Changes between Initial Version and Version 1 of Ticket #3892


Ignore:
Timestamp:
Oct 30, 2020, 10:24:49 AM (5 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #3892

    • Property Component Unassigned → Structure Editing
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → chain merge not reordering residues

  • Ticket #3892 – Description

    initial v1  
    1818restore_snapshot for "RotamerRestraintMgr" returned None 
    1919
    20 Log from Thu Oct 29 17:29:15 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    21 © 2016-2020 Regents of the University of California. All rights reserved. 
    22 
    23 > open
    24 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/working.cxs
    25 
    26 restore_snapshot for "RotamerRestraintMgr" returned None 
    27 
    28 Log from Thu Oct 29 16:35:33 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    29 © 2016-2020 Regents of the University of California. All rights reserved. 
    30 
    31 > open working.cxs
    32 
    33 restore_snapshot for "RotamerRestraintMgr" returned None 
    34 
    35 restore_snapshot for "RotamerRestraintMgr" returned None 
    36 
    37 Log from Wed Oct 28 21:12:33 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    38 © 2016-2020 Regents of the University of California. All rights reserved. 
    39 
    40 > open working.cxs
    41 
    42 restore_snapshot for "RotamerRestraintMgr" returned None 
    43 
    44 restore_snapshot for "RotamerRestraintMgr" returned None 
    45 
    46 Log from Tue Oct 27 22:03:57 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    47 © 2016-2020 Regents of the University of California. All rights reserved. 
    48 
    49 > open working.cxs
    50 
    51 restore_snapshot for "RotamerRestraintMgr" returned None 
    52 
    53 Log from Fri Oct 23 21:33:44 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    54 © 2016-2020 Regents of the University of California. All rights reserved. 
    55 
    56 > open working.cxs
    57 
    58 restore_snapshot for "RotamerRestraintMgr" returned None 
    59 
    60 Log from Fri Oct 23 12:38:35 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    61 © 2016-2020 Regents of the University of California. All rights reserved. 
    62 
    63 > open working.cxs
    64 
    65 restore_snapshot for "RotamerRestraintMgr" returned None 
    66 
    67 restore_snapshot for "RotamerRestraintMgr" returned None 
    68 
    69 Log from Thu Oct 22 21:38:47 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    70 © 2016-2020 Regents of the University of California. All rights reserved. 
    71 
    72 > open working_3.cxs
    73 
    74 restore_snapshot for "RotamerRestraintMgr" returned None 
    75 
    76 restore_snapshot for "RotamerRestraintMgr" returned None 
    77 
    78 Log from Thu Oct 22 17:00:13 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    79 © 2016-2020 Regents of the University of California. All rights reserved. 
    80 
    81 > open
    82 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/reopened.cxs
    83 
    84 restore_snapshot for "RotamerRestraintMgr" returned None 
    85 
    86 Log from Thu Oct 22 16:23:14 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    87 © 2016-2020 Regents of the University of California. All rights reserved. 
    88 
    89 > open working_2.cxs
    90 
    91 restore_snapshot for "RotamerRestraintMgr" returned None 
    92 
    93 Log from Thu Oct 22 16:02:14 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    94 © 2016-2020 Regents of the University of California. All rights reserved. 
    95 
    96 > open
    97 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cxs
    98 
    99 restore_snapshot for "RotamerRestraintMgr" returned None 
    100 
    101 Log from Thu Oct 22 13:56:05 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    102 © 2016-2020 Regents of the University of California. All rights reserved. 
    103 
    104 > open ../old_model_in_map_1b.cxs
    105 
    106 Log from Thu Oct 22 06:57:21 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    107 © 2016-2020 Regents of the University of California. All rights reserved. 
    108 
    109 > open model1b_working.cxs
    110 
    111 restore_snapshot for "RotamerRestraintMgr" returned None 
    112 
    113 Log from Wed Oct 21 20:17:18 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    114 © 2016-2020 Regents of the University of California. All rights reserved. 
    115 
    116 > open model1b_working.cxs
    117 
    118 restore_snapshot for "RotamerRestraintMgr" returned None 
    119 
    120 Log from Wed Oct 21 20:13:59 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    121 © 2016-2020 Regents of the University of California. All rights reserved. 
    122 
    123 > open
    124 > /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/model1b_working.cxs
    125 
    126 restore_snapshot for "RotamerRestraintMgr" returned None 
    127 
    128 Log from Wed Oct 21 19:55:36 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    129 © 2016-2020 Regents of the University of California. All rights reserved. 
    130 How to cite UCSF ChimeraX 
    131 
    132 > open /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/rc-
    133 > dlh1-model1b_rearranged.pdb format pdb
    134 
    135 Chain information for rc-dlh1-model1b_rearranged.pdb #1 
    136 --- 
    137 Chain | Description 
    138 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    139 description available 
    140 Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available 
    141 Ag | No description available 
    142 B | No description available 
    143 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX Ba Bb
    144 Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available 
    145 C | No description available 
    146 C1 | No description available 
    147 H1 | No description available 
    148 H2 | No description available 
    149 L | No description available 
    150 M | No description available 
    151  
    152 
    153 > open
    154 > /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/class1b_26A.mrc
    155 
    156 Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    157 0.0224, step 2, values float32 
    158 
    159 > clipper associate #2 toModel #1
    160 
    161 Chain information for rc-dlh1-model1b_rearranged.pdb 
    162 --- 
    163 Chain | Description 
    164 1.2/AA 1.2/AB 1.2/AC 1.2/AD 1.2/AE 1.2/AF 1.2/AG 1.2/AH 1.2/AI 1.2/AJ 1.2/AK
    165 1.2/AL 1.2/AM 1.2/AN 1.2/AO 1.2/AP 1.2/AQ 1.2/AR 1.2/AS 1.2/AT 1.2/AU 1.2/AV
    166 1.2/AW 1.2/AX | No description available 
    167 1.2/Aa 1.2/Ab 1.2/Ac 1.2/Ad 1.2/Ae 1.2/Af 1.2/Ah 1.2/Ai 1.2/Aj 1.2/Ak 1.2/Al
    168 1.2/Am 1.2/An 1.2/Ao 1.2/Ap | No description available 
    169 1.2/Ag | No description available 
    170 1.2/B | No description available 
    171 1.2/BA 1.2/BB 1.2/BC 1.2/BD 1.2/BE 1.2/BF 1.2/BG 1.2/BH 1.2/BI 1.2/BJ 1.2/BK
    172 1.2/BL 1.2/BM 1.2/BN 1.2/BO 1.2/BP 1.2/BQ 1.2/BR 1.2/BS 1.2/BT 1.2/BU 1.2/BV
    173 1.2/BW 1.2/BX 1.2/Ba 1.2/Bb 1.2/Bc 1.2/Bd 1.2/Be 1.2/Bf 1.2/Bg 1.2/Bh 1.2/Bi
    174 1.2/Bj 1.2/Bk 1.2/Bl 1.2/Bm 1.2/Bn 1.2/Bo 1.2/Bp | No description available 
    175 1.2/C | No description available 
    176 1.2/C1 | No description available 
    177 1.2/H1 | No description available 
    178 1.2/H2 | No description available 
    179 1.2/L | No description available 
    180 1.2/M | No description available 
    181  
    182 
    183 > delete :GPC@HO45
    184 
    185 > ui tool show Shell
    186 
    187 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    188 UserWarning: IPython History requires SQLite, your history will not be saved 
    189 warn("IPython History requires SQLite, your history will not be saved") 
    190 
    191 > select ~protein
    192 
    193 10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 8 models selected 
    194 
    195 > ui tool show ISOLDE
    196 
    197 > set selectionWidth 4
    198 
    199 Done loading forcefield 
    200 
    201 > select ~protein
    202 
    203 10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 13 models selected 
    204 
    205 > addh
    206 
    207 Summary of feedback from adding hydrogens to rc-dlh1-model1b_rearranged.pdb
    208 #1.2 
    209 --- 
    210 warning | Skipped 8 atom(s) with bad connectivities; see log for details 
    211 notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2)
    212 chain AA; guessing termini instead 
    213 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AB;
    214 guessing termini instead 
    215 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AC;
    216 guessing termini instead 
    217 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AD;
    218 guessing termini instead 
    219 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AE;
    220 guessing termini instead 
    221 82 messages similar to the above omitted 
    222 Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2, /AC
    223 HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2, /AJ
    224 HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2, /AQ
    225 HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2, /AX
    226 HIS 2, /Aa MET 1, /Ab MET 1, /Ac MET 1, /Ad MET 1, /Ae MET 1, /Af MET 1, /Ag
    227 MET 1, /Ah MET 1, /Ai MET 1, /Aj MET 1, /Ak MET 1, /Al MET 1, /Am MET 1, /An
    228 MET 1, /Ao MET 1, /Ap MET 1, /B PRO 25, /BA MET 1, /BB MET 1, /BC MET 1, /BD
    229 MET 1, /BE MET 1, /BF MET 1, /BG MET 1, /BH MET 1, /BI MET 1, /BJ MET 1, /BK
    230 MET 1, /BL MET 1, /BM MET 1, /BN MET 1, /BO MET 1, /BP MET 1, /BQ MET 1, /BR
    231 MET 1, /BS MET 1, /BT MET 1, /BU MET 1, /BV MET 1, /BW MET 1, /BX MET 1, /Ba
    232 MET 1, /Bb MET 1, /Bc MET 1, /Bd MET 1, /Be MET 1, /Bf MET 1, /Bg MET 1, /Bh
    233 MET 1, /Bi MET 1, /Bj MET 1, /Bk MET 1, /Bl MET 1, /Bm MET 1, /Bn MET 1, /Bo
    234 MET 1, /Bp MET 1, /C ALA 15, /H1 MET 1, /H2 SER 1, /L ALA 1, /M MET 1 
    235 Chain-initial residues that are not actual N termini: /C1 GLN 1, /H2 ARG 38 
    236 Chain-final residues that are actual C termini: /BA PHE 38, /BB PHE 38, /BC
    237 PHE 38, /BD PHE 38, /BE PHE 38, /BF PHE 38, /BG PHE 38, /BH PHE 38, /BI PHE
    238 38, /BJ PHE 38, /BK PHE 38, /BL PHE 38, /BM PHE 38, /BN PHE 38, /BO PHE 38,
    239 /BP PHE 38, /BQ PHE 38, /BR PHE 38, /BS PHE 38, /BT PHE 38, /BU PHE 38, /BV
    240 PHE 38, /BW PHE 38, /BX PHE 38, /Ba PHE 38, /Bb PHE 38, /Bc PHE 38, /Bd PHE
    241 38, /Be PHE 38, /Bf PHE 38, /Bg PHE 38, /Bh PHE 38, /Bi PHE 38, /Bj PHE 38,
    242 /Bk PHE 38, /Bl PHE 38, /Bm PHE 38, /Bn PHE 38, /Bo PHE 38, /Bp PHE 38 
    243 Chain-final residues that are not actual C termini: /AA PRO 48, /AB PRO 48,
    244 /AC PRO 48, /AD PRO 48, /AE PRO 48, /AF PRO 48, /AG PRO 48, /AH PRO 48, /AI
    245 PRO 48, /AJ PRO 48, /AK PRO 48, /AL PRO 48, /AM PRO 48, /AN PRO 48, /AO PRO
    246 48, /AP PRO 48, /AQ PRO 48, /AR PRO 48, /AS PRO 48, /AT PRO 48, /AU PRO 48,
    247 /AV PRO 48, /AW PRO 48, /AX PRO 48, /Aa ALA 60, /Ab ALA 60, /Ac ALA 60, /Ad
    248 ALA 60, /Ae ALA 60, /Af ALA 60, /Ag LEU 67, /Ah ALA 60, /Ai ALA 60, /Aj ALA
    249 60, /Ak ALA 60, /Al ALA 60, /Am ALA 60, /An ALA 60, /Ao ALA 60, /Ap ALA 60, /B
    250 ILE 123, /C ILE 313, /C1 LEU 92, /H1 HIS 67, /H2 ILE 181, /H2 ARG 36, /L TRP
    251 272, /M TYR 324 
    252 Skipping possible acceptor with bad geometry: /C ARG 302 O 
    253 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O 
    254  
    255 Skipping possible acceptor with bad geometry: /C ARG 302 OXT 
    256 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT 
    257  
    258 Skipping possible acceptor with bad geometry: /C ARG 302 OXT 
    259 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT 
    260  
    261 Skipping possible acceptor with bad geometry: /C ARG 302 O 
    262 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O 
    263  
    264 Skipping possible acceptor with bad geometry: /C ARG 302 O 
    265 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O 
    266  
    267 3 messages similar to the above omitted 
    268 4746 hydrogen bonds 
    269 Adding 'H' to /H2 ARG 38 
    270 /AA PRO 48 is not terminus, removing H atom from 'C' 
    271 /AB PRO 48 is not terminus, removing H atom from 'C' 
    272 /AC PRO 48 is not terminus, removing H atom from 'C' 
    273 /AD PRO 48 is not terminus, removing H atom from 'C' 
    274 /AE PRO 48 is not terminus, removing H atom from 'C' 
    275 42 messages similar to the above omitted 
    276 44090 hydrogens added 
    277  
    278 
    279 > save model1b_working.cxs
    280 
    281 opened ChimeraX session 
    282 
    283 > select up
    284 
    285 101 atoms, 100 bonds, 1 residue, 1 model selected 
    286 
    287 > show sel
    288 
    289 > select clear
    290 
    291 > style sel ball
    292 
    293 Changed 100 atom styles 
    294 
    295 > select :GPC
    296 
    297 4013 atoms, 3973 bonds, 40 residues, 1 model selected 
    298 
    299 > show sel
    300 
    301 > select :GPC@HC19
    302 
    303 40 atoms, 40 residues, 1 model selected 
    304 
    305 > select :GPC
    306 
    307 4013 atoms, 3973 bonds, 40 residues, 1 model selected 
    308 
    309 > delete sel
    310 
    311 MD template USER_BCL for residue BCL L604 contains extra atoms that are not in
    312 a coordinate template, and are not directly connected to existing atoms. Since
    313 MD templates do not explicitly provide geometry,these atoms will not be built. 
    314 
    315 > select sel&@CBD
    316 
    317 1 atom, 1 residue, 1 model selected 
    318 
    319 > style sel sphere
    320 
    321 Changed 1 atom style 
    322 
    323 > style sel stick
    324 
    325 Changed 1 atom style 
    326 
    327 > select up
    328 
    329 139 atoms, 147 bonds, 1 residue, 1 model selected 
    330 Deleted the following atoms from residue BCL L604: HHC1, HHD1 
    331 Deleted the following atoms from residue BCL L602: HHD2, HHC2, HHD1, HHC1 
    332 Deleted the following atoms from residue BPH L606: H12, H92, HHD1, H41, H93,
    333 H91, H52, H11, HHD2, H43, H61, H51, H62, H42, H71, H72 
    334 
    335 > save model1b_working.cxs
    336 
    337 opened ChimeraX session 
    338 Deleted the following atoms from residue MQ8 M405: H272, H9, H502, H122, C49,
    339 C46, H172, H503, C50, H461, H471, H222, H11, H422, H492, H6, H472, C48, H462,
    340 H7, H501, C47, H8, H491, H372, H322 
    341 Deleted the following atoms from residue BCL M601: HHD2, HHD1 
    342 Deleted the following atoms from residue BCL M603: HHD1, HHD2, HHC1, HHC2 
    343 Deleted the following atoms from residue BPH M605: H11, H62, H72, H42, H12,
    344 H91, H52, H71, HHD2, H93, H51, H92, HHD1, H61, H43, H41 
    345 Residue RCC M701 has only 0 connected atoms in common with template GPC. At
    346 least 3 matching atoms are needed. 
    347 
    348 > save model1b_working.cxs
    349 
    350 > delete sel
    351 
    352 > save model1b_working.cxs
    353 
    354 opened ChimeraX session 
    355 
    356 > open
    357 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb
    358 
    359 Summary of feedback from opening
    360 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb 
    361 --- 
    362 warnings | Ignored bad PDB record found on line 317 
    363 LINK NE2 HIS AA 29 MG BCL AA 57 
    364  
    365 Ignored bad PDB record found on line 318 
    366 LINK NE2 HIS AB 29 MG BCL AB 57 
    367  
    368 Ignored bad PDB record found on line 319 
    369 LINK NE2 HIS AC 29 MG BCL AC 57 
    370  
    371 Ignored bad PDB record found on line 320 
    372 LINK NE2 HIS AD 29 MG BCL AD 57 
    373  
    374 Ignored bad PDB record found on line 321 
    375 LINK NE2 HIS AE 29 MG BCL AE 57 
    376  
    377 75 messages similar to the above omitted 
    378 Start residue of secondary structure not found: HELIX 1 1 PROAA 10 PHEAA 36 1
    379 26 
    380 Start residue of secondary structure not found: HELIX 2 2 ALAAA 40 LYSAA 45 1
    381 5 
    382 Start residue of secondary structure not found: HELIX 3 3 ARGAB 3 TRPAB 5 1 2 
    383 Start residue of secondary structure not found: HELIX 4 4 PROAB 10 GLNAB 35 1
    384 25 
    385 Start residue of secondary structure not found: HELIX 5 5 ALAAB 40 LEUAB 42 1
    386 2 
    387 207 messages similar to the above omitted 
    388  
    389 Chain information for working_noh_real_space_refined.pdb #2 
    390 --- 
    391 Chain | Description 
    392 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    393 description available 
    394 BA BC BF BG BH BJ BK BL BM BN BO BP BQ BR BS BT BU BX ba bb bc bd be bf bg bh
    395 bi bj bk bl bm bo bp | No description available 
    396 BB BD BE BI BV BW bn | No description available 
    397 C | No description available 
    398 H1 | No description available 
    399 H2 | No description available 
    400 L | No description available 
    401 M | No description available 
    402 UA | No description available 
    403 UB | No description available 
    404 UC | No description available 
    405 aa | No description available 
    406 ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available 
    407  
    408 
    409 > matchmaker #2 to #1
    410 
    411 Parameters 
    412 --- 
    413 Chain pairing | bb 
    414 Alignment algorithm | Needleman-Wunsch 
    415 Similarity matrix | BLOSUM-62 
    416 SS fraction | 0.3 
    417 Gap open (HH/SS/other) | 18/18/6 
    418 Gap extend | 1 
    419 SS matrix |  |  | H | S | O 
    420 ---|---|---|--- 
    421 H | 6 | -9 | -6 
    422 S |  | 6 | -6 
    423 O |  |  | 4 
    424 Iteration cutoff | 2 
    425  
    426 Matchmaker rc-dlh1-model1b_rearranged.pdb, chain M (#1.2) with
    427 working_noh_real_space_refined.pdb, chain M (#2), sequence alignment score =
    428 1582 
    429 RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 324 pairs:
    430 1.723) 
    431  
    432 
    433 > delete #2/UA,UB,UC
    434 
    435 > open
    436 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc
    437 
    438 Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    439 0.0224, step 2, values float32 
    440 
    441 > clipper associate #3 toModel #2
    442 
    443 Chain information for working_noh_real_space_refined.pdb 
    444 --- 
    445 Chain | Description 
    446 2.2/AA 2.2/AB 2.2/AC 2.2/AD 2.2/AE 2.2/AF 2.2/AG 2.2/AH 2.2/AI 2.2/AJ 2.2/AK
    447 2.2/AL 2.2/AM 2.2/AN 2.2/AO 2.2/AP 2.2/AQ 2.2/AR 2.2/AS 2.2/AT 2.2/AU 2.2/AV
    448 2.2/AW 2.2/AX | No description available 
    449 2.2/BA 2.2/BC 2.2/BF 2.2/BG 2.2/BH 2.2/BJ 2.2/BK 2.2/BL 2.2/BM 2.2/BN 2.2/BO
    450 2.2/BP 2.2/BQ 2.2/BR 2.2/BS 2.2/BT 2.2/BU 2.2/BX 2.2/ba 2.2/bb 2.2/bc 2.2/bd
    451 2.2/be 2.2/bf 2.2/bg 2.2/bh 2.2/bi 2.2/bj 2.2/bk 2.2/bl 2.2/bm 2.2/bo 2.2/bp |
    452 No description available 
    453 2.2/BB 2.2/BD 2.2/BE 2.2/BI 2.2/BV 2.2/BW 2.2/bn | No description available 
    454 2.2/C | No description available 
    455 2.2/H1 | No description available 
    456 2.2/H2 | No description available 
    457 2.2/L | No description available 
    458 2.2/M | No description available 
    459 2.2/aa | No description available 
    460 2.2/ab 2.2/ac 2.2/ad 2.2/ae 2.2/af 2.2/ag 2.2/ah 2.2/ai 2.2/aj 2.2/ak 2.2/al
    461 2.2/am 2.2/an 2.2/ao 2.2/ap | No description available 
    462  
    463 
    464 > select #2:GPC
    465 
    466 1800 atoms, 1760 bonds, 40 residues, 1 model selected 
    467 
    468 > select #2:RCC
    469 
    470 Nothing selected 
    471 
    472 > select #1:RCC
    473 
    474 100 atoms, 99 bonds, 1 residue, 1 model selected 
    475 
    476 > select #2:GPC
    477 
    478 1800 atoms, 1760 bonds, 40 residues, 1 model selected 
    479 
    480 > select #1:GPC
    481 
    482 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    483 
    484 > select #2:GPC
    485 
    486 1800 atoms, 1760 bonds, 40 residues, 1 model selected 
    487 
    488 > delete sel
    489 
    490 > ui tool show Shell
    491 
    492 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    493 UserWarning: IPython History requires SQLite, your history will not be saved 
    494 warn("IPython History requires SQLite, your history will not be saved") 
    495 
    496 > delete #2:GP1
    497 
    498 > select #1:RCC
    499 
    500 100 atoms, 99 bonds, 1 residue, 1 model selected 
    501 
    502 > select #1:RCC,GCC
    503 
    504 100 atoms, 99 bonds, 1 residue, 1 model selected 
    505 
    506 > select #1:RCC,GPC
    507 
    508 4100 atoms, 4059 bonds, 41 residues, 1 model selected 
    509 
    510 > close #1
    511 
    512 > addh
    513 
    514 Summary of feedback from adding hydrogens to
    515 working_noh_real_space_refined.pdb #2.2 
    516 --- 
    517 notes | No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2)
    518 chain AA; guessing termini instead 
    519 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    520 AB; guessing termini instead 
    521 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    522 AC; guessing termini instead 
    523 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    524 AD; guessing termini instead 
    525 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    526 AE; guessing termini instead 
    527 80 messages similar to the above omitted 
    528 Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2, /AC
    529 HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2, /AJ
    530 HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2, /AQ
    531 HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2, /AX
    532 HIS 2, /BA GLY 6, /BB GLY 5, /BC GLY 6, /BD GLY 5, /BE GLY 5, /BF GLY 6, /BG
    533 GLY 6, /BH GLY 6, /BI GLY 5, /BJ GLY 6, /BK GLY 6, /BL GLY 6, /BM GLY 6, /BN
    534 GLY 6, /BO GLY 6, /BP GLY 6, /BQ GLY 6, /BR GLY 6, /BS GLY 6, /BT GLY 6, /BU
    535 GLY 6, /BV GLY 5, /BW GLY 5, /BX GLY 6, /C ALA 15, /H1 MET 1, /H2 SER 1, /L
    536 ALA 1, /M MET 1, /aa HIS 2, /ab MET 1, /ac MET 1, /ad MET 1, /ae MET 1, /af
    537 MET 1, /ag MET 1, /ah MET 1, /ai MET 1, /aj MET 1, /ak MET 1, /al MET 1, /am
    538 MET 1, /an MET 1, /ao MET 1, /ap MET 1, /ba GLY 6, /bb GLY 6, /bc GLY 6, /bd
    539 GLY 6, /be GLY 6, /bf GLY 6, /bg GLY 6, /bh GLY 6, /bi GLY 6, /bj GLY 6, /bk
    540 GLY 6, /bl GLY 6, /bm GLY 6, /bn GLY 5, /bo GLY 6, /bp GLY 6 
    541 Chain-initial residues that are not actual N termini: 
    542 Chain-final residues that are actual C termini: /BA PHE 44, /BB PHE 44, /BC
    543 PHE 44, /BD PHE 44, /BE PHE 44, /BF PHE 44, /BG PHE 44, /BH PHE 44, /BI PHE
    544 44, /BJ PHE 44, /BK PHE 44, /BL PHE 44, /BM PHE 44, /BN PHE 44, /BO PHE 44,
    545 /BP PHE 44, /BQ PHE 44, /BR PHE 44, /BS PHE 44, /BT PHE 44, /BU PHE 44, /BV
    546 PHE 44, /BW PHE 44, /BX PHE 44, /C ARG 302, /H2 ILE 181, /L LYS 273, /ba PHE
    547 44, /bb PHE 44, /bc PHE 44, /bd PHE 44, /be PHE 44, /bf PHE 44, /bg PHE 44,
    548 /bh PHE 44, /bi PHE 44, /bj PHE 44, /bk PHE 44, /bl PHE 44, /bm PHE 44, /bn
    549 PHE 44, /bo PHE 44, /bp PHE 44 
    550 Chain-final residues that are not actual C termini: /AA TYR 46, /AB TYR 46,
    551 /AC TYR 46, /AD TYR 46, /AE TYR 46, /AF TYR 46, /AG TYR 46, /AH TYR 46, /AI
    552 TYR 46, /AJ TYR 46, /AK TYR 46, /AL TYR 46, /AM TYR 46, /AN TYR 46, /AO TYR
    553 46, /AP TYR 46, /AQ TYR 46, /AR TYR 46, /AS TYR 46, /AT TYR 46, /AU TYR 46,
    554 /AV TYR 46, /AW TYR 46, /AX TYR 46, /H1 LYS 53, /M TYR 324, /aa ALA 60, /ab
    555 ALA 60, /ac ALA 60, /ad ALA 60, /ae ALA 60, /af ALA 60, /ag ALA 60, /ah ALA
    556 60, /ai ALA 60, /aj ALA 60, /ak ALA 60, /al ALA 60, /am ALA 60, /an ALA 60,
    557 /ao ALA 60, /ap ALA 60 
    558 4864 hydrogen bonds 
    559 /AA TYR 46 is not terminus, removing H atom from 'C' 
    560 /AB TYR 46 is not terminus, removing H atom from 'C' 
    561 /AC TYR 46 is not terminus, removing H atom from 'C' 
    562 /AD TYR 46 is not terminus, removing H atom from 'C' 
    563 /AE TYR 46 is not terminus, removing H atom from 'C' 
    564 37 messages similar to the above omitted 
    565 43714 hydrogens added 
    566  
    567 
    568 > hide HC
    569 
    570 > select ~protein
    571 
    572 16594 atoms, 16919 bonds, 365 pseudobonds, 133 residues, 8 models selected 
    573 
    574 > select clear
    575 
    576 > save old_model_in_map_1b.cxs
    577 
    578 opened ChimeraX session 
    579 
    580 > isolde start
    581 
    582 > set selectionWidth 4
    583 
    584 Done loading forcefield 
    585 
    586 > select :GPC
    587 
    588 4013 atoms, 3973 bonds, 40 residues, 1 model selected 
    589 
    590 > ui tool show Shell
    591 
    592 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    593 UserWarning: IPython History requires SQLite, your history will not be saved 
    594 warn("IPython History requires SQLite, your history will not be saved") 
    595 
    596 > select clear
    597 
    598 > delete sel
    599 
    600 > delete sel
    601 
    602 > delete sel
    603 
    604 > delete sel
    605 
    606 > save ready.cxs
    607 
    608 > select gpc
    609 
    610 Expected an objects specifier or a keyword 
    611 
    612 > select :GPC
    613 
    614 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    615 
    616 > select :GPC
    617 
    618 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    619 
    620 > show sel
    621 
    622 > select clear
    623 
    624 > show sel
    625 
    626 > save ready.cxs
    627 
    628 > volume gaussian #1 bfactor 50
    629 
    630 > volume gaussian #2 bfactor 50
    631 
    632 > clipper associate #1 toModel #2
    633 
    634 > hide HC
    635 
    636 > select #1
    637 
    638 Nothing selected 
    639 
    640 > select #2
    641 
    642 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    643 
    644 > clipper set contourSensitivity 0.25
    645 
    646 > select clear
    647 
    648 > set bgColor white
    649 
    650 > select #1
    651 
    652 Nothing selected 
    653 
    654 > select #2
    655 
    656 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    657 
    658 > select clear
    659 
    660 > select #2
    661 
    662 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    663 
    664 > select #1
    665 
    666 Nothing selected 
    667 
    668 > select #2
    669 
    670 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    671 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    672 more memory-efficient implementation. 
    673 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    674 more memory-efficient implementation. 
    675 
    676 > select clear
    677 
    678 > open
    679 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb
    680 
    681 Summary of feedback from opening
    682 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb 
    683 --- 
    684 warnings | Start residue of secondary structure not found: HELIX 1 1 ILE B 5
    685 TYR B 9 1 5 
    686 Start residue of secondary structure not found: HELIX 2 2 ARG B 22 ARG B 52 1
    687 31 
    688 Start residue of secondary structure not found: HELIX 3 3 VAL B 55 ARG B 86 1
    689 32 
    690  
    691 Chain information for assigned_sequence.pdb #1 
    692 --- 
    693 Chain | Description 
    694 Ba | No description available 
    695  
    696 
    697 > open
    698 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb
    699 
    700 Summary of feedback from opening
    701 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb 
    702 --- 
    703 warnings | Start residue of secondary structure not found: HELIX 1 1 THR C 19
    704 GLY C 21 1 3 
    705 Start residue of secondary structure not found: HELIX 2 2 VAL C 28 VAL C 31 1
    706 4 
    707 Start residue of secondary structure not found: HELIX 3 3 VAL C 32 HIS C 34 1
    708 3 
    709 Start residue of secondary structure not found: HELIX 4 4 GLY C 61 ILE C 64 1
    710 4 
    711 Start residue of secondary structure not found: HELIX 5 5 MET C 71 LYS C 74 1
    712 4 
    713 3 messages similar to the above omitted 
    714  
    715 Chain information for sequence_assigned.pdb #3 
    716 --- 
    717 Chain | Description 
    718 C1 | No description available 
    719  
    720 
    721 > open
    722 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/rc-
    723 > dlh1-model1b_rearranged.pdb
    724 
    725 Chain information for rc-dlh1-model1b_rearranged.pdb #4 
    726 --- 
    727 Chain | Description 
    728 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    729 description available 
    730 Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available 
    731 Ag | No description available 
    732 B | No description available 
    733 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX Ba Bb
    734 Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available 
    735 C | No description available 
    736 C1 | No description available 
    737 H1 | No description available 
    738 H2 | No description available 
    739 L | No description available 
    740 M | No description available 
    741  
    742 
    743 > hide #!4 models
    744 
    745 > select #3
    746 
    747 1472 atoms, 1487 bonds, 92 residues, 1 model selected 
    748 
    749 > save working.cxs
    750 
    751 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    752 
    753 > hide #3 models
    754 
    755 > select #1
    756 
    757 1516 atoms, 1537 bonds, 99 residues, 1 model selected 
    758 
    759 > select #2/Ba
    760 
    761 100 atoms, 99 bonds, 1 residue, 1 model selected 
    762 
    763 > view sel
    764 
    765 > select #1
    766 
    767 1516 atoms, 1537 bonds, 99 residues, 1 model selected 
    768 
    769 > select clear
    770 
    771 > select /AA
    772 
    773 1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected 
    774 
    775 > select /BA
    776 
    777 1151 atoms, 1189 bonds, 4 pseudobonds, 79 residues, 3 models selected 
    778 
    779 > isolde stepto /AA
    780 
    781 Multiple residues selected! Going to the first... 
    782 
    783 > select /AA
    784 
    785 1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected 
    786 
    787 > select clear
    788 
    789 > select clear
    790 
    791 > select /AA
    792 
    793 1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected 
    794 
    795 > select clear
    796 
    797 > sequence chain /AA
    798 
    799 Chains must have same sequence 
    800 
    801 > sequence chain #1/AA
    802 
    803 Chains must have same sequence 
    804 
    805 > sequence chain #2/AA
    806 
    807 Alignment identifier is 2.2/AA 
    808 
    809 > select /AA
    810 
    811 1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected 
    812 
    813 > select clear
    814 
    815 > select clear
    816 
    817 > select /AA
    818 
    819 1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected 
    820 
    821 > select clear
    822 
    823 > select clear
    824 
    825 > show #!4 models
    826 
    827 > select #4/AS
    828 
    829 540 atoms, 558 bonds, 4 pseudobonds, 49 residues, 2 models selected 
    830 
    831 > select clear
    832 
    833 > select #4
    834 
    835 51294 atoms, 53027 bonds, 354 pseudobonds, 5083 residues, 3 models selected 
    836 
    837 > style sel stick
    838 
    839 Changed 51294 atom styles 
    840 
    841 > select clear
    842 
    843 > hide #!4 models
    844 
    845 > select clear
    846 
    847 > isolde stepto /C
    848 
    849 Multiple residues selected! Going to the first... 
    850 
    851 > select /C:15-200
    852 
    853 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    854 
    855 > select clear
    856 
    857 > show #!4 models
    858 
    859 > hide #!4 models
    860 
    861 > show #!4 models
    862 
    863 > hide #!4 models
    864 
    865 > isolde stepto
    866 
    867 > isolde stepto
    868 
    869 > isolde stepto
    870 
    871 > show #!4 models
    872 
    873 > hide #!4 models
    874 
    875 reverting to start 
    876 
    877 > select /C1
    878 
    879 4416 atoms, 4461 bonds, 276 residues, 3 models selected 
    880 
    881 > isolde ignore /C1:30-300
    882 
    883 ISOLDE: currently ignoring 63 residues in model 2.2 
    884 ISOLDE: currently ignoring 63 residues in model 3 
    885 ISOLDE: currently ignoring 63 residues in model 4 
    886 
    887 > select /C:15-200
    888 
    889 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    890 
    891 > select /M:311-400
    892 
    893 359 atoms, 361 bonds, 28 residues, 2 models selected 
    894 
    895 > select clear
    896 
    897 > isolde ~ignore
    898 
    899 > show #!4 models
    900 
    901 > hide #!4 models
    902 
    903 > save working.cxs
    904 
    905 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    906 
    907 > select /C:15-200
    908 
    909 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    910 
    911 > select clear
    912 
    913 > isolde stepto
    914 
    915 > hide #1 models
    916 
    917 > isolde ignore /C2
    918 
    919 ISOLDE: currently ignoring 99 residues in model 2.2 
    920 
    921 > select /H2:120-129
    922 
    923 241 atoms, 251 bonds, 20 residues, 2 models selected 
    924 
    925 > select clear
    926 
    927 > select clear
    928 
    929 > isolde ~ignore
    930 
    931 > select up
    932 
    933 22 atoms, 21 bonds, 1 residue, 1 model selected 
    934 
    935 > isolde ignore sel
    936 
    937 ISOLDE: currently ignoring 1 residues in model 2.2 
    938 
    939 > isolde ~ignore
    940 
    941 > select clear
    942 
    943 > select up
    944 
    945 24 atoms, 23 bonds, 1 residue, 1 model selected 
    946 
    947 > isolde ignore sel
    948 
    949 ISOLDE: currently ignoring 1 residues in model 2.2 
    950 
    951 > isolde ~ignore
    952 
    953 > select up
    954 
    955 14 atoms, 13 bonds, 1 residue, 1 model selected 
    956 
    957 > select up
    958 
    959 105 atoms, 108 bonds, 7 residues, 1 model selected 
    960 
    961 > isolde ignore sel
    962 
    963 ISOLDE: currently ignoring 8 residues in model 2.2 
    964 
    965 > select up
    966 
    967 10 atoms, 9 bonds, 1 residue, 1 model selected 
    968 
    969 > select up
    970 
    971 939 atoms, 951 bonds, 60 residues, 1 model selected 
    972 
    973 > select clear
    974 
    975 > show #!4 models
    976 
    977 > select clear
    978 
    979 > hide #!4 models
    980 
    981 > select clear
    982 
    983 > select clear
    984 
    985 > select clear
    986 
    987 > select clear
    988 
    989 > select clear
    990 
    991 > save working.cxs
    992 
    993 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    994 
    995 > select /C:15-200
    996 
    997 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    998 
    999 > select clear
    1000 
    1001 > isolde stepto /C
    1002 
    1003 Multiple residues selected! Going to the first... 
    1004 
    1005 > select clear
    1006 
    1007 > isolde stepto
    1008 
    1009 > isolde stepto
    1010 
    1011 > isolde stepto
    1012 
    1013 > select clear
    1014 
    1015 > show #!4 models
    1016 
    1017 > hide #!4 models
    1018 
    1019 > isolde stepto
    1020 
    1021 > isolde stepto
    1022 
    1023 > isolde stepto
    1024 
    1025 > show #!4 models
    1026 
    1027 > hide #!4 models
    1028 
    1029 > isolde stepto
    1030 
    1031 > isolde stepto
    1032 
    1033 > isolde stepto
    1034 
    1035 > isolde stepto
    1036 
    1037 > isolde stepto
    1038 
    1039 > isolde stepto
    1040 
    1041 > select clear
    1042 
    1043 > isolde stepto
    1044 
    1045 > isolde stepto
    1046 
    1047 > isolde stepto
    1048 
    1049 > isolde stepto
    1050 
    1051 > isolde stepto
    1052 
    1053 > isolde stepto
    1054 
    1055 > isolde stepto
    1056 
    1057 > isolde stepto
    1058 
    1059 > show #!4 models
    1060 
    1061 > hide #!4 models
    1062 
    1063 > show #!4 models
    1064 
    1065 > hide #!4 models
    1066 
    1067 > select clear
    1068 
    1069 > select up
    1070 
    1071 14 atoms, 14 bonds, 1 residue, 1 model selected 
    1072 
    1073 > select up
    1074 
    1075 450 atoms, 459 bonds, 30 residues, 1 model selected 
    1076 
    1077 > select clear
    1078 
    1079 > select clear
    1080 
    1081 > select /C:64-200
    1082 
    1083 3217 atoms, 3269 bonds, 274 residues, 2 models selected 
    1084 
    1085 > select clear
    1086 
    1087 > select clear
    1088 
    1089 > select clear
    1090 
    1091 > isolde stepto /C:64
    1092 
    1093 Multiple residues selected! Going to the first... 
    1094 
    1095 > isolde stepto
    1096 
    1097 > isolde stepto
    1098 
    1099 > isolde stepto
    1100 
    1101 > isolde stepto
    1102 
    1103 > isolde stepto
    1104 
    1105 > isolde stepto
    1106 
    1107 > isolde stepto
    1108 
    1109 > isolde stepto
    1110 
    1111 > isolde stepto
    1112 
    1113 > isolde stepto
    1114 
    1115 > isolde stepto
    1116 
    1117 > isolde stepto
    1118 
    1119 > isolde stepto
    1120 
    1121 > isolde stepto
    1122 
    1123 > isolde stepto
    1124 
    1125 > isolde stepto
    1126 
    1127 > isolde stepto
    1128 
    1129 > isolde stepto
    1130 
    1131 > isolde stepto
    1132 
    1133 > isolde stepto
    1134 
    1135 > isolde stepto
    1136 
    1137 > select clear
    1138 
    1139 > isolde stepto
    1140 
    1141 > isolde stepto
    1142 
    1143 > isolde stepto
    1144 
    1145 > isolde stepto
    1146 
    1147 > isolde stepto
    1148 
    1149 > isolde stepto
    1150 
    1151 > isolde stepto
    1152 
    1153 > isolde stepto
    1154 
    1155 > isolde stepto
    1156 
    1157 > isolde stepto
    1158 
    1159 > isolde stepto
    1160 
    1161 > isolde stepto
    1162 
    1163 > isolde stepto
    1164 
    1165 > isolde stepto
    1166 
    1167 > select clear
    1168 
    1169 > delete sel
    1170 
    1171 > select /C:99-200
    1172 
    1173 2415 atoms, 2455 bonds, 204 residues, 2 models selected 
    1174 
    1175 > select clear
    1176 
    1177 > select clear
    1178 
    1179 > select clear
    1180 
    1181 > isolde stepto
    1182 
    1183 > isolde stepto
    1184 
    1185 > isolde stepto
    1186 
    1187 > isolde stepto
    1188 
    1189 > isolde stepto
    1190 
    1191 > isolde stepto
    1192 
    1193 > isolde stepto
    1194 
    1195 > isolde stepto
    1196 
    1197 > select clear
    1198 
    1199 > isolde stepto
    1200 
    1201 > isolde stepto
    1202 
    1203 > isolde stepto
    1204 
    1205 > isolde stepto
    1206 
    1207 > isolde stepto
    1208 
    1209 > isolde stepto
    1210 
    1211 > isolde stepto
    1212 
    1213 > isolde stepto
    1214 
    1215 > select clear
    1216 
    1217 > isolde stepto
    1218 
    1219 > isolde stepto
    1220 
    1221 > isolde stepto
    1222 
    1223 > isolde stepto
    1224 
    1225 > isolde stepto
    1226 
    1227 > isolde stepto
    1228 
    1229 > isolde stepto
    1230 
    1231 > isolde stepto
    1232 
    1233 > isolde stepto
    1234 
    1235 > isolde stepto
    1236 
    1237 > isolde stepto
    1238 
    1239 > isolde stepto
    1240 
    1241 > isolde stepto
    1242 
    1243 > isolde stepto
    1244 
    1245 > isolde stepto
    1246 
    1247 > isolde stepto
    1248 
    1249 > isolde stepto
    1250 
    1251 > isolde stepto
    1252 
    1253 > isolde stepto
    1254 
    1255 > isolde stepto
    1256 
    1257 > isolde stepto
    1258 
    1259 > isolde stepto
    1260 
    1261 > isolde stepto
    1262 
    1263 > isolde stepto
    1264 
    1265 > isolde stepto
    1266 
    1267 > isolde stepto
    1268 
    1269 > isolde stepto
    1270 
    1271 > isolde stepto
    1272 
    1273 > isolde stepto
    1274 
    1275 > isolde stepto
    1276 
    1277 > isolde stepto
    1278 
    1279 > isolde stepto
    1280 
    1281 > isolde stepto
    1282 
    1283 > isolde stepto
    1284 
    1285 > isolde stepto
    1286 
    1287 > isolde stepto
    1288 
    1289 > isolde stepto
    1290 
    1291 > isolde stepto
    1292 
    1293 > isolde stepto
    1294 
    1295 > isolde stepto
    1296 
    1297 > isolde stepto
    1298 
    1299 > isolde stepto
    1300 
    1301 > isolde stepto
    1302 
    1303 > isolde stepto
    1304 
    1305 > isolde stepto
    1306 
    1307 > isolde stepto
    1308 
    1309 > isolde stepto
    1310 
    1311 > show #!4 models
    1312 
    1313 > hide #!4 models
    1314 
    1315 > show #!4 models
    1316 
    1317 > hide #!4 models
    1318 
    1319 > isolde stepto
    1320 
    1321 > isolde stepto
    1322 
    1323 > isolde stepto
    1324 
    1325 > isolde stepto
    1326 
    1327 > isolde stepto
    1328 
    1329 > isolde stepto
    1330 
    1331 > isolde stepto
    1332 
    1333 > isolde stepto
    1334 
    1335 > isolde stepto
    1336 
    1337 > isolde stepto
    1338 
    1339 > isolde stepto
    1340 
    1341 > isolde stepto
    1342 
    1343 > show #!4 models
    1344 
    1345 > hide #!4 models
    1346 
    1347 > select /C:179-189
    1348 
    1349 241 atoms, 241 bonds, 22 residues, 2 models selected 
    1350 
    1351 > select #2/C:179-189
    1352 
    1353 162 atoms, 162 bonds, 11 residues, 1 model selected 
    1354 
    1355 > select clear
    1356 
    1357 > isolde stepto
    1358 
    1359 > isolde stepto
    1360 
    1361 > select clear
    1362 
    1363 > isolde stepto
    1364 
    1365 > isolde stepto
    1366 
    1367 > isolde stepto
    1368 
    1369 > isolde stepto
    1370 
    1371 > isolde stepto
    1372 
    1373 > isolde stepto
    1374 
    1375 > isolde stepto
    1376 
    1377 > select clear
    1378 
    1379 > isolde stepto
    1380 
    1381 > isolde stepto
    1382 
    1383 > isolde stepto
    1384 
    1385 > isolde stepto
    1386 
    1387 > isolde stepto
    1388 
    1389 > isolde stepto
    1390 
    1391 > isolde stepto
    1392 
    1393 > isolde stepto
    1394 
    1395 > isolde stepto
    1396 
    1397 > isolde stepto
    1398 
    1399 > isolde stepto
    1400 
    1401 > isolde stepto
    1402 
    1403 > isolde stepto
    1404 
    1405 > isolde stepto
    1406 
    1407 > isolde stepto
    1408 
    1409 > isolde stepto
    1410 
    1411 > isolde stepto
    1412 
    1413 > isolde stepto
    1414 
    1415 > isolde stepto
    1416 
    1417 > isolde stepto
    1418 
    1419 > isolde stepto
    1420 
    1421 > isolde stepto
    1422 
    1423 > isolde stepto
    1424 
    1425 > isolde stepto
    1426 
    1427 > isolde stepto
    1428 
    1429 > isolde stepto
    1430 
    1431 > isolde stepto
    1432 
    1433 > isolde stepto
    1434 
    1435 > save working.cxs
    1436 
    1437 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    1438 
    1439 > select /C:200-400
    1440 
    1441 2486 atoms, 2541 bonds, 217 residues, 2 models selected 
    1442 
    1443 > select clear
    1444 
    1445 > select clear
    1446 
    1447 > isolde stepto
    1448 
    1449 > isolde stepto
    1450 
    1451 > isolde stepto
    1452 
    1453 > isolde stepto
    1454 
    1455 > isolde stepto
    1456 
    1457 > isolde stepto
    1458 
    1459 > isolde stepto
    1460 
    1461 > isolde stepto
    1462 
    1463 > isolde stepto
    1464 
    1465 > isolde stepto
    1466 
    1467 > isolde stepto
    1468 
    1469 > isolde stepto
    1470 
    1471 > isolde stepto
    1472 
    1473 > isolde stepto
    1474 
    1475 > isolde stepto
    1476 
    1477 > isolde stepto
    1478 
    1479 > isolde stepto
    1480 
    1481 > isolde stepto
    1482 
    1483 > isolde stepto
    1484 
    1485 > isolde stepto
    1486 
    1487 > isolde stepto
    1488 
    1489 > isolde stepto
    1490 
    1491 > isolde stepto
    1492 
    1493 > isolde stepto
    1494 
    1495 > isolde stepto
    1496 
    1497 > isolde stepto
    1498 
    1499 > isolde stepto
    1500 
    1501 > isolde stepto
    1502 
    1503 > isolde stepto
    1504 
    1505 > isolde stepto
    1506 
    1507 > isolde stepto
    1508 
    1509 > isolde stepto
    1510 
    1511 > isolde stepto
    1512 
    1513 > isolde stepto
    1514 
    1515 > isolde stepto
    1516 
    1517 > isolde stepto
    1518 
    1519 > isolde stepto
    1520 
    1521 > isolde stepto
    1522 
    1523 > isolde stepto
    1524 
    1525 > select clear
    1526 
    1527 > isolde stepto
    1528 
    1529 > isolde stepto
    1530 
    1531 > isolde stepto
    1532 
    1533 > isolde stepto
    1534 
    1535 > isolde stepto
    1536 
    1537 > isolde stepto
    1538 
    1539 > isolde stepto
    1540 
    1541 > isolde stepto
    1542 
    1543 > isolde stepto
    1544 
    1545 > isolde stepto
    1546 
    1547 > isolde stepto
    1548 
    1549 > isolde stepto
    1550 
    1551 > isolde stepto
    1552 
    1553 > isolde stepto
    1554 
    1555 > isolde stepto
    1556 
    1557 > isolde stepto
    1558 
    1559 > isolde stepto
    1560 
    1561 > isolde stepto
    1562 
    1563 > isolde stepto
    1564 
    1565 > isolde stepto
    1566 
    1567 > isolde stepto
    1568 
    1569 > isolde stepto
    1570 
    1571 > isolde stepto
    1572 
    1573 > isolde stepto
    1574 
    1575 > isolde stepto
    1576 
    1577 > isolde stepto
    1578 
    1579 > isolde stepto
    1580 
    1581 > select clear
    1582 
    1583 > isolde stepto
    1584 
    1585 > isolde stepto
    1586 
    1587 > isolde stepto
    1588 
    1589 > isolde stepto
    1590 
    1591 > isolde stepto
    1592 
    1593 > isolde stepto
    1594 
    1595 > isolde stepto
    1596 
    1597 > isolde stepto
    1598 
    1599 > isolde stepto
    1600 
    1601 > isolde stepto
    1602 
    1603 > isolde stepto
    1604 
    1605 > isolde stepto
    1606 
    1607 > isolde stepto
    1608 
    1609 > isolde stepto
    1610 
    1611 > isolde stepto
    1612 
    1613 > isolde stepto
    1614 
    1615 > isolde stepto
    1616 
    1617 > isolde stepto
    1618 
    1619 > isolde stepto
    1620 
    1621 > isolde stepto
    1622 
    1623 > isolde stepto
    1624 
    1625 > isolde stepto
    1626 
    1627 > isolde stepto
    1628 
    1629 > isolde stepto
    1630 
    1631 > show #!4 models
    1632 
    1633 > save working.cxs
    1634 
    1635 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    1636 
    1637 > select #4/C:303-313
    1638 
    1639 83 atoms, 87 bonds, 11 residues, 1 model selected 
    1640 
    1641 > select clear
    1642 
    1643 > hide #!4 models
    1644 
    1645 > select #2/C:303-400
    1646 
    1647 83 atoms, 87 bonds, 11 residues, 1 model selected 
    1648 
    1649 > show sel
    1650 
    1651 > delete sell
    1652 
    1653 Missing or invalid "atoms" argument: invalid atoms specifier 
    1654 
    1655 > delete sel
    1656 
    1657 > addh #4
    1658 
    1659 Summary of feedback from adding hydrogens to rc-dlh1-model1b_rearranged.pdb #4 
    1660 --- 
    1661 warning | Skipped 8 atom(s) with bad connectivities; see log for details 
    1662 notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain
    1663 AA; guessing termini instead 
    1664 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AB;
    1665 guessing termini instead 
    1666 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AC;
    1667 guessing termini instead 
    1668 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AD;
    1669 guessing termini instead 
    1670 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AE;
    1671 guessing termini instead 
    1672 82 messages similar to the above omitted 
    1673 Chain-initial residues that are actual N termini: rc-
    1674 dlh1-model1b_rearranged.pdb #4/AA HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AB
    1675 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AC HIS 2, rc-
    1676 dlh1-model1b_rearranged.pdb #4/AD HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AE
    1677 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AF HIS 2, rc-
    1678 dlh1-model1b_rearranged.pdb #4/AG HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AH
    1679 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AI HIS 2, rc-
    1680 dlh1-model1b_rearranged.pdb #4/AJ HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AK
    1681 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AL HIS 2, rc-
    1682 dlh1-model1b_rearranged.pdb #4/AM HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AN
    1683 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AO HIS 2, rc-
    1684 dlh1-model1b_rearranged.pdb #4/AP HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AQ
    1685 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AR HIS 2, rc-
    1686 dlh1-model1b_rearranged.pdb #4/AS HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AT
    1687 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AU HIS 2, rc-
    1688 dlh1-model1b_rearranged.pdb #4/AV HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AW
    1689 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AX HIS 2, rc-
    1690 dlh1-model1b_rearranged.pdb #4/Aa MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ab
    1691 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ac MET 1, rc-
    1692 dlh1-model1b_rearranged.pdb #4/Ad MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ae
    1693 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Af MET 1, rc-
    1694 dlh1-model1b_rearranged.pdb #4/Ag MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ah
    1695 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ai MET 1, rc-
    1696 dlh1-model1b_rearranged.pdb #4/Aj MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ak
    1697 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Al MET 1, rc-
    1698 dlh1-model1b_rearranged.pdb #4/Am MET 1, rc-dlh1-model1b_rearranged.pdb #4/An
    1699 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ao MET 1, rc-
    1700 dlh1-model1b_rearranged.pdb #4/Ap MET 1, rc-dlh1-model1b_rearranged.pdb #4/B
    1701 PRO 25, rc-dlh1-model1b_rearranged.pdb #4/BA MET 1, rc-
    1702 dlh1-model1b_rearranged.pdb #4/BB MET 1, rc-dlh1-model1b_rearranged.pdb #4/BC
    1703 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BD MET 1, rc-
    1704 dlh1-model1b_rearranged.pdb #4/BE MET 1, rc-dlh1-model1b_rearranged.pdb #4/BF
    1705 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BG MET 1, rc-
    1706 dlh1-model1b_rearranged.pdb #4/BH MET 1, rc-dlh1-model1b_rearranged.pdb #4/BI
    1707 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BJ MET 1, rc-
    1708 dlh1-model1b_rearranged.pdb #4/BK MET 1, rc-dlh1-model1b_rearranged.pdb #4/BL
    1709 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BM MET 1, rc-
    1710 dlh1-model1b_rearranged.pdb #4/BN MET 1, rc-dlh1-model1b_rearranged.pdb #4/BO
    1711 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BP MET 1, rc-
    1712 dlh1-model1b_rearranged.pdb #4/BQ MET 1, rc-dlh1-model1b_rearranged.pdb #4/BR
    1713 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BS MET 1, rc-
    1714 dlh1-model1b_rearranged.pdb #4/BT MET 1, rc-dlh1-model1b_rearranged.pdb #4/BU
    1715 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BV MET 1, rc-
    1716 dlh1-model1b_rearranged.pdb #4/BW MET 1, rc-dlh1-model1b_rearranged.pdb #4/BX
    1717 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ba MET 1, rc-
    1718 dlh1-model1b_rearranged.pdb #4/Bb MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bc
    1719 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bd MET 1, rc-
    1720 dlh1-model1b_rearranged.pdb #4/Be MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bf
    1721 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bg MET 1, rc-
    1722 dlh1-model1b_rearranged.pdb #4/Bh MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bi
    1723 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bj MET 1, rc-
    1724 dlh1-model1b_rearranged.pdb #4/Bk MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bl
    1725 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bm MET 1, rc-
    1726 dlh1-model1b_rearranged.pdb #4/Bn MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bo
    1727 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bp MET 1, rc-
    1728 dlh1-model1b_rearranged.pdb #4/C ALA 15, rc-dlh1-model1b_rearranged.pdb #4/H1
    1729 MET 1, rc-dlh1-model1b_rearranged.pdb #4/H2 SER 1, rc-
    1730 dlh1-model1b_rearranged.pdb #4/L ALA 1, rc-dlh1-model1b_rearranged.pdb #4/M
    1731 MET 1 
    1732 Chain-initial residues that are not actual N termini: rc-
    1733 dlh1-model1b_rearranged.pdb #4/C1 GLN 1, rc-dlh1-model1b_rearranged.pdb #4/H2
    1734 ARG 38 
    1735 Chain-final residues that are actual C termini: rc-dlh1-model1b_rearranged.pdb
    1736 #4/BA PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BB PHE 38, rc-
    1737 dlh1-model1b_rearranged.pdb #4/BC PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BD
    1738 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BE PHE 38, rc-
    1739 dlh1-model1b_rearranged.pdb #4/BF PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BG
    1740 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BH PHE 38, rc-
    1741 dlh1-model1b_rearranged.pdb #4/BI PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BJ
    1742 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BK PHE 38, rc-
    1743 dlh1-model1b_rearranged.pdb #4/BL PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BM
    1744 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BN PHE 38, rc-
    1745 dlh1-model1b_rearranged.pdb #4/BO PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BP
    1746 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BQ PHE 38, rc-
    1747 dlh1-model1b_rearranged.pdb #4/BR PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BS
    1748 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BT PHE 38, rc-
    1749 dlh1-model1b_rearranged.pdb #4/BU PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BV
    1750 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BW PHE 38, rc-
    1751 dlh1-model1b_rearranged.pdb #4/BX PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Ba
    1752 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bb PHE 38, rc-
    1753 dlh1-model1b_rearranged.pdb #4/Bc PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bd
    1754 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Be PHE 38, rc-
    1755 dlh1-model1b_rearranged.pdb #4/Bf PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bg
    1756 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bh PHE 38, rc-
    1757 dlh1-model1b_rearranged.pdb #4/Bi PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bj
    1758 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bk PHE 38, rc-
    1759 dlh1-model1b_rearranged.pdb #4/Bl PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bm
    1760 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bn PHE 38, rc-
    1761 dlh1-model1b_rearranged.pdb #4/Bo PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bp
    1762 PHE 38 
    1763 Chain-final residues that are not actual C termini: rc-
    1764 dlh1-model1b_rearranged.pdb #4/AA PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AB
    1765 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48, rc-
    1766 dlh1-model1b_rearranged.pdb #4/AD PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AE
    1767 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AF PRO 48, rc-
    1768 dlh1-model1b_rearranged.pdb #4/AG PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AH
    1769 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AI PRO 48, rc-
    1770 dlh1-model1b_rearranged.pdb #4/AJ PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AK
    1771 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AL PRO 48, rc-
    1772 dlh1-model1b_rearranged.pdb #4/AM PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AN
    1773 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AO PRO 48, rc-
    1774 dlh1-model1b_rearranged.pdb #4/AP PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AQ
    1775 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AR PRO 48, rc-
    1776 dlh1-model1b_rearranged.pdb #4/AS PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AT
    1777 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AU PRO 48, rc-
    1778 dlh1-model1b_rearranged.pdb #4/AV PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AW
    1779 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AX PRO 48, rc-
    1780 dlh1-model1b_rearranged.pdb #4/Aa ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ab
    1781 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ac ALA 60, rc-
    1782 dlh1-model1b_rearranged.pdb #4/Ad ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ae
    1783 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Af ALA 60, rc-
    1784 dlh1-model1b_rearranged.pdb #4/Ag LEU 67, rc-dlh1-model1b_rearranged.pdb #4/Ah
    1785 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ai ALA 60, rc-
    1786 dlh1-model1b_rearranged.pdb #4/Aj ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ak
    1787 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Al ALA 60, rc-
    1788 dlh1-model1b_rearranged.pdb #4/Am ALA 60, rc-dlh1-model1b_rearranged.pdb #4/An
    1789 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ao ALA 60, rc-
    1790 dlh1-model1b_rearranged.pdb #4/Ap ALA 60, rc-dlh1-model1b_rearranged.pdb #4/B
    1791 ILE 123, rc-dlh1-model1b_rearranged.pdb #4/C ILE 313, rc-
    1792 dlh1-model1b_rearranged.pdb #4/C1 LEU 92, rc-dlh1-model1b_rearranged.pdb #4/H1
    1793 HIS 67, rc-dlh1-model1b_rearranged.pdb #4/H2 ILE 181, rc-
    1794 dlh1-model1b_rearranged.pdb #4/H2 ARG 36, rc-dlh1-model1b_rearranged.pdb #4/L
    1795 TRP 272, rc-dlh1-model1b_rearranged.pdb #4/M TYR 324 
    1796 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1797 #4/C ARG 302 O 
    1798 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1799 dlh1-model1b_rearranged.pdb #4/C ARG 302 O 
    1800  
    1801 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1802 #4/C ARG 302 OXT 
    1803 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1804 dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT 
    1805  
    1806 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1807 #4/C ARG 302 OXT 
    1808 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1809 dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT 
    1810  
    1811 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1812 #4/C ARG 302 O 
    1813 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1814 dlh1-model1b_rearranged.pdb #4/C ARG 302 O 
    1815  
    1816 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1817 #4/C ARG 302 O 
    1818 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1819 dlh1-model1b_rearranged.pdb #4/C ARG 302 O 
    1820  
    1821 3 messages similar to the above omitted 
    1822 4768 hydrogen bonds 
    1823 Adding 'H' to rc-dlh1-model1b_rearranged.pdb #4/H2 ARG 38 
    1824 rc-dlh1-model1b_rearranged.pdb #4/AA PRO 48 is not terminus, removing H atom
    1825 from 'C' 
    1826 rc-dlh1-model1b_rearranged.pdb #4/AB PRO 48 is not terminus, removing H atom
    1827 from 'C' 
    1828 rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48 is not terminus, removing H atom
    1829 from 'C' 
    1830 rc-dlh1-model1b_rearranged.pdb #4/AD PRO 48 is not terminus, removing H atom
    1831 from 'C' 
    1832 rc-dlh1-model1b_rearranged.pdb #4/AE PRO 48 is not terminus, removing H atom
    1833 from 'C' 
    1834 42 messages similar to the above omitted 
    1835 44090 hydrogens added 
    1836  
    1837 
    1838 > select #2/C:303-400
    1839 
    1840 157 atoms, 161 bonds, 11 residues, 1 model selected 
    1841 
    1842 > select clear
    1843 
    1844 > isolde stepto
    1845 
    1846 > isolde stepto
    1847 
    1848 > isolde stepto
    1849 
    1850 > isolde stepto
    1851 
    1852 > isolde stepto
    1853 
    1854 > isolde stepto
    1855 
    1856 > isolde stepto
    1857 
    1858 > isolde stepto
    1859 
    1860 > isolde stepto
    1861 
    1862 > isolde stepto
    1863 
    1864 > isolde stepto
    1865 
    1866 > isolde stepto
    1867 
    1868 > isolde stepto
    1869 
    1870 > show #!4 models
    1871 
    1872 > hide #!4 models
    1873 
    1874 > select up
    1875 
    1876 12 atoms, 11 bonds, 1 residue, 1 model selected 
    1877 
    1878 > select up
    1879 
    1880 874 atoms, 890 bonds, 53 residues, 1 model selected 
    1881 
    1882 > select #2/H1:3-100
    1883 
    1884 838 atoms, 854 bonds, 51 residues, 1 model selected 
    1885 
    1886 > show #!4 models
    1887 
    1888 > hide #!4 models
    1889 
    1890 > isolde stepto
    1891 
    1892 > isolde stepto
    1893 
    1894 > isolde stepto
    1895 
    1896 > isolde stepto
    1897 
    1898 > isolde stepto
    1899 
    1900 > isolde stepto
    1901 
    1902 > isolde stepto
    1903 
    1904 > isolde stepto
    1905 
    1906 > isolde stepto
    1907 
    1908 > isolde stepto
    1909 
    1910 > isolde stepto
    1911 
    1912 > isolde stepto
    1913 
    1914 > isolde stepto
    1915 
    1916 > isolde stepto
    1917 
    1918 > isolde stepto
    1919 
    1920 > isolde stepto
    1921 
    1922 > isolde stepto
    1923 
    1924 > isolde stepto
    1925 
    1926 > isolde stepto
    1927 
    1928 > isolde stepto
    1929 
    1930 > isolde stepto
    1931 
    1932 > isolde stepto
    1933 
    1934 > isolde stepto
    1935 
    1936 > isolde stepto
    1937 
    1938 > isolde stepto
    1939 
    1940 > isolde stepto
    1941 
    1942 > isolde stepto
    1943 
    1944 > isolde stepto
    1945 
    1946 > isolde stepto
    1947 
    1948 > isolde stepto
    1949 
    1950 > isolde stepto
    1951 
    1952 > isolde stepto
    1953 
    1954 > isolde stepto
    1955 
    1956 > isolde stepto
    1957 
    1958 > isolde stepto
    1959 
    1960 > isolde stepto
    1961 
    1962 > isolde stepto
    1963 
    1964 > isolde stepto
    1965 
    1966 > isolde stepto
    1967 
    1968 > show #!4 models
    1969 
    1970 > hide #!4 models
    1971 
    1972 > select up
    1973 
    1974 38 atoms, 40 bonds, 2 residues, 1 model selected 
    1975 
    1976 > select clear
    1977 
    1978 > select clear
    1979 
    1980 > select #1
    1981 
    1982 1516 atoms, 1537 bonds, 99 residues, 1 model selected 
    1983 
    1984 > select #2
    1985 
    1986 94789 atoms, 96857 bonds, 14 pseudobonds, 5061 residues, 22 models selected 
    1987 
    1988 > style sel sphere
    1989 
    1990 Changed 94789 atom styles 
    1991 
    1992 > select clear
    1993 
    1994 > style #!2.2 stick
    1995 
    1996 Changed 94789 atom styles 
    1997 
    1998 > delete sel
    1999 
    2000 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2001 bonded heavy atom. 
    2002 
    2003 > delete sel
    2004 
    2005 > delete sel
    2006 
    2007 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2008 bonded heavy atom. 
    2009 
    2010 > delete sel
    2011 
    2012 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2013 bonded heavy atom. 
    2014 
    2015 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2016 bonded heavy atom. 
    2017 
    2018 > select #2/H2
    2019 
    2020 2777 atoms, 2816 bonds, 180 residues, 1 model selected 
    2021 
    2022 > select clear
    2023 
    2024 > isolde jumpto
    2025 
    2026 > select #2/H2:3-100
    2027 
    2028 1476 atoms, 1499 bonds, 97 residues, 1 model selected 
    2029 
    2030 > select clear
    2031 
    2032 > select clear
    2033 
    2034 > isolde stepto
    2035 
    2036 > isolde stepto
    2037 
    2038 > isolde stepto
    2039 
    2040 > isolde stepto
    2041 
    2042 > isolde stepto
    2043 
    2044 > isolde stepto
    2045 
    2046 > isolde stepto
    2047 
    2048 > isolde stepto
    2049 
    2050 > isolde stepto
    2051 
    2052 > isolde stepto
    2053 
    2054 > isolde stepto
    2055 
    2056 > isolde stepto
    2057 
    2058 > isolde stepto
    2059 
    2060 > isolde stepto
    2061 
    2062 > select #2/H2:3-100
    2063 
    2064 1476 atoms, 1499 bonds, 97 residues, 1 model selected 
    2065 
    2066 > select clear
    2067 
    2068 > isolde stepto
    2069 
    2070 > isolde stepto
    2071 
    2072 > isolde stepto
    2073 
    2074 > isolde stepto
    2075 
    2076 > isolde stepto
    2077 
    2078 > isolde stepto
    2079 
    2080 > isolde stepto
    2081 
    2082 > isolde stepto
    2083 
    2084 > isolde stepto
    2085 
    2086 > isolde stepto
    2087 
    2088 > isolde stepto
    2089 
    2090 > isolde stepto
    2091 
    2092 > isolde stepto
    2093 
    2094 > isolde stepto
    2095 
    2096 > isolde stepto
    2097 
    2098 > isolde stepto
    2099 
    2100 > isolde stepto
    2101 
    2102 > isolde stepto
    2103 
    2104 > isolde stepto
    2105 
    2106 > isolde stepto
    2107 
    2108 > isolde stepto
    2109 
    2110 > isolde stepto
    2111 
    2112 > isolde stepto
    2113 
    2114 > isolde stepto
    2115 
    2116 > isolde stepto
    2117 
    2118 > isolde stepto
    2119 
    2120 > isolde stepto
    2121 
    2122 > isolde stepto
    2123 
    2124 > isolde stepto
    2125 
    2126 > isolde stepto
    2127 
    2128 > isolde stepto
    2129 
    2130 > isolde stepto
    2131 
    2132 > isolde stepto
    2133 
    2134 > isolde stepto
    2135 
    2136 > isolde stepto
    2137 
    2138 > isolde stepto
    2139 
    2140 > isolde stepto
    2141 
    2142 > isolde stepto
    2143 
    2144 > isolde stepto
    2145 
    2146 > isolde stepto
    2147 
    2148 > isolde stepto
    2149 
    2150 > isolde stepto
    2151 
    2152 > isolde stepto
    2153 
    2154 > isolde stepto
    2155 
    2156 > isolde stepto
    2157 
    2158 > isolde stepto
    2159 
    2160 > isolde stepto
    2161 
    2162 > isolde stepto
    2163 
    2164 > isolde stepto
    2165 
    2166 > isolde stepto
    2167 
    2168 > isolde stepto
    2169 
    2170 > isolde stepto
    2171 
    2172 > isolde stepto
    2173 
    2174 > isolde stepto
    2175 
    2176 > isolde stepto
    2177 
    2178 > isolde stepto
    2179 
    2180 > isolde stepto
    2181 
    2182 > isolde stepto
    2183 
    2184 > isolde stepto
    2185 
    2186 > isolde stepto
    2187 
    2188 > isolde stepto
    2189 
    2190 > isolde stepto
    2191 
    2192 > isolde stepto
    2193 
    2194 > isolde stepto
    2195 
    2196 > isolde stepto
    2197 
    2198 > isolde stepto
    2199 
    2200 > isolde stepto
    2201 
    2202 > isolde stepto
    2203 
    2204 > isolde stepto
    2205 
    2206 > isolde stepto
    2207 
    2208 > isolde stepto
    2209 
    2210 > isolde stepto
    2211 
    2212 > isolde stepto
    2213 
    2214 > isolde stepto
    2215 
    2216 > isolde stepto
    2217 
    2218 > isolde stepto
    2219 
    2220 > isolde stepto
    2221 
    2222 > isolde stepto
    2223 
    2224 > isolde stepto
    2225 
    2226 > select #2/H1:95-205
    2227 
    2228 Nothing selected 
    2229 
    2230 > select #2/H1:95-205
    2231 
    2232 Nothing selected 
    2233 
    2234 > select #2/H2:95-205
    2235 
    2236 1376 atoms, 1394 bonds, 87 residues, 1 model selected 
    2237 
    2238 > select clear
    2239 
    2240 > isolde stepto
    2241 
    2242 > isolde stepto
    2243 
    2244 > isolde stepto
    2245 
    2246 > isolde stepto
    2247 
    2248 > isolde stepto
    2249 
    2250 > isolde stepto
    2251 
    2252 > isolde stepto
    2253 
    2254 > isolde stepto
    2255 
    2256 > isolde stepto
    2257 
    2258 > isolde stepto
    2259 
    2260 > select clear
    2261 
    2262 > isolde stepto
    2263 
    2264 > isolde stepto
    2265 
    2266 > isolde stepto
    2267 
    2268 > isolde stepto
    2269 
    2270 > isolde stepto
    2271 
    2272 > isolde stepto
    2273 
    2274 > isolde stepto
    2275 
    2276 > isolde stepto
    2277 
    2278 > isolde stepto
    2279 
    2280 > isolde stepto
    2281 
    2282 > isolde stepto
    2283 
    2284 > isolde stepto
    2285 
    2286 > isolde stepto
    2287 
    2288 > isolde stepto
    2289 
    2290 > isolde stepto
    2291 
    2292 > isolde stepto
    2293 
    2294 > isolde stepto
    2295 
    2296 > isolde stepto
    2297 
    2298 > isolde stepto
    2299 
    2300 > isolde stepto
    2301 
    2302 > isolde stepto
    2303 
    2304 > isolde stepto
    2305 
    2306 > isolde stepto
    2307 
    2308 > isolde stepto
    2309 
    2310 > isolde stepto
    2311 
    2312 > isolde stepto
    2313 
    2314 > isolde stepto
    2315 
    2316 > isolde stepto
    2317 
    2318 > isolde stepto
    2319 
    2320 > isolde stepto
    2321 
    2322 > isolde stepto
    2323 
    2324 > isolde stepto
    2325 
    2326 > isolde stepto
    2327 
    2328 > isolde stepto
    2329 
    2330 > isolde stepto
    2331 
    2332 > isolde stepto
    2333 
    2334 > isolde stepto
    2335 
    2336 > isolde stepto
    2337 
    2338 > isolde stepto
    2339 
    2340 > isolde stepto
    2341 
    2342 > isolde stepto
    2343 
    2344 > isolde stepto
    2345 
    2346 > isolde stepto
    2347 
    2348 > isolde stepto
    2349 
    2350 > isolde stepto
    2351 
    2352 > isolde stepto
    2353 
    2354 > isolde stepto
    2355 
    2356 > isolde stepto
    2357 
    2358 > isolde stepto
    2359 
    2360 > isolde stepto
    2361 
    2362 > isolde stepto
    2363 
    2364 > isolde stepto
    2365 
    2366 > isolde stepto
    2367 
    2368 > isolde stepto
    2369 
    2370 > isolde stepto
    2371 
    2372 > isolde stepto
    2373 
    2374 > isolde stepto
    2375 
    2376 > isolde stepto
    2377 
    2378 > isolde stepto
    2379 
    2380 > isolde stepto
    2381 
    2382 > isolde stepto
    2383 
    2384 > isolde stepto
    2385 
    2386 > isolde stepto
    2387 
    2388 > isolde stepto
    2389 
    2390 > isolde stepto
    2391 
    2392 > isolde stepto
    2393 
    2394 > isolde stepto
    2395 
    2396 > isolde stepto
    2397 
    2398 > isolde stepto
    2399 
    2400 > isolde stepto
    2401 
    2402 > isolde stepto
    2403 
    2404 > isolde stepto
    2405 
    2406 > isolde stepto
    2407 
    2408 > isolde stepto
    2409 
    2410 > isolde stepto
    2411 
    2412 > isolde stepto
    2413 
    2414 > isolde stepto
    2415 
    2416 > save working.cxs
    2417 
    2418 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    2419 
    2420 > isolde stepto
    2421 
    2422 > select #2/L:1-100
    2423 
    2424 1563 atoms, 1592 bonds, 100 residues, 1 model selected 
    2425 
    2426 > select clear
    2427 
    2428 > isolde stepto
    2429 
    2430 > isolde stepto
    2431 
    2432 > isolde stepto
    2433 
    2434 > isolde stepto
    2435 
    2436 > isolde stepto
    2437 
    2438 > isolde stepto
    2439 
    2440 > isolde stepto
    2441 
    2442 > isolde stepto
    2443 
    2444 > isolde stepto
    2445 
    2446 > isolde stepto
    2447 
    2448 > select clear
    2449 
    2450 > isolde stepto
    2451 
    2452 > isolde stepto
    2453 
    2454 > isolde stepto
    2455 
    2456 > isolde stepto
    2457 
    2458 > isolde stepto
    2459 
    2460 > isolde stepto
    2461 
    2462 > isolde stepto
    2463 
    2464 > isolde stepto
    2465 
    2466 > isolde stepto
    2467 
    2468 > isolde stepto
    2469 
    2470 > isolde stepto
    2471 
    2472 > isolde stepto
    2473 
    2474 > isolde stepto
    2475 
    2476 > isolde stepto
    2477 
    2478 > isolde stepto
    2479 
    2480 > isolde stepto
    2481 
    2482 > isolde stepto
    2483 
    2484 > isolde stepto
    2485 
    2486 > isolde stepto
    2487 
    2488 > isolde stepto
    2489 
    2490 > isolde stepto
    2491 
    2492 > isolde stepto
    2493 
    2494 > isolde stepto
    2495 
    2496 > isolde stepto
    2497 
    2498 > isolde stepto
    2499 
    2500 > isolde stepto
    2501 
    2502 > isolde stepto
    2503 
    2504 > select clear
    2505 
    2506 > isolde stepto
    2507 
    2508 > isolde stepto
    2509 
    2510 > isolde stepto
    2511 
    2512 > isolde stepto
    2513 
    2514 > isolde stepto
    2515 
    2516 > isolde stepto
    2517 
    2518 > isolde stepto
    2519 
    2520 > isolde stepto
    2521 
    2522 > isolde stepto
    2523 
    2524 > isolde stepto
    2525 
    2526 > isolde stepto
    2527 
    2528 > isolde stepto
    2529 
    2530 > isolde stepto
    2531 
    2532 > isolde stepto
    2533 
    2534 > isolde stepto
    2535 
    2536 > isolde stepto
    2537 
    2538 > isolde stepto
    2539 
    2540 > isolde stepto
    2541 
    2542 > isolde stepto
    2543 
    2544 > isolde stepto
    2545 
    2546 > isolde stepto
    2547 
    2548 > isolde stepto
    2549 
    2550 > isolde stepto
    2551 
    2552 > isolde stepto
    2553 
    2554 > isolde stepto
    2555 
    2556 > isolde stepto
    2557 
    2558 > isolde stepto
    2559 
    2560 > isolde stepto
    2561 
    2562 > isolde stepto
    2563 
    2564 > isolde stepto
    2565 
    2566 > isolde stepto
    2567 
    2568 > isolde stepto
    2569 
    2570 > isolde stepto
    2571 
    2572 > isolde stepto
    2573 
    2574 > isolde stepto
    2575 
    2576 > isolde stepto
    2577 
    2578 > isolde stepto
    2579 
    2580 > isolde stepto
    2581 
    2582 > isolde stepto
    2583 
    2584 > isolde stepto
    2585 
    2586 > isolde stepto
    2587 
    2588 > isolde stepto
    2589 
    2590 > isolde stepto
    2591 
    2592 > isolde stepto
    2593 
    2594 > isolde stepto
    2595 
    2596 > isolde stepto
    2597 
    2598 > isolde stepto
    2599 
    2600 > isolde stepto
    2601 
    2602 > isolde stepto
    2603 
    2604 > isolde stepto
    2605 
    2606 > isolde stepto
    2607 
    2608 > isolde stepto
    2609 
    2610 > isolde stepto
    2611 
    2612 > isolde stepto
    2613 
    2614 > isolde stepto
    2615 
    2616 > isolde stepto
    2617 
    2618 > isolde stepto
    2619 
    2620 > isolde stepto
    2621 
    2622 > isolde stepto
    2623 
    2624 > isolde stepto
    2625 
    2626 > isolde stepto
    2627 
    2628 > isolde stepto
    2629 
    2630 > isolde stepto
    2631 
    2632 > isolde stepto
    2633 
    2634 > isolde stepto
    2635 
    2636 > isolde stepto
    2637 
    2638 > isolde stepto
    2639 
    2640 > isolde stepto
    2641 
    2642 > isolde stepto
    2643 
    2644 > isolde stepto
    2645 
    2646 > isolde stepto
    2647 
    2648 > isolde stepto
    2649 
    2650 > isolde stepto
    2651 
    2652 > select #2/L:100-300
    2653 
    2654 2756 atoms, 2816 bonds, 174 residues, 1 model selected 
    2655 
    2656 > select clear
    2657 
    2658 > select clear
    2659 
    2660 > isolde stepto
    2661 
    2662 > isolde stepto
    2663 
    2664 > isolde stepto
    2665 
    2666 > select clear
    2667 
    2668 > isolde stepto
    2669 
    2670 > isolde stepto
    2671 
    2672 > isolde stepto
    2673 
    2674 > isolde stepto
    2675 
    2676 > isolde stepto
    2677 
    2678 > isolde stepto
    2679 
    2680 > isolde stepto
    2681 
    2682 > isolde stepto
    2683 
    2684 > isolde stepto
    2685 
    2686 > isolde stepto
    2687 
    2688 > isolde stepto
    2689 
    2690 > isolde stepto
    2691 
    2692 > isolde stepto
    2693 
    2694 > isolde stepto
    2695 
    2696 > isolde stepto
    2697 
    2698 > isolde stepto
    2699 
    2700 > isolde stepto
    2701 
    2702 > isolde stepto
    2703 
    2704 > isolde stepto
    2705 
    2706 > isolde stepto
    2707 
    2708 > isolde stepto
    2709 
    2710 > isolde stepto
    2711 
    2712 > isolde stepto
    2713 
    2714 > isolde stepto
    2715 
    2716 > isolde stepto
    2717 
    2718 > isolde stepto
    2719 
    2720 > isolde stepto
    2721 
    2722 > isolde stepto
    2723 
    2724 > isolde stepto
    2725 
    2726 > isolde stepto
    2727 
    2728 > isolde stepto
    2729 
    2730 > isolde stepto
    2731 
    2732 > isolde stepto
    2733 
    2734 > isolde stepto
    2735 
    2736 > isolde stepto
    2737 
    2738 > isolde stepto
    2739 
    2740 > isolde stepto
    2741 
    2742 > isolde stepto
    2743 
    2744 > isolde stepto
    2745 
    2746 > isolde stepto
    2747 
    2748 > isolde stepto
    2749 
    2750 > isolde stepto
    2751 
    2752 > isolde stepto
    2753 
    2754 > isolde stepto
    2755 
    2756 > isolde stepto
    2757 
    2758 > isolde stepto
    2759 
    2760 > isolde stepto
    2761 
    2762 > isolde stepto
    2763 
    2764 > isolde stepto
    2765 
    2766 > isolde stepto
    2767 
    2768 > isolde stepto
    2769 
    2770 > isolde stepto
    2771 
    2772 > isolde stepto
    2773 
    2774 > isolde stepto
    2775 
    2776 > isolde stepto
    2777 
    2778 > isolde stepto
    2779 
    2780 > isolde stepto
    2781 
    2782 > isolde stepto
    2783 
    2784 > isolde stepto
    2785 
    2786 > isolde stepto
    2787 
    2788 > isolde stepto
    2789 
    2790 > isolde stepto
    2791 
    2792 > isolde stepto
    2793 
    2794 > isolde stepto
    2795 
    2796 > isolde stepto
    2797 
    2798 > isolde stepto
    2799 
    2800 > isolde stepto
    2801 
    2802 > isolde stepto
    2803 
    2804 > isolde stepto
    2805 
    2806 > isolde stepto
    2807 
    2808 > isolde stepto
    2809 
    2810 > isolde stepto
    2811 
    2812 > isolde stepto
    2813 
    2814 > isolde stepto
    2815 
    2816 > isolde stepto
    2817 
    2818 > isolde stepto
    2819 
    2820 > isolde stepto
    2821 
    2822 > isolde stepto
    2823 
    2824 > isolde stepto
    2825 
    2826 > isolde stepto
    2827 
    2828 > isolde stepto
    2829 
    2830 > isolde stepto
    2831 
    2832 > isolde stepto
    2833 
    2834 > isolde stepto
    2835 
    2836 > isolde stepto
    2837 
    2838 > isolde stepto
    2839 
    2840 > isolde stepto
    2841 
    2842 > isolde stepto
    2843 
    2844 > isolde stepto
    2845 
    2846 > isolde stepto
    2847 
    2848 > select clear
    2849 
    2850 > isolde stepto
    2851 
    2852 > isolde stepto
    2853 
    2854 > isolde stepto
    2855 
    2856 > isolde stepto
    2857 
    2858 > select clear
    2859 
    2860 > isolde stepto
    2861 
    2862 > isolde stepto
    2863 
    2864 > isolde stepto
    2865 
    2866 > select clear
    2867 
    2868 > isolde stepto
    2869 
    2870 > isolde stepto
    2871 
    2872 > isolde stepto
    2873 
    2874 > isolde stepto
    2875 
    2876 > isolde stepto
    2877 
    2878 > isolde stepto
    2879 
    2880 > isolde stepto
    2881 
    2882 > isolde stepto
    2883 
    2884 > isolde stepto
    2885 
    2886 > isolde stepto
    2887 
    2888 > isolde stepto
    2889 
    2890 > isolde stepto
    2891 
    2892 > isolde stepto
    2893 
    2894 > isolde stepto
    2895 
    2896 > isolde stepto
    2897 
    2898 > swapaa mousemode sel ILE
    2899 
    2900 > select up
    2901 
    2902 19 atoms, 18 bonds, 1 residue, 1 model selected 
    2903 
    2904 > color sel bychain
    2905 
    2906 > color sel byhetero
    2907 
    2908 > select #2/L:227-400
    2909 
    2910 777 atoms, 798 bonds, 47 residues, 1 model selected 
    2911 
    2912 > hide HC
    2913 
    2914 > select up
    2915 
    2916 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2917 
    2918 > color sel byhetero
    2919 
    2920 > select clear
    2921 
    2922 > color bychain
    2923 
    2924 > color byhetero
    2925 
    2926 > hide HC
    2927 
    2928 > select #2/L:227-400
    2929 
    2930 777 atoms, 798 bonds, 47 residues, 1 model selected 
    2931 
    2932 > select clear
    2933 
    2934 > isolde stepto
    2935 
    2936 > isolde stepto
    2937 
    2938 > isolde stepto
    2939 
    2940 > isolde stepto
    2941 
    2942 > isolde stepto
    2943 
    2944 > isolde stepto
    2945 
    2946 > isolde stepto
    2947 
    2948 > isolde stepto
    2949 
    2950 > isolde stepto
    2951 
    2952 > isolde stepto
    2953 
    2954 > isolde stepto
    2955 
    2956 > isolde stepto
    2957 
    2958 > isolde stepto
    2959 
    2960 > isolde stepto
    2961 
    2962 > isolde stepto
    2963 
    2964 > isolde stepto
    2965 
    2966 > isolde stepto
    2967 
    2968 > isolde stepto
    2969 
    2970 > isolde stepto
    2971 
    2972 > isolde stepto
    2973 
    2974 > select clear
    2975 
    2976 > show H&~HC
    2977 
    2978 > select clear
    2979 
    2980 > show H&~HC
    2981 
    2982 > show ~H
    2983 
    2984 > select #2/L:227-400
    2985 
    2986 777 atoms, 798 bonds, 47 residues, 1 model selected 
    2987 
    2988 > select clear
    2989 
    2990 > select clear
    2991 
    2992 > isolde stepto
    2993 
    2994 > isolde stepto
    2995 
    2996 > isolde stepto
    2997 
    2998 > isolde stepto
    2999 
    3000 > isolde stepto
    3001 
    3002 > isolde stepto
    3003 
    3004 > isolde stepto
    3005 
    3006 > isolde stepto
    3007 
    3008 > isolde stepto
    3009 
    3010 > isolde stepto
    3011 
    3012 > isolde stepto
    3013 
    3014 > isolde stepto
    3015 
    3016 > isolde stepto
    3017 
    3018 > isolde stepto
    3019 
    3020 > isolde stepto
    3021 
    3022 > isolde stepto
    3023 
    3024 > isolde stepto
    3025 
    3026 > isolde stepto
    3027 
    3028 > isolde stepto
    3029 
    3030 > isolde stepto
    3031 
    3032 > isolde stepto
    3033 
    3034 > isolde stepto
    3035 
    3036 > isolde stepto
    3037 
    3038 > isolde stepto
    3039 
    3040 > isolde stepto
    3041 
    3042 > isolde stepto
    3043 
    3044 > isolde stepto
    3045 
    3046 > select #2/M
    3047 
    3048 5833 atoms, 5950 bonds, 6 pseudobonds, 330 residues, 2 models selected 
    3049 
    3050 > select #2/M:1-50
    3051 
    3052 763 atoms, 772 bonds, 50 residues, 1 model selected 
    3053 
    3054 > select clear
    3055 
    3056 > isolde stepto
    3057 
    3058 > isolde stepto
    3059 
    3060 > isolde stepto
    3061 
    3062 > isolde stepto
    3063 
    3064 > isolde stepto
    3065 
    3066 > isolde stepto
    3067 
    3068 > isolde stepto
    3069 
    3070 > isolde stepto
    3071 
    3072 > isolde stepto
    3073 
    3074 > isolde stepto
    3075 
    3076 > isolde stepto
    3077 
    3078 > isolde stepto
    3079 
    3080 > isolde stepto
    3081 
    3082 > isolde stepto
    3083 
    3084 > select clear
    3085 
    3086 > select clear
    3087 
    3088 > isolde stepto
    3089 
    3090 > isolde stepto
    3091 
    3092 > isolde stepto
    3093 
    3094 > isolde stepto
    3095 
    3096 > isolde stepto
    3097 
    3098 > isolde stepto
    3099 
    3100 > isolde stepto
    3101 
    3102 > isolde stepto
    3103 
    3104 > isolde stepto
    3105 
    3106 > isolde stepto
    3107 
    3108 > isolde stepto
    3109 
    3110 > isolde stepto
    3111 
    3112 > isolde stepto
    3113 
    3114 > isolde stepto
    3115 
    3116 > isolde stepto
    3117 
    3118 > isolde stepto
    3119 
    3120 > isolde stepto
    3121 
    3122 > isolde stepto
    3123 
    3124 > isolde stepto
    3125 
    3126 > isolde stepto
    3127 
    3128 > isolde stepto
    3129 
    3130 > isolde stepto
    3131 
    3132 > isolde stepto
    3133 
    3134 > isolde stepto
    3135 
    3136 > isolde stepto
    3137 
    3138 > isolde stepto
    3139 
    3140 > isolde stepto
    3141 
    3142 > isolde stepto
    3143 
    3144 > isolde stepto
    3145 
    3146 > isolde stepto
    3147 
    3148 > isolde stepto
    3149 
    3150 > isolde stepto
    3151 
    3152 > isolde stepto
    3153 
    3154 > isolde stepto
    3155 
    3156 > isolde stepto
    3157 
    3158 > isolde stepto
    3159 
    3160 > isolde stepto
    3161 
    3162 > isolde stepto
    3163 
    3164 > isolde stepto
    3165 
    3166 > isolde stepto
    3167 
    3168 > isolde stepto
    3169 
    3170 > isolde stepto
    3171 
    3172 > isolde stepto
    3173 
    3174 > select #2/M:58-158
    3175 
    3176 1664 atoms, 1698 bonds, 101 residues, 1 model selected 
    3177 
    3178 > select clear
    3179 
    3180 > select #2/M:58-158
    3181 
    3182 1664 atoms, 1698 bonds, 101 residues, 1 model selected 
    3183 
    3184 > select clear
    3185 
    3186 > isolde stepto
    3187 
    3188 > isolde stepto
    3189 
    3190 > isolde stepto
    3191 
    3192 > isolde stepto
    3193 
    3194 > isolde stepto
    3195 
    3196 > isolde stepto
    3197 
    3198 > isolde stepto
    3199 
    3200 > isolde stepto
    3201 
    3202 > select clear
    3203 
    3204 > isolde stepto
    3205 
    3206 > isolde stepto
    3207 
    3208 > isolde stepto
    3209 
    3210 > isolde stepto
    3211 
    3212 > sequence chain #2/M
    3213 
    3214 Alignment identifier is 2.2/M 
    3215 
    3216 > select #2/M:58-158
    3217 
    3218 1665 atoms, 1699 bonds, 101 residues, 1 model selected 
    3219 
    3220 > select clear
    3221 
    3222 > select clear
    3223 
    3224 > isolde stepto
    3225 
    3226 > isolde stepto
    3227 
    3228 > isolde stepto
    3229 
    3230 > isolde stepto
    3231 
    3232 > select clear
    3233 
    3234 > isolde stepto
    3235 
    3236 > isolde stepto
    3237 
    3238 > isolde stepto
    3239 
    3240 > isolde stepto
    3241 
    3242 > isolde stepto
    3243 
    3244 > isolde stepto
    3245 
    3246 > isolde stepto
    3247 
    3248 > select clear
    3249 
    3250 > isolde stepto
    3251 
    3252 > isolde stepto
    3253 
    3254 > isolde stepto
    3255 
    3256 > isolde stepto
    3257 
    3258 > isolde stepto
    3259 
    3260 > isolde stepto
    3261 
    3262 > isolde stepto
    3263 
    3264 > isolde stepto
    3265 
    3266 > isolde stepto
    3267 
    3268 > isolde stepto
    3269 
    3270 > isolde stepto
    3271 
    3272 > isolde stepto
    3273 
    3274 > isolde stepto
    3275 
    3276 > isolde stepto
    3277 
    3278 > isolde stepto
    3279 
    3280 > isolde stepto
    3281 
    3282 > isolde stepto
    3283 
    3284 > isolde stepto
    3285 
    3286 > isolde stepto
    3287 
    3288 > isolde stepto
    3289 
    3290 > isolde stepto
    3291 
    3292 > isolde stepto
    3293 
    3294 > isolde stepto
    3295 
    3296 > isolde stepto
    3297 
    3298 > isolde stepto
    3299 
    3300 > select clear
    3301 
    3302 > isolde stepto
    3303 
    3304 > isolde stepto
    3305 
    3306 > isolde stepto
    3307 
    3308 > isolde stepto
    3309 
    3310 > select clear
    3311 
    3312 > isolde stepto
    3313 
    3314 > isolde stepto
    3315 
    3316 > isolde stepto
    3317 
    3318 > isolde stepto
    3319 
    3320 > isolde stepto
    3321 
    3322 > isolde stepto
    3323 
    3324 > isolde stepto
    3325 
    3326 > isolde stepto
    3327 
    3328 > isolde stepto
    3329 
    3330 > isolde stepto
    3331 
    3332 > isolde stepto
    3333 
    3334 > isolde stepto
    3335 
    3336 > isolde stepto
    3337 
    3338 > isolde stepto
    3339 
    3340 > isolde stepto
    3341 
    3342 > isolde stepto
    3343 
    3344 > isolde stepto
    3345 
    3346 > isolde stepto
    3347 
    3348 > isolde stepto
    3349 
    3350 > isolde stepto
    3351 
    3352 > isolde stepto
    3353 
    3354 > isolde stepto
    3355 
    3356 > isolde stepto
    3357 
    3358 > isolde stepto
    3359 
    3360 > isolde stepto
    3361 
    3362 > isolde stepto
    3363 
    3364 > isolde stepto
    3365 
    3366 > isolde stepto
    3367 
    3368 > isolde stepto
    3369 
    3370 > isolde stepto
    3371 
    3372 > isolde stepto
    3373 
    3374 > isolde stepto
    3375 
    3376 > isolde stepto
    3377 
    3378 > isolde stepto
    3379 
    3380 > isolde stepto
    3381 
    3382 > isolde stepto
    3383 
    3384 > isolde stepto
    3385 
    3386 > isolde stepto
    3387 
    3388 > isolde stepto
    3389 
    3390 > isolde stepto
    3391 
    3392 > isolde stepto
    3393 
    3394 > isolde stepto
    3395 
    3396 > isolde stepto
    3397 
    3398 > isolde stepto
    3399 
    3400 > isolde stepto
    3401 
    3402 > isolde stepto
    3403 
    3404 > isolde stepto
    3405 
    3406 > isolde stepto
    3407 
    3408 > isolde stepto
    3409 
    3410 > isolde stepto
    3411 
    3412 > isolde stepto
    3413 
    3414 > isolde stepto
    3415 
    3416 > isolde stepto
    3417 
    3418 > isolde stepto
    3419 
    3420 > isolde stepto
    3421 
    3422 > isolde stepto
    3423 
    3424 > isolde stepto
    3425 
    3426 > isolde stepto
    3427 
    3428 > isolde stepto
    3429 
    3430 > isolde stepto
    3431 
    3432 > isolde stepto
    3433 
    3434 > isolde stepto
    3435 
    3436 > isolde stepto
    3437 
    3438 > isolde stepto
    3439 
    3440 > isolde stepto
    3441 
    3442 > isolde stepto
    3443 
    3444 > isolde stepto
    3445 
    3446 > isolde stepto
    3447 
    3448 > delete sel
    3449 
    3450 > select #2/M:178-400
    3451 
    3452 2337 atoms, 2378 bonds, 147 residues, 1 model selected 
    3453 
    3454 > select clear
    3455 
    3456 > select clear
    3457 
    3458 > select clear
    3459 
    3460 > isolde stepto
    3461 
    3462 > isolde stepto
    3463 
    3464 > isolde stepto
    3465 
    3466 > isolde stepto
    3467 
    3468 > select clear
    3469 
    3470 > isolde stepto
    3471 
    3472 > isolde stepto
    3473 
    3474 > isolde stepto
    3475 
    3476 > isolde stepto
    3477 
    3478 > isolde stepto
    3479 
    3480 > isolde stepto
    3481 
    3482 > isolde stepto
    3483 
    3484 > isolde stepto
    3485 
    3486 > isolde stepto
    3487 
    3488 > isolde stepto
    3489 
    3490 > isolde stepto
    3491 
    3492 > isolde stepto
    3493 
    3494 > isolde stepto
    3495 
    3496 > isolde stepto
    3497 
    3498 > isolde stepto
    3499 
    3500 > isolde stepto
    3501 
    3502 > isolde stepto
    3503 
    3504 > isolde stepto
    3505 
    3506 > isolde stepto
    3507 
    3508 > isolde stepto
    3509 
    3510 > isolde stepto
    3511 
    3512 > isolde stepto
    3513 
    3514 > isolde stepto
    3515 
    3516 > isolde stepto
    3517 
    3518 > isolde stepto
    3519 
    3520 > isolde stepto
    3521 
    3522 > isolde stepto
    3523 
    3524 > isolde stepto
    3525 
    3526 > isolde stepto
    3527 
    3528 > isolde stepto
    3529 
    3530 > isolde stepto
    3531 
    3532 > isolde stepto
    3533 
    3534 > select clear
    3535 
    3536 > isolde stepto
    3537 
    3538 > select clear
    3539 
    3540 > isolde stepto
    3541 
    3542 > isolde stepto
    3543 
    3544 > isolde stepto
    3545 
    3546 > isolde stepto
    3547 
    3548 > isolde stepto
    3549 
    3550 > isolde stepto
    3551 
    3552 > isolde stepto
    3553 
    3554 > isolde stepto
    3555 
    3556 > isolde stepto
    3557 
    3558 > isolde stepto
    3559 
    3560 > isolde stepto
    3561 
    3562 > isolde stepto
    3563 
    3564 > isolde stepto
    3565 
    3566 > isolde stepto
    3567 
    3568 > isolde stepto
    3569 
    3570 > isolde stepto
    3571 
    3572 > isolde stepto
    3573 
    3574 > isolde stepto
    3575 
    3576 > isolde stepto
    3577 
    3578 > isolde stepto
    3579 
    3580 > isolde stepto
    3581 
    3582 > isolde stepto
    3583 
    3584 > isolde stepto
    3585 
    3586 > isolde stepto
    3587 
    3588 > isolde stepto
    3589 
    3590 > isolde stepto
    3591 
    3592 > isolde stepto
    3593 
    3594 > isolde stepto
    3595 
    3596 > isolde stepto
    3597 
    3598 > isolde stepto
    3599 
    3600 > isolde stepto
    3601 
    3602 > isolde stepto
    3603 
    3604 > isolde stepto
    3605 
    3606 > isolde stepto
    3607 
    3608 > isolde stepto
    3609 
    3610 > isolde stepto
    3611 
    3612 > isolde stepto
    3613 
    3614 > isolde stepto
    3615 
    3616 > isolde stepto
    3617 
    3618 > isolde stepto
    3619 
    3620 > isolde stepto
    3621 
    3622 > isolde stepto
    3623 
    3624 > isolde stepto
    3625 
    3626 > isolde stepto
    3627 
    3628 > isolde stepto
    3629 
    3630 > isolde stepto
    3631 
    3632 > isolde stepto
    3633 
    3634 > isolde stepto
    3635 
    3636 > isolde stepto
    3637 
    3638 > select clear
    3639 
    3640 > isolde stepto
    3641 
    3642 > isolde stepto
    3643 
    3644 > isolde stepto
    3645 
    3646 > isolde stepto
    3647 
    3648 > isolde stepto
    3649 
    3650 > isolde stepto
    3651 
    3652 > isolde stepto
    3653 
    3654 > isolde stepto
    3655 
    3656 > isolde stepto
    3657 
    3658 > isolde stepto
    3659 
    3660 > isolde stepto
    3661 
    3662 > isolde stepto
    3663 
    3664 > isolde stepto
    3665 
    3666 > isolde stepto
    3667 
    3668 > isolde stepto
    3669 
    3670 > isolde stepto
    3671 
    3672 > isolde stepto
    3673 
    3674 > isolde stepto
    3675 
    3676 > isolde stepto
    3677 
    3678 > isolde stepto
    3679 
    3680 > isolde stepto
    3681 
    3682 > isolde stepto
    3683 
    3684 > isolde stepto
    3685 
    3686 > isolde stepto
    3687 
    3688 > isolde stepto
    3689 
    3690 > isolde stepto
    3691 
    3692 > isolde stepto
    3693 
    3694 > isolde stepto
    3695 
    3696 > isolde stepto
    3697 
    3698 > isolde stepto
    3699 
    3700 > isolde stepto
    3701 
    3702 > select clear
    3703 
    3704 > isolde stepto
    3705 
    3706 > isolde stepto
    3707 
    3708 > isolde stepto
    3709 
    3710 > select clear
    3711 
    3712 > isolde stepto
    3713 
    3714 > isolde stepto
    3715 
    3716 > isolde stepto
    3717 
    3718 > isolde stepto
    3719 
    3720 > isolde stepto
    3721 
    3722 > isolde stepto
    3723 
    3724 > isolde stepto
    3725 
    3726 > isolde stepto
    3727 
    3728 > isolde stepto
    3729 
    3730 > isolde stepto
    3731 
    3732 > isolde stepto
    3733 
    3734 > isolde stepto
    3735 
    3736 > isolde stepto
    3737 
    3738 > isolde stepto
    3739 
    3740 > isolde stepto
    3741 
    3742 > select clear
    3743 
    3744 > isolde stepto
    3745 
    3746 > isolde stepto
    3747 
    3748 > isolde stepto
    3749 
    3750 > isolde stepto
    3751 
    3752 > isolde stepto
    3753 
    3754 > isolde stepto
    3755 
    3756 > select clear
    3757 
    3758 > isolde stepto
    3759 
    3760 > isolde stepto
    3761 
    3762 > isolde stepto
    3763 
    3764 > isolde stepto
    3765 
    3766 > isolde stepto
    3767 
    3768 > save working.cxs
    3769 
    3770 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    3771 
    3772 > show #!4 models
    3773 
    3774 > hide #!4 models
    3775 
    3776 > swapaa mousemode sel GLY
    3777 
    3778 > select up
    3779 
    3780 16 atoms, 15 bonds, 1 residue, 1 model selected 
    3781 
    3782 > select up
    3783 
    3784 255 atoms, 259 bonds, 18 residues, 1 model selected 
    3785 
    3786 > isolde ignore sel
    3787 
    3788 ISOLDE: currently ignoring 26 residues in model 2.2 
    3789 
    3790 > select clear
    3791 
    3792 > isolde ~ignore
    3793 
    3794 > select up
    3795 
    3796 23 atoms, 21 bonds, 2 residues, 1 model selected 
    3797 
    3798 > select clear
    3799 
    3800 > delete sel
    3801 
    3802 > delete sel
    3803 
    3804 > select clear
    3805 
    3806 > save working.cxs
    3807 
    3808 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    3809 
    3810 > ui tool show "Build Structure"
    3811 
    3812 > build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
    3813 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3814 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3815 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3816 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3817 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3818 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3819 > rotLib Dunbrack
    3820 
    3821 Chain information for custom built #5 
    3822 --- 
    3823 Chain | Description 
    3824 A | No description available 
    3825  
    3826 
    3827 > build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
    3828 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3829 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3830 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3831 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3832 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3833 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3834 > rotLib Dunbrack
    3835 
    3836 Chain information for custom built #6 
    3837 --- 
    3838 Chain | Description 
    3839 A | No description available 
    3840  
    3841 
    3842 > close #5
    3843 
    3844 > select #6
    3845 
    3846 258 atoms, 263 bonds, 36 residues, 1 model selected 
    3847 
    3848 > show sel&:1
    3849 
    3850 > ui mousemode right "translate selected models"
    3851 
    3852 > ui mousemode right "rotate selected models"
    3853 
    3854 > ui mousemode right "translate selected models"
    3855 
    3856 > ui mousemode right "rotate selected models"
    3857 
    3858 > ui mousemode right "translate selected models"
    3859 
    3860 > hide #6 models
    3861 
    3862 > delete #2/M:332-367
    3863 
    3864 > addh #6
    3865 
    3866 Summary of feedback from adding hydrogens to custom built #6 
    3867 --- 
    3868 notes | No usable SEQRES records for custom built (#6) chain A; guessing
    3869 termini instead 
    3870 Chain-initial residues that are actual N termini: custom built #6/A PHE 1 
    3871 Chain-initial residues that are not actual N termini: 
    3872 Chain-final residues that are actual C termini: custom built #6/A GLN 36 
    3873 Chain-final residues that are not actual C termini: 
    3874 37 hydrogen bonds 
    3875 250 hydrogens added 
    3876  
    3877 
    3878 > isolde ignore #2/C
    3879 
    3880 ISOLDE: currently ignoring 303 residues in model 2.2 
    3881 
    3882 > select #2/M:332-367
    3883 
    3884 506 atoms, 511 bonds, 36 residues, 1 model selected 
    3885 
    3886 > hide HC
    3887 
    3888 > delete #2/M:339-367
    3889 
    3890 > isolde ~ignore
    3891 
    3892 > select clear
    3893 
    3894 > select clear
    3895 
    3896 > select up
    3897 
    3898 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3899 
    3900 > select up
    3901 
    3902 92 atoms, 94 bonds, 6 residues, 1 model selected 
    3903 
    3904 > select clear
    3905 
    3906 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    3907 bonded heavy atom. 
    3908 
    3909 > select up
    3910 
    3911 14 atoms, 14 bonds, 1 residue, 1 model selected 
    3912 
    3913 > delete sel
    3914 
    3915 > save ser_M331_O_glycan.jpg
    3916 
    3917 > open 3e80
    3918 
    3919 3e80 title: 
    3920 Structure of Heparinase II complexed with heparan sulfate degradation
    3921 disaccharide product [more info...] 
    3922  
    3923 Chain information for 3e80 #5 
    3924 --- 
    3925 Chain | Description 
    3926 A B C | Heparinase II protein 
    3927  
    3928 Non-standard residues in 3e80 #5 
    3929 --- 
    3930 GCD — 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid 
    3931 GCU — alpha-D-glucopyranuronic acid 
    3932 MAN — alpha-D-mannopyranose 
    3933 NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose 
    3934 PO4 — phosphate ion 
    3935 RAM — alpha-L-rhamnopyranose 
    3936 XYS — alpha-D-xylopyranose 
    3937 ZN — zinc ion 
    3938  
    3939 3e80 mmCIF Assemblies 
    3940 --- 
    3941 1| author_and_software_defined_assembly 
    3942 2| author_and_software_defined_assembly 
    3943 3| author_and_software_defined_assembly 
    3944  
    3945 
    3946 > addh #5
    3947 
    3948 Summary of feedback from adding hydrogens to 3e80 #5 
    3949 --- 
    3950 warning | Not adding hydrogens to 3e80 #5/C LEU 732 CB because it is missing
    3951 heavy-atom bond partners 
    3952 notes | Termini for 3e80 (#5) chain A determined from SEQRES records 
    3953 Termini for 3e80 (#5) chain B determined from SEQRES records 
    3954 Termini for 3e80 (#5) chain C determined from SEQRES records 
    3955 Chain-initial residues that are actual N termini: 
    3956 Chain-initial residues that are not actual N termini: 3e80 #5/A PCA 26, 3e80
    3957 #5/B PCA 26, 3e80 #5/C PCA 26 
    3958 Chain-final residues that are actual C termini: 3e80 #5/A ARG 772, 3e80 #5/B
    3959 ARG 772, 3e80 #5/C ARG 772 
    3960 Chain-final residues that are not actual C termini: 
    3961 Missing OXT added to C-terminal residue 3e80 #5/A ARG 772 
    3962 Missing OXT added to C-terminal residue 3e80 #5/B ARG 772 
    3963 Missing OXT added to C-terminal residue 3e80 #5/C ARG 772 
    3964 3540 hydrogen bonds 
    3965 Adding 'H' to 3e80 #5/A PCA 26 
    3966 Adding 'H' to 3e80 #5/B PCA 26 
    3967 Adding 'H' to 3e80 #5/C PCA 26 
    3968 18911 hydrogens added 
    3969  
    3970 
    3971 > select #5
    3972 
    3973 37630 atoms, 37586 bonds, 17 pseudobonds, 2807 residues, 2 models selected 
    3974 
    3975 > hide #!2 models
    3976 
    3977 > select clear
    3978 
    3979 > select clear
    3980 
    3981 > select #5/B:134|(#5/E:1-4)
    3982 
    3983 90 atoms, 93 bonds, 5 residues, 1 model selected 
    3984 
    3985 > hide #5&~sel
    3986 
    3987 > ~cartoon #5
    3988 
    3989 > show #!2 models
    3990 
    3991 > ui mousemode right "translate selected models"
    3992 
    3993 > ui mousemode right "rotate selected models"
    3994 
    3995 > ui mousemode right "translate selected models"
    3996 
    3997 > ui mousemode right "rotate selected models"
    3998 
    3999 > ui mousemode right "translate selected models"
    4000 
    4001 > select (#5/E:1-4)
    4002 
    4003 77 atoms, 80 bonds, 4 residues, 1 model selected 
    4004 
    4005 > save working.cxs
    4006 
    4007 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4008 Restoring stepper: working_noh_real_space_refined.pdb 
    4009 opened ChimeraX session 
    4010 
    4011 > open
    4012 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb
    4013 
    4014 Summary of feedback from opening
    4015 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb 
    4016 --- 
    4017 warnings | End residue of secondary structure not found: HELIX 55 55 THR C 19
    4018 GLY C 21 1 3 
    4019 Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C 34
    4020 1 7 
    4021 Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C 55
    4022 1 3 
    4023 Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C 69
    4024 1 6 
    4025 Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C 81
    4026 1 7 
    4027 Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C 91
    4028 1 3 
    4029 5 messages similar to the above omitted 
    4030 Cannot find LINK/SSBOND residue GCU (2 ) 
    4031 Cannot find LINK/SSBOND residue XYS (3 ) 
    4032 Cannot find LINK/SSBOND residue RAM (4 ) 
    4033 Cannot find LINK/SSBOND residue MAN (1 ) 
    4034 Cannot find LINK/SSBOND residue GCU (2 ) 
    4035 3 messages similar to the above omitted 
    4036  
    4037 Chain information for working.pdb #7 
    4038 --- 
    4039 Chain | Description 
    4040 AA | No description available 
    4041 AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    4042 description available 
    4043 BA BC BF BG BH BJ BK BL BM BN BO BP BQ BR BS BT BU BX ba bb bc bd be bf bg bh
    4044 bi bj bk bl bm bo bp | No description available 
    4045 BB BD BE BI BV BW bn | No description available 
    4046 C | No description available 
    4047 C1 | No description available 
    4048 C2 | No description available 
    4049 H1 | No description available 
    4050 H2 | No description available 
    4051 L | No description available 
    4052 M | No description available 
    4053 aa | No description available 
    4054 ab ac ad ae af ag ah ai aj am an ao ap | No description available 
    4055 ak | No description available 
    4056  
    4057 
    4058 > select clear
    4059 
    4060 > hide #7&protein
    4061 
    4062 > hide #!5 models
    4063 
    4064 > select #7/CG
    4065 
    4066 78 atoms, 81 bonds, 4 residues, 1 model selected 
    4067 
    4068 > hide #!7 models
    4069 
    4070 > delete sel
    4071 
    4072 > select clear
    4073 
    4074 > select clear
    4075 
    4076 > view #2/M:330
    4077 
    4078 > show #!7 models
    4079 
    4080 > select #7/MG
    4081 
    4082 78 atoms, 81 bonds, 4 residues, 1 model selected 
    4083 
    4084 > hide #!7 models
    4085 
    4086 > delete sel
    4087 
    4088 > select clear
    4089 
    4090 > select clear
    4091 
    4092 > save M331_glycan.jpg
    4093 
    4094 > save working.cxs
    4095 
    4096 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4097 
    4098 > select #2/ak
    4099 
    4100 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    4101 
    4102 > ui tool show "Build Structure"
    4103 
    4104 > build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
    4105 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    4106 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    4107 
    4108 Chain information for custom built #8 
    4109 --- 
    4110 Chain | Description 
    4111 A | No description available 
    4112  
    4113 
    4114 > addh #8
    4115 
    4116 Summary of feedback from adding hydrogens to custom built #8 
    4117 --- 
    4118 notes | No usable SEQRES records for custom built (#8) chain A; guessing
    4119 termini instead 
    4120 Chain-initial residues that are actual N termini: custom built #8/A ALA 1 
    4121 Chain-initial residues that are not actual N termini: 
    4122 Chain-final residues that are actual C termini: custom built #8/A ARG 11 
    4123 Chain-final residues that are not actual C termini: 
    4124 0 hydrogen bonds 
    4125 80 hydrogens added 
    4126  
    4127 
    4128 > select #8
    4129 
    4130 158 atoms, 160 bonds, 11 residues, 1 model selected 
    4131 
    4132 > show sel
    4133 
    4134 > ui mousemode right "translate selected atoms"
    4135 
    4136 > ui mousemode right "rotate selected models"
    4137 
    4138 > ui mousemode right "translate selected models"
    4139 
    4140 > ui mousemode right "rotate selected models"
    4141 
    4142 > ui mousemode right "translate selected models"
    4143 
    4144 > ui mousemode right "rotate selected models"
    4145 
    4146 > ui mousemode right "translate selected models"
    4147 
    4148 > save working_2.cxs
    4149 
    4150 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4151 Restoring stepper: working_noh_real_space_refined.pdb 
    4152 opened ChimeraX session 
    4153 
    4154 > save
    4155 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
    4156 > models #2
    4157 
    4158 > close #2
    4159 
    4160 > open
    4161 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
    4162 
    4163 Summary of feedback from opening
    4164 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb 
    4165 --- 
    4166 warnings | End residue of secondary structure not found: HELIX 55 55 THR C 19
    4167 GLY C 21 1 3 
    4168 Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C 34
    4169 1 7 
    4170 Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C 55
    4171 1 3 
    4172 Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C 69
    4173 1 6 
    4174 Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C 81
    4175 1 7 
    4176 Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C 91
    4177 1 3 
    4178 5 messages similar to the above omitted 
    4179 Cannot find LINK/SSBOND residue GCU (2 ) 
    4180 Cannot find LINK/SSBOND residue XYS (3 ) 
    4181 Cannot find LINK/SSBOND residue RAM (4 ) 
    4182 Cannot find LINK/SSBOND residue MAN (1 ) 
    4183 Cannot find LINK/SSBOND residue GCU (2 ) 
    4184 3 messages similar to the above omitted 
    4185  
    4186 Chain information for working_2.pdb #8 
    4187 --- 
    4188 Chain | Description 
    4189 AA | No description available 
    4190 AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    4191 description available 
    4192 BA BC BF BG BH BJ BK BL BM BN BO BP BQ BR BS BT BU BX ba bb bc bd be bf bg bh
    4193 bi bj bk bl bm bo bp | No description available 
    4194 BB BD BE BI BV BW bn | No description available 
    4195 C | No description available 
    4196 C1 | No description available 
    4197 C2 | No description available 
    4198 H1 | No description available 
    4199 H2 | No description available 
    4200 L | No description available 
    4201 M | No description available 
    4202 aa | No description available 
    4203 ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available 
    4204  
    4205 
    4206 > open
    4207 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc
    4208 
    4209 Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    4210 0.0224, step 2, values float32 
    4211 
    4212 > clipper associate #9 toModel #8
    4213 
    4214 Chain information for working_2.pdb 
    4215 --- 
    4216 Chain | Description 
    4217 8.2/AA | No description available 
    4218 8.2/AB 8.2/AC 8.2/AD 8.2/AE 8.2/AF 8.2/AG 8.2/AH 8.2/AI 8.2/AJ 8.2/AK 8.2/AL
    4219 8.2/AM 8.2/AN 8.2/AO 8.2/AP 8.2/AQ 8.2/AR 8.2/AS 8.2/AT 8.2/AU 8.2/AV 8.2/AW
    4220 8.2/AX | No description available 
    4221 8.2/BA 8.2/BC 8.2/BF 8.2/BG 8.2/BH 8.2/BJ 8.2/BK 8.2/BL 8.2/BM 8.2/BN 8.2/BO
    4222 8.2/BP 8.2/BQ 8.2/BR 8.2/BS 8.2/BT 8.2/BU 8.2/BX 8.2/ba 8.2/bb 8.2/bc 8.2/bd
    4223 8.2/be 8.2/bf 8.2/bg 8.2/bh 8.2/bi 8.2/bj 8.2/bk 8.2/bl 8.2/bm 8.2/bo 8.2/bp |
    4224 No description available 
    4225 8.2/BB 8.2/BD 8.2/BE 8.2/BI 8.2/BV 8.2/BW 8.2/bn | No description available 
    4226 8.2/C | No description available 
    4227 8.2/C1 | No description available 
    4228 8.2/C2 | No description available 
    4229 8.2/H1 | No description available 
    4230 8.2/H2 | No description available 
    4231 8.2/L | No description available 
    4232 8.2/M | No description available 
    4233 8.2/aa | No description available 
    4234 8.2/ab 8.2/ac 8.2/ad 8.2/ae 8.2/af 8.2/ag 8.2/ah 8.2/ai 8.2/aj 8.2/ak 8.2/al
    4235 8.2/am 8.2/an 8.2/ao 8.2/ap | No description available 
    4236  
    4237 
    4238 > close #1
    4239 
    4240 > close #2
    4241 
    4242 > select #3
    4243 
    4244 508 atoms, 513 bonds, 36 residues, 8 models selected 
    4245 
    4246 > hide #!4 models
    4247 
    4248 > select #8/ak
    4249 
    4250 1079 atoms, 1095 bonds, 4 pseudobonds, 61 residues, 2 models selected 
    4251 
    4252 > hide #!3 models
    4253 
    4254 > show #!3 models
    4255 
    4256 > close #4
    4257 
    4258 > view #3
    4259 
    4260 > show #3
    4261 
    4262 > hide #!3 models
    4263 
    4264 > show #!3 models
    4265 
    4266 > view #3
    4267 
    4268 > close #3
    4269 
    4270 > close #5
    4271 
    4272 > close #6
    4273 
    4274 > close #7
    4275 
    4276 > volume gaussian #8 bfactor 50
    4277 
    4278 > clipper associate #1 toModel #8
    4279 
    4280 > select clear
    4281 
    4282 > save reopened.cxs
    4283 
    4284 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4285 Traceback (most recent call last): 
    4286 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4287 packages/chimerax/core/session.py", line 280, in process 
    4288 data = sm.take_snapshot(obj, session, self.state_flags) 
    4289 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4290 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4291 data = {'structure': self.structure, 
    4292 File "cymol.pyx", line 1437, in
    4293 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4294 RuntimeError: Residue already deleted 
    4295  
    4296 The above exception was the direct cause of the following exception: 
    4297  
    4298 Traceback (most recent call last): 
    4299 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4300 packages/chimerax/core/session.py", line 259, in discovery 
    4301 self.processed[key] = self.process(obj, parents) 
    4302 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4303 packages/chimerax/core/session.py", line 283, in process 
    4304 raise RuntimeError(msg) from e 
    4305 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4306 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4307 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4308  
    4309 During handling of the above exception, another exception occurred: 
    4310  
    4311 Traceback (most recent call last): 
    4312 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4313 packages/chimerax/core/session.py", line 826, in save 
    4314 session.save(output, version=version, include_maps=include_maps) 
    4315 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4316 packages/chimerax/core/session.py", line 583, in save 
    4317 mgr.discovery(self._state_containers) 
    4318 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4319 packages/chimerax/core/session.py", line 261, in discovery 
    4320 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4321 ValueError: error processing: 'isolde residue stepper 1' ->
    4322 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4323 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4324 saving session data for 'isolde residue stepper 1' ->
    4325 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4326 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4327  
    4328 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4329 saving session data for 'isolde residue stepper 1' -> -> 
    4330  
    4331 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4332 packages/chimerax/core/session.py", line 261, in discovery 
    4333 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4334  
    4335 See log for complete Python traceback. 
    4336  
    4337 Traceback (most recent call last): 
    4338 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4339 packages/chimerax/core/session.py", line 280, in process 
    4340 data = sm.take_snapshot(obj, session, self.state_flags) 
    4341 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4342 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4343 data = {'structure': self.structure, 
    4344 File "cymol.pyx", line 1437, in
    4345 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4346 RuntimeError: Residue already deleted 
    4347  
    4348 The above exception was the direct cause of the following exception: 
    4349  
    4350 Traceback (most recent call last): 
    4351 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4352 packages/chimerax/core/session.py", line 259, in discovery 
    4353 self.processed[key] = self.process(obj, parents) 
    4354 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4355 packages/chimerax/core/session.py", line 283, in process 
    4356 raise RuntimeError(msg) from e 
    4357 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4358 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4359 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4360  
    4361 During handling of the above exception, another exception occurred: 
    4362  
    4363 Traceback (most recent call last): 
    4364 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4365 packages/chimerax/cmd_line/tool.py", line 275, in execute 
    4366 cmd.run(cmd_text) 
    4367 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4368 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4369 result = ci.function(session, **kw_args) 
    4370 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4371 packages/chimerax/save_command/cmd.py", line 66, in cmd_save 
    4372 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    4373 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4374 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4375 result = ci.function(session, **kw_args) 
    4376 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4377 packages/chimerax/save_command/cmd.py", line 79, in provider_save 
    4378 mgr).save(session, path, **provider_kw) 
    4379 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4380 packages/chimerax/core_formats/__init__.py", line 79, in save 
    4381 return cxs_save(session, path, **kw) 
    4382 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4383 packages/chimerax/core/session.py", line 826, in save 
    4384 session.save(output, version=version, include_maps=include_maps) 
    4385 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4386 packages/chimerax/core/session.py", line 583, in save 
    4387 mgr.discovery(self._state_containers) 
    4388 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4389 packages/chimerax/core/session.py", line 261, in discovery 
    4390 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4391 ValueError: error processing: 'isolde residue stepper 1' ->
    4392 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4393 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4394 saving session data for 'isolde residue stepper 1' ->
    4395 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4396 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4397  
    4398 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4399 saving session data for 'isolde residue stepper 1' -> -> 
    4400  
    4401 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4402 packages/chimerax/core/session.py", line 261, in discovery 
    4403 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4404  
    4405 See log for complete Python traceback. 
    4406  
    4407 
    4408 > isolde stepto sel
    4409 
    4410 > select up
    4411 
    4412 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4413 
    4414 > save reopened.cxs
    4415 
    4416 Taking snapshot of stepper: working_2.pdb 
    4417 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4418 Traceback (most recent call last): 
    4419 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4420 packages/chimerax/core/session.py", line 280, in process 
    4421 data = sm.take_snapshot(obj, session, self.state_flags) 
    4422 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4423 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4424 data = {'structure': self.structure, 
    4425 File "cymol.pyx", line 1437, in
    4426 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4427 RuntimeError: Residue already deleted 
    4428  
    4429 The above exception was the direct cause of the following exception: 
    4430  
    4431 Traceback (most recent call last): 
    4432 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4433 packages/chimerax/core/session.py", line 259, in discovery 
    4434 self.processed[key] = self.process(obj, parents) 
    4435 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4436 packages/chimerax/core/session.py", line 283, in process 
    4437 raise RuntimeError(msg) from e 
    4438 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4439 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4440 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4441  
    4442 During handling of the above exception, another exception occurred: 
    4443  
    4444 Traceback (most recent call last): 
    4445 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4446 packages/chimerax/core/session.py", line 826, in save 
    4447 session.save(output, version=version, include_maps=include_maps) 
    4448 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4449 packages/chimerax/core/session.py", line 583, in save 
    4450 mgr.discovery(self._state_containers) 
    4451 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4452 packages/chimerax/core/session.py", line 261, in discovery 
    4453 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4454 ValueError: error processing: 'isolde residue stepper 1' ->
    4455 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4456 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4457 saving session data for 'isolde residue stepper 1' ->
    4458 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4459 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4460  
    4461 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4462 saving session data for 'isolde residue stepper 1' -> -> 
    4463  
    4464 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4465 packages/chimerax/core/session.py", line 261, in discovery 
    4466 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4467  
    4468 See log for complete Python traceback. 
    4469  
    4470 Traceback (most recent call last): 
    4471 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4472 packages/chimerax/core/session.py", line 280, in process 
    4473 data = sm.take_snapshot(obj, session, self.state_flags) 
    4474 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4475 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4476 data = {'structure': self.structure, 
    4477 File "cymol.pyx", line 1437, in
    4478 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4479 RuntimeError: Residue already deleted 
    4480  
    4481 The above exception was the direct cause of the following exception: 
    4482  
    4483 Traceback (most recent call last): 
    4484 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4485 packages/chimerax/core/session.py", line 259, in discovery 
    4486 self.processed[key] = self.process(obj, parents) 
    4487 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4488 packages/chimerax/core/session.py", line 283, in process 
    4489 raise RuntimeError(msg) from e 
    4490 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4491 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4492 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4493  
    4494 During handling of the above exception, another exception occurred: 
    4495  
    4496 Traceback (most recent call last): 
    4497 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4498 packages/chimerax/cmd_line/tool.py", line 275, in execute 
    4499 cmd.run(cmd_text) 
    4500 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4501 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4502 result = ci.function(session, **kw_args) 
    4503 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4504 packages/chimerax/save_command/cmd.py", line 66, in cmd_save 
    4505 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    4506 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4507 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4508 result = ci.function(session, **kw_args) 
    4509 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4510 packages/chimerax/save_command/cmd.py", line 79, in provider_save 
    4511 mgr).save(session, path, **provider_kw) 
    4512 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4513 packages/chimerax/core_formats/__init__.py", line 79, in save 
    4514 return cxs_save(session, path, **kw) 
    4515 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4516 packages/chimerax/core/session.py", line 826, in save 
    4517 session.save(output, version=version, include_maps=include_maps) 
    4518 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4519 packages/chimerax/core/session.py", line 583, in save 
    4520 mgr.discovery(self._state_containers) 
    4521 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4522 packages/chimerax/core/session.py", line 261, in discovery 
    4523 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4524 ValueError: error processing: 'isolde residue stepper 1' ->
    4525 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4526 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4527 saving session data for 'isolde residue stepper 1' ->
    4528 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4529 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4530  
    4531 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4532 saving session data for 'isolde residue stepper 1' -> -> 
    4533  
    4534 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4535 packages/chimerax/core/session.py", line 261, in discovery 
    4536 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4537  
    4538 See log for complete Python traceback. 
    4539  
    4540 
    4541 > save reopened.cxs
    4542 
    4543 Taking snapshot of stepper: working_2.pdb 
    4544 
    4545 > ui tool show "Build Structure"
    4546 
    4547 > build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
    4548 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    4549 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    4550 
    4551 Chain information for custom built #1 
    4552 --- 
    4553 Chain | Description 
    4554 A | No description available 
    4555  
    4556 
    4557 > addh #1
    4558 
    4559 Summary of feedback from adding hydrogens to custom built #1 
    4560 --- 
    4561 notes | No usable SEQRES records for custom built (#1) chain A; guessing
    4562 termini instead 
    4563 Chain-initial residues that are actual N termini: custom built #1/A ALA 1 
    4564 Chain-initial residues that are not actual N termini: 
    4565 Chain-final residues that are actual C termini: custom built #1/A ARG 11 
    4566 Chain-final residues that are not actual C termini: 
    4567 0 hydrogen bonds 
    4568 80 hydrogens added 
    4569  
    4570 
    4571 > select #1
    4572 
    4573 158 atoms, 160 bonds, 11 residues, 1 model selected 
    4574 
    4575 > show sel
    4576 
    4577 > ui mousemode right "translate selected models"
    4578 
    4579 > ui mousemode right "rotate selected models"
    4580 
    4581 > ui mousemode right "translate selected models"
    4582 
    4583 > save reopened.cxs
    4584 
    4585 Taking snapshot of stepper: working_2.pdb 
    4586 Restoring stepper: working_2.pdb 
    4587 opened ChimeraX session 
    4588 
    4589 > ui tool show Shell
    4590 
    4591 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    4592 UserWarning: IPython History requires SQLite, your history will not be saved 
    4593 warn("IPython History requires SQLite, your history will not be saved") 
    4594 
    4595 > isolde start
    4596 
    4597 > set selectionWidth 4
    4598 
    4599 Done loading forcefield 
    4600 
    4601 > select clear
    4602 
    4603 > select clear
    4604 
    4605 > select ~protein
    4606 
    4607 16729 atoms, 17062 bonds, 366 pseudobonds, 140 residues, 23 models selected 
    4608 
    4609 > select /ak
    4610 
    4611 1238 atoms, 1261 bonds, 72 residues, 1 model selected 
    4612 
    4613 > hide #!1 models
    4614 
    4615 > select up
    4616 
    4617 45 atoms, 44 bonds, 2 residues, 1 model selected 
    4618 
    4619 > select up
    4620 
    4621 71 atoms, 71 bonds, 4 residues, 1 model selected 
    4622 
    4623 > isolde ignore sel
    4624 
    4625 ISOLDE: currently ignoring 4 residues in model 8.2 
    4626 
    4627 > select up
    4628 
    4629 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4630 
    4631 > select up
    4632 
    4633 939 atoms, 951 bonds, 60 residues, 1 model selected 
    4634 
    4635 > select up
    4636 
    4637 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    4638 
    4639 > select up
    4640 
    4641 1179 atoms, 1198 bonds, 62 residues, 1 model selected 
    4642 
    4643 > isolde ignore sel
    4644 
    4645 ISOLDE: currently ignoring 66 residues in model 8.2 
    4646 
    4647 > select up
    4648 
    4649 20 atoms, 19 bonds, 1 residue, 1 model selected 
    4650 
    4651 > select up
    4652 
    4653 159 atoms, 161 bonds, 11 residues, 1 model selected 
    4654 
    4655 Chain CG, residue 1 specifies more than one residue! The simulation can still
    4656 run, but this will probably cause problems later if not rectified by
    4657 renumbering. 
    4658 
    4659 Chain CG, residue 2 specifies more than one residue! The simulation can still
    4660 run, but this will probably cause problems later if not rectified by
    4661 renumbering. 
    4662 
    4663 Chain CG, residue 3 specifies more than one residue! The simulation can still
    4664 run, but this will probably cause problems later if not rectified by
    4665 renumbering. 
    4666 
    4667 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4668 run, but this will probably cause problems later if not rectified by
    4669 renumbering. 
    4670 
    4671 Chain CG, residue 1 specifies more than one residue! The simulation can still
    4672 run, but this will probably cause problems later if not rectified by
    4673 renumbering. 
    4674 
    4675 Chain CG, residue 2 specifies more than one residue! The simulation can still
    4676 run, but this will probably cause problems later if not rectified by
    4677 renumbering. 
    4678 
    4679 Chain CG, residue 3 specifies more than one residue! The simulation can still
    4680 run, but this will probably cause problems later if not rectified by
    4681 renumbering. 
    4682 
    4683 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4684 run, but this will probably cause problems later if not rectified by
    4685 renumbering. 
    4686 
    4687 > delete sel
    4688 
    4689 > delete sel
    4690 
    4691 > delete sel
    4692 
    4693 > delete sel
    4694 
    4695 > select up
    4696 
    4697 99 atoms, 102 bonds, 4 residues, 1 model selected 
    4698 
    4699 > select clear
    4700 
    4701 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4702 run, but this will probably cause problems later if not rectified by
    4703 renumbering. 
    4704 
    4705 > select /ak
    4706 
    4707 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    4708 
    4709 > select up
    4710 
    4711 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4712 
    4713 > select up
    4714 
    4715 155 atoms, 157 bonds, 11 residues, 1 model selected 
    4716 
    4717 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4718 run, but this will probably cause problems later if not rectified by
    4719 renumbering. 
    4720 
    4721 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4722 run, but this will probably cause problems later if not rectified by
    4723 renumbering. 
    4724 
    4725 > select /MG
    4726 
    4727 99 atoms, 102 bonds, 4 residues, 1 model selected 
    4728 
    4729 > select up
    4730 
    4731 42 atoms, 42 bonds, 1 residue, 1 model selected 
    4732 
    4733 > select clear
    4734 
    4735 > select sel&:MG
    4736 
    4737 Nothing selected 
    4738 
    4739 > select sel&/MG
    4740 
    4741 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4742 
    4743 > select up
    4744 
    4745 42 atoms, 42 bonds, 1 residue, 1 model selected 
    4746 
    4747 > select clear
    4748 
    4749 > select up
    4750 
    4751 99 atoms, 102 bonds, 4 residues, 1 model selected 
    4752 
    4753 > select clear
    4754 
    4755 > select up
    4756 
    4757 42 atoms, 42 bonds, 1 residue, 1 model selected 
    4758 
    4759 > delete sel
    4760 
    4761 > isolde add ligand RAM
    4762 
    4763 Deleted the following atoms from residue RAM CG4: O1, HO1 
    4764 
    4765 > ui mousemode right "translate selected atoms"
    4766 
    4767 > clipper set contourSensitivity 0.25
    4768 
    4769 > select clear
    4770 
    4771 > isolde add ligand RAM
    4772 
    4773 Deleted the following atoms from residue RAM MG4: HO1, O1 
    4774 
    4775 > delete sel
    4776 
    4777 > isolde add ligand RAM
    4778 
    4779 Deleted the following atoms from residue RAM MG4: HO1, O1 
    4780 
    4781 > ui mousemode right "translate selected atoms"
    4782 
    4783 > select clear
    4784 
    4785 > select /ak
    4786 
    4787 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    4788 
    4789 > select up
    4790 
    4791 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4792 
    4793 > select up
    4794 
    4795 155 atoms, 157 bonds, 11 residues, 1 model selected 
    4796 
    4797 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4798 run, but this will probably cause problems later if not rectified by
    4799 renumbering. 
    4800 
    4801 > select clear
    4802 
    4803 > select up
    4804 
    4805 15 atoms, 14 bonds, 1 residue, 1 model selected 
    4806 
    4807 > select up
    4808 
    4809 155 atoms, 157 bonds, 11 residues, 1 model selected 
    4810 
    4811 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4812 run, but this will probably cause problems later if not rectified by
    4813 renumbering. 
    4814 
    4815 > select clear
    4816 
    4817 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4818 run, but this will probably cause problems later if not rectified by
    4819 renumbering. 
    4820 
    4821 > select clear
    4822 
    4823 > isolde ~ignore
    4824 
    4825 > save working_3.cxs
    4826 
    4827 Taking snapshot of stepper: working_2.pdb 
    4828 Restoring stepper: working_2.pdb 
    4829 opened ChimeraX session 
    4830 
    4831 > select /ak
    4832 
    4833 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    4834 
    4835 > select clear
    4836 
    4837 > dssp
    4838 
    4839 > select /AA
    4840 
    4841 981 atoms, 1002 bonds, 48 residues, 1 model selected 
    4842 
    4843 > isolde stepto /AB
    4844 
    4845 Multiple residues selected! Going to the first... 
    4846 
    4847 > clipper set contourSensitivity 0.25
    4848 
    4849 > select /AB
    4850 
    4851 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    4852 
    4853 > select clear
    4854 
    4855 > isolde stepto
    4856 
    4857 > isolde stepto
    4858 
    4859 > isolde stepto
    4860 
    4861 > isolde stepto
    4862 
    4863 > isolde stepto
    4864 
    4865 > isolde stepto
    4866 
    4867 > isolde stepto
    4868 
    4869 > isolde stepto
    4870 
    4871 > isolde stepto
    4872 
    4873 > isolde stepto
    4874 
    4875 > isolde stepto
    4876 
    4877 > isolde stepto
    4878 
    4879 > isolde stepto
    4880 
    4881 > isolde stepto
    4882 
    4883 > isolde stepto
    4884 
    4885 > isolde stepto
    4886 
    4887 > isolde stepto
    4888 
    4889 > isolde stepto
    4890 
    4891 > isolde stepto
    4892 
    4893 > isolde stepto
    4894 
    4895 > isolde stepto
    4896 
    4897 > isolde stepto
    4898 
    4899 > isolde stepto
    4900 
    4901 > isolde stepto
    4902 
    4903 > isolde stepto
    4904 
    4905 > isolde stepto
    4906 
    4907 > isolde stepto
    4908 
    4909 > isolde stepto
    4910 
    4911 > isolde stepto
    4912 
    4913 > isolde stepto
    4914 
    4915 > isolde stepto
    4916 
    4917 > isolde stepto
    4918 
    4919 > isolde stepto
    4920 
    4921 > isolde stepto
    4922 
    4923 > isolde stepto
    4924 
    4925 > isolde stepto
    4926 
    4927 > isolde stepto
    4928 
    4929 > isolde stepto
    4930 
    4931 > isolde stepto
    4932 
    4933 > isolde stepto
    4934 
    4935 > isolde stepto
    4936 
    4937 > isolde stepto
    4938 
    4939 > isolde stepto
    4940 
    4941 > isolde stepto
    4942 
    4943 > select clear
    4944 
    4945 > select clear
    4946 
    4947 > isolde stepto
    4948 
    4949 > isolde stepto
    4950 
    4951 > isolde stepto
    4952 
    4953 > isolde stepto
    4954 
    4955 > select /AC
    4956 
    4957 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    4958 
    4959 > select clear
    4960 
    4961 > isolde stepto
    4962 
    4963 > isolde stepto
    4964 
    4965 > isolde stepto
    4966 
    4967 > isolde stepto
    4968 
    4969 > isolde stepto
    4970 
    4971 > isolde stepto
    4972 
    4973 > isolde stepto
    4974 
    4975 > isolde stepto
    4976 
    4977 > isolde stepto
    4978 
    4979 > isolde stepto
    4980 
    4981 > isolde stepto
    4982 
    4983 > isolde stepto
    4984 
    4985 > isolde stepto
    4986 
    4987 > isolde stepto
    4988 
    4989 > isolde stepto
    4990 
    4991 > isolde stepto
    4992 
    4993 > isolde stepto
    4994 
    4995 > isolde stepto
    4996 
    4997 > isolde stepto
    4998 
    4999 > isolde stepto
    5000 
    5001 > isolde stepto
    5002 
    5003 > isolde stepto
    5004 
    5005 > isolde stepto
    5006 
    5007 > isolde stepto
    5008 
    5009 > isolde stepto
    5010 
    5011 > isolde stepto
    5012 
    5013 > isolde stepto
    5014 
    5015 > isolde stepto
    5016 
    5017 > isolde stepto
    5018 
    5019 > isolde stepto
    5020 
    5021 > isolde stepto
    5022 
    5023 > isolde stepto
    5024 
    5025 > isolde stepto
    5026 
    5027 > isolde stepto
    5028 
    5029 > isolde stepto
    5030 
    5031 > isolde stepto
    5032 
    5033 > isolde stepto
    5034 
    5035 > isolde stepto
    5036 
    5037 > isolde stepto
    5038 
    5039 > isolde stepto
    5040 
    5041 > select clear
    5042 
    5043 > isolde stepto
    5044 
    5045 > isolde stepto
    5046 
    5047 > isolde stepto
    5048 
    5049 > isolde stepto
    5050 
    5051 > isolde stepto
    5052 
    5053 > isolde stepto prev
    5054 
    5055 > isolde ignore sel
    5056 
    5057 ISOLDE: currently ignoring 1 residues in model 8.2 
    5058 
    5059 > select clear
    5060 
    5061 > isolde stepto
    5062 
    5063 > isolde stepto
    5064 
    5065 > isolde stepto
    5066 
    5067 > select /AD
    5068 
    5069 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5070 
    5071 > select clear
    5072 
    5073 > isolde stepto
    5074 
    5075 > isolde stepto
    5076 
    5077 > isolde stepto
    5078 
    5079 > isolde stepto
    5080 
    5081 > isolde stepto
    5082 
    5083 > isolde stepto
    5084 
    5085 > isolde stepto
    5086 
    5087 > isolde stepto
    5088 
    5089 > isolde stepto
    5090 
    5091 > isolde stepto
    5092 
    5093 > isolde stepto
    5094 
    5095 > isolde stepto
    5096 
    5097 > isolde stepto
    5098 
    5099 > isolde stepto
    5100 
    5101 > isolde stepto
    5102 
    5103 > isolde stepto
    5104 
    5105 > isolde stepto
    5106 
    5107 > isolde stepto
    5108 
    5109 > isolde stepto
    5110 
    5111 > isolde stepto
    5112 
    5113 > isolde stepto
    5114 
    5115 > isolde stepto
    5116 
    5117 > isolde stepto
    5118 
    5119 > isolde stepto
    5120 
    5121 > isolde stepto
    5122 
    5123 > isolde stepto
    5124 
    5125 > isolde stepto
    5126 
    5127 > isolde stepto
    5128 
    5129 > isolde stepto
    5130 
    5131 > isolde stepto
    5132 
    5133 > isolde stepto
    5134 
    5135 > isolde stepto
    5136 
    5137 > isolde stepto
    5138 
    5139 > isolde stepto
    5140 
    5141 > isolde stepto
    5142 
    5143 > isolde stepto
    5144 
    5145 > isolde stepto
    5146 
    5147 > isolde stepto
    5148 
    5149 > isolde stepto
    5150 
    5151 > isolde stepto
    5152 
    5153 > isolde stepto
    5154 
    5155 > isolde stepto
    5156 
    5157 > isolde stepto
    5158 
    5159 > isolde stepto
    5160 
    5161 > select clear
    5162 
    5163 > isolde stepto
    5164 
    5165 > isolde stepto
    5166 
    5167 > isolde stepto
    5168 
    5169 > select /AE
    5170 
    5171 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5172 
    5173 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5174 bonded heavy atom. 
    5175 
    5176 > select clear
    5177 
    5178 > isolde stepto
    5179 
    5180 > isolde stepto
    5181 
    5182 > isolde stepto
    5183 
    5184 > isolde stepto
    5185 
    5186 > isolde stepto
    5187 
    5188 > isolde stepto
    5189 
    5190 > isolde stepto
    5191 
    5192 > isolde stepto
    5193 
    5194 > isolde stepto
    5195 
    5196 > isolde stepto
    5197 
    5198 > isolde stepto
    5199 
    5200 > isolde stepto
    5201 
    5202 > isolde stepto
    5203 
    5204 > isolde stepto
    5205 
    5206 > isolde stepto
    5207 
    5208 > isolde stepto
    5209 
    5210 > isolde stepto
    5211 
    5212 > isolde stepto
    5213 
    5214 > isolde stepto
    5215 
    5216 > isolde stepto
    5217 
    5218 > isolde stepto
    5219 
    5220 > isolde stepto
    5221 
    5222 > isolde stepto
    5223 
    5224 > isolde stepto
    5225 
    5226 > isolde stepto
    5227 
    5228 > isolde stepto
    5229 
    5230 > isolde stepto
    5231 
    5232 > isolde stepto
    5233 
    5234 > isolde stepto
    5235 
    5236 > isolde stepto
    5237 
    5238 > isolde stepto
    5239 
    5240 > isolde stepto
    5241 
    5242 > isolde stepto
    5243 
    5244 > isolde stepto
    5245 
    5246 > isolde stepto
    5247 
    5248 > isolde stepto
    5249 
    5250 > isolde stepto
    5251 
    5252 > isolde stepto
    5253 
    5254 > isolde stepto
    5255 
    5256 > select clear
    5257 
    5258 > isolde stepto
    5259 
    5260 > isolde stepto
    5261 
    5262 > isolde stepto
    5263 
    5264 > isolde stepto
    5265 
    5266 > isolde stepto
    5267 
    5268 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5269 bonded heavy atom. 
    5270 
    5271 > select clear
    5272 
    5273 > select clear
    5274 
    5275 > isolde stepto
    5276 
    5277 > isolde stepto
    5278 
    5279 > isolde stepto
    5280 
    5281 > isolde stepto
    5282 
    5283 > select /AF
    5284 
    5285 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5286 
    5287 > select clear
    5288 
    5289 > isolde stepto
    5290 
    5291 > isolde stepto
    5292 
    5293 > isolde stepto
    5294 
    5295 > isolde stepto
    5296 
    5297 > isolde stepto
    5298 
    5299 > isolde stepto
    5300 
    5301 > isolde stepto
    5302 
    5303 > isolde stepto
    5304 
    5305 > isolde stepto
    5306 
    5307 > isolde stepto
    5308 
    5309 > isolde stepto
    5310 
    5311 > isolde stepto
    5312 
    5313 > isolde stepto
    5314 
    5315 > isolde stepto
    5316 
    5317 > isolde stepto
    5318 
    5319 > isolde stepto
    5320 
    5321 > isolde stepto
    5322 
    5323 > isolde stepto
    5324 
    5325 > isolde stepto
    5326 
    5327 > isolde stepto
    5328 
    5329 > isolde stepto
    5330 
    5331 > isolde stepto
    5332 
    5333 > isolde stepto
    5334 
    5335 > isolde stepto
    5336 
    5337 > isolde stepto
    5338 
    5339 > isolde stepto
    5340 
    5341 > isolde stepto
    5342 
    5343 > isolde stepto
    5344 
    5345 > isolde stepto
    5346 
    5347 > isolde stepto
    5348 
    5349 > isolde stepto
    5350 
    5351 > isolde stepto
    5352 
    5353 > isolde stepto
    5354 
    5355 > isolde stepto
    5356 
    5357 > isolde stepto
    5358 
    5359 > isolde stepto
    5360 
    5361 > isolde stepto
    5362 
    5363 > isolde stepto
    5364 
    5365 > isolde stepto
    5366 
    5367 > isolde stepto
    5368 
    5369 > isolde stepto
    5370 
    5371 > isolde stepto
    5372 
    5373 > isolde stepto
    5374 
    5375 > isolde stepto
    5376 
    5377 > swapaa mousemode sel PRO
    5378 
    5379 Traceback (most recent call last): 
    5380 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5381 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    5382 self.start_sim() 
    5383 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5384 packages/chimerax/isolde/isolde.py", line 2724, in start_sim 
    5385 main_sel = self._last_main_sel = self._get_main_sim_selection() 
    5386 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5387 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    5388 raise TypeError('You must select at least one atom from the current ' 
    5389 TypeError: You must select at least one atom from the current working model
    5390 prior to starting a simulation! 
    5391  
    5392 TypeError: You must select at least one atom from the current working model
    5393 prior to starting a simulation! 
    5394  
    5395 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5396 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    5397 raise TypeError('You must select at least one atom from the current ' 
    5398  
    5399 See log for complete Python traceback. 
    5400  
    5401 
    5402 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5403 bonded heavy atom. 
    5404 
    5405 > select clear
    5406 
    5407 > isolde stepto
    5408 
    5409 > isolde stepto
    5410 
    5411 > isolde stepto
    5412 
    5413 > isolde stepto
    5414 
    5415 > select /AG
    5416 
    5417 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5418 
    5419 > select clear
    5420 
    5421 > isolde stepto
    5422 
    5423 > isolde stepto
    5424 
    5425 > isolde stepto
    5426 
    5427 > isolde stepto
    5428 
    5429 > isolde stepto
    5430 
    5431 > isolde stepto
    5432 
    5433 > isolde stepto
    5434 
    5435 > isolde stepto
    5436 
    5437 > isolde stepto
    5438 
    5439 > isolde stepto
    5440 
    5441 > isolde stepto
    5442 
    5443 > isolde stepto
    5444 
    5445 > isolde stepto
    5446 
    5447 > select /AG
    5448 
    5449 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5450 
    5451 > select /AG, ak
    5452 
    5453 2214 atoms, 2258 bonds, 120 residues, 1 model selected 
    5454 
    5455 > select /AG
    5456 
    5457 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5458 
    5459 > select clear
    5460 
    5461 > isolde stepto
    5462 
    5463 > isolde stepto
    5464 
    5465 > isolde stepto
    5466 
    5467 > isolde stepto
    5468 
    5469 > isolde stepto
    5470 
    5471 > isolde stepto
    5472 
    5473 > isolde stepto
    5474 
    5475 > isolde stepto
    5476 
    5477 > isolde stepto
    5478 
    5479 > isolde stepto
    5480 
    5481 > isolde stepto
    5482 
    5483 > isolde stepto
    5484 
    5485 > isolde stepto
    5486 
    5487 > isolde stepto
    5488 
    5489 > isolde stepto
    5490 
    5491 > isolde stepto
    5492 
    5493 > isolde stepto
    5494 
    5495 > isolde stepto
    5496 
    5497 > isolde stepto
    5498 
    5499 > isolde stepto
    5500 
    5501 > isolde stepto
    5502 
    5503 > isolde stepto
    5504 
    5505 > isolde stepto
    5506 
    5507 > isolde stepto
    5508 
    5509 > isolde stepto
    5510 
    5511 > isolde stepto
    5512 
    5513 > isolde stepto
    5514 
    5515 > select clear
    5516 
    5517 > isolde stepto
    5518 
    5519 > isolde stepto
    5520 
    5521 > isolde stepto
    5522 
    5523 > isolde stepto
    5524 
    5525 > select clear
    5526 
    5527 > select clear
    5528 
    5529 > isolde stepto
    5530 
    5531 > isolde stepto
    5532 
    5533 > isolde stepto
    5534 
    5535 > isolde stepto
    5536 
    5537 > select /AH
    5538 
    5539 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5540 
    5541 > select clear
    5542 
    5543 > isolde stepto
    5544 
    5545 > isolde stepto
    5546 
    5547 > isolde stepto
    5548 
    5549 > isolde stepto
    5550 
    5551 > isolde stepto
    5552 
    5553 > isolde stepto
    5554 
    5555 > isolde stepto
    5556 
    5557 > isolde stepto
    5558 
    5559 > isolde stepto
    5560 
    5561 > isolde stepto
    5562 
    5563 > isolde stepto
    5564 
    5565 > isolde stepto
    5566 
    5567 > isolde stepto
    5568 
    5569 > isolde stepto
    5570 
    5571 > isolde stepto
    5572 
    5573 > isolde stepto
    5574 
    5575 > isolde stepto
    5576 
    5577 > isolde stepto
    5578 
    5579 > isolde stepto
    5580 
    5581 > isolde stepto
    5582 
    5583 > isolde stepto
    5584 
    5585 > isolde stepto
    5586 
    5587 > isolde stepto
    5588 
    5589 > isolde stepto
    5590 
    5591 > isolde stepto
    5592 
    5593 > isolde stepto
    5594 
    5595 > isolde stepto
    5596 
    5597 > isolde stepto
    5598 
    5599 > isolde stepto
    5600 
    5601 > isolde stepto
    5602 
    5603 > isolde stepto
    5604 
    5605 > isolde stepto
    5606 
    5607 > isolde stepto
    5608 
    5609 > isolde stepto
    5610 
    5611 > isolde stepto
    5612 
    5613 > isolde stepto
    5614 
    5615 > isolde stepto
    5616 
    5617 > isolde stepto
    5618 
    5619 > isolde stepto
    5620 
    5621 > isolde stepto
    5622 
    5623 > isolde stepto
    5624 
    5625 > isolde stepto
    5626 
    5627 > isolde stepto
    5628 
    5629 > isolde stepto
    5630 
    5631 > select clear
    5632 
    5633 > isolde stepto
    5634 
    5635 > isolde stepto
    5636 
    5637 > isolde stepto
    5638 
    5639 > isolde stepto
    5640 
    5641 > select /AI
    5642 
    5643 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5644 
    5645 > select clear
    5646 
    5647 > isolde stepto
    5648 
    5649 > isolde stepto
    5650 
    5651 > isolde stepto
    5652 
    5653 > isolde stepto
    5654 
    5655 > isolde stepto
    5656 
    5657 > isolde stepto
    5658 
    5659 > isolde stepto
    5660 
    5661 > isolde stepto
    5662 
    5663 > isolde stepto
    5664 
    5665 > isolde stepto
    5666 
    5667 > isolde stepto
    5668 
    5669 > isolde stepto
    5670 
    5671 > isolde stepto
    5672 
    5673 > isolde stepto
    5674 
    5675 > isolde stepto
    5676 
    5677 > isolde stepto
    5678 
    5679 > isolde stepto
    5680 
    5681 > isolde stepto
    5682 
    5683 > isolde stepto
    5684 
    5685 > isolde stepto
    5686 
    5687 > isolde stepto
    5688 
    5689 > isolde stepto
    5690 
    5691 > isolde stepto
    5692 
    5693 > isolde stepto
    5694 
    5695 > isolde stepto
    5696 
    5697 > isolde stepto
    5698 
    5699 > isolde stepto
    5700 
    5701 > isolde stepto
    5702 
    5703 > isolde stepto
    5704 
    5705 > isolde stepto
    5706 
    5707 > isolde stepto
    5708 
    5709 > isolde stepto
    5710 
    5711 > isolde stepto
    5712 
    5713 > isolde stepto
    5714 
    5715 > isolde stepto
    5716 
    5717 > isolde stepto
    5718 
    5719 > isolde stepto
    5720 
    5721 > isolde stepto
    5722 
    5723 > isolde stepto
    5724 
    5725 > isolde stepto
    5726 
    5727 > isolde stepto
    5728 
    5729 > isolde stepto
    5730 
    5731 > isolde stepto
    5732 
    5733 > isolde stepto
    5734 
    5735 > select clear
    5736 
    5737 > isolde stepto
    5738 
    5739 > isolde stepto
    5740 
    5741 > isolde stepto
    5742 
    5743 > isolde stepto
    5744 
    5745 > save working_4.cxs
    5746 
    5747 Taking snapshot of stepper: working_2.pdb 
    5748 
    5749 > select /AJ
    5750 
    5751 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5752 
    5753 > select clear
    5754 
    5755 > select clear
    5756 
    5757 > select clear
    5758 
    5759 > isolde stepto
    5760 
    5761 > isolde stepto
    5762 
    5763 > isolde stepto
    5764 
    5765 > isolde stepto
    5766 
    5767 > isolde stepto
    5768 
    5769 > isolde stepto
    5770 
    5771 > isolde stepto
    5772 
    5773 > isolde stepto
    5774 
    5775 > isolde stepto
    5776 
    5777 > isolde stepto
    5778 
    5779 > isolde stepto
    5780 
    5781 > isolde stepto
    5782 
    5783 > isolde stepto
    5784 
    5785 > isolde stepto
    5786 
    5787 > isolde stepto
    5788 
    5789 > isolde stepto
    5790 
    5791 > isolde stepto
    5792 
    5793 > isolde stepto
    5794 
    5795 > isolde stepto
    5796 
    5797 > select clear
    5798 
    5799 > isolde stepto
    5800 
    5801 > isolde stepto
    5802 
    5803 > isolde stepto
    5804 
    5805 > isolde stepto
    5806 
    5807 > isolde stepto
    5808 
    5809 > isolde stepto
    5810 
    5811 > isolde stepto
    5812 
    5813 > isolde stepto
    5814 
    5815 > isolde stepto
    5816 
    5817 > isolde stepto
    5818 
    5819 > isolde stepto
    5820 
    5821 > isolde stepto
    5822 
    5823 > isolde stepto
    5824 
    5825 > isolde stepto
    5826 
    5827 > isolde stepto
    5828 
    5829 > isolde stepto
    5830 
    5831 > isolde stepto
    5832 
    5833 > isolde stepto
    5834 
    5835 > isolde stepto
    5836 
    5837 > isolde stepto
    5838 
    5839 > isolde stepto
    5840 
    5841 > isolde stepto
    5842 
    5843 > isolde stepto
    5844 
    5845 > isolde stepto
    5846 
    5847 > isolde stepto
    5848 
    5849 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5850 bonded heavy atom. 
    5851 
    5852 > select clear
    5853 
    5854 > isolde stepto
    5855 
    5856 > isolde stepto
    5857 
    5858 > isolde stepto
    5859 
    5860 > isolde stepto
    5861 
    5862 > select /AK
    5863 
    5864 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5865 
    5866 > select clear
    5867 
    5868 > select /AK
    5869 
    5870 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5871 
    5872 > select clear
    5873 
    5874 > isolde stepto
    5875 
    5876 > isolde stepto
    5877 
    5878 > isolde stepto
    5879 
    5880 > isolde stepto
    5881 
    5882 > isolde stepto
    5883 
    5884 > isolde stepto
    5885 
    5886 > isolde stepto
    5887 
    5888 > isolde stepto
    5889 
    5890 > isolde stepto
    5891 
    5892 > isolde stepto
    5893 
    5894 > isolde stepto
    5895 
    5896 > isolde stepto
    5897 
    5898 > isolde stepto
    5899 
    5900 > isolde stepto
    5901 
    5902 > isolde stepto
    5903 
    5904 > isolde stepto
    5905 
    5906 > isolde stepto
    5907 
    5908 > isolde stepto
    5909 
    5910 > isolde stepto
    5911 
    5912 > isolde stepto
    5913 
    5914 > isolde stepto
    5915 
    5916 > isolde stepto
    5917 
    5918 > isolde stepto
    5919 
    5920 > isolde stepto
    5921 
    5922 > isolde stepto
    5923 
    5924 > isolde stepto
    5925 
    5926 > isolde stepto
    5927 
    5928 > isolde stepto
    5929 
    5930 > isolde stepto
    5931 
    5932 > isolde stepto
    5933 
    5934 > isolde stepto
    5935 
    5936 > isolde stepto
    5937 
    5938 > isolde stepto
    5939 
    5940 > isolde stepto
    5941 
    5942 > isolde stepto
    5943 
    5944 > isolde stepto
    5945 
    5946 > isolde stepto
    5947 
    5948 > isolde stepto
    5949 
    5950 > isolde stepto
    5951 
    5952 > isolde stepto
    5953 
    5954 > isolde stepto
    5955 
    5956 > isolde stepto
    5957 
    5958 > isolde stepto
    5959 
    5960 > isolde stepto
    5961 
    5962 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5963 bonded heavy atom. 
    5964 
    5965 > select clear
    5966 
    5967 > isolde stepto
    5968 
    5969 > isolde stepto
    5970 
    5971 > isolde stepto
    5972 
    5973 > isolde stepto
    5974 
    5975 > select /AL
    5976 
    5977 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5978 
    5979 > select clear
    5980 
    5981 > isolde stepto
    5982 
    5983 > isolde stepto
    5984 
    5985 > isolde stepto
    5986 
    5987 > isolde stepto
    5988 
    5989 > isolde stepto
    5990 
    5991 > isolde stepto
    5992 
    5993 > isolde stepto
    5994 
    5995 > isolde stepto
    5996 
    5997 > isolde stepto
    5998 
    5999 > isolde stepto
    6000 
    6001 > isolde stepto
    6002 
    6003 > isolde stepto
    6004 
    6005 > isolde stepto
    6006 
    6007 > isolde stepto
    6008 
    6009 > isolde stepto
    6010 
    6011 > isolde stepto
    6012 
    6013 > isolde stepto
    6014 
    6015 > isolde stepto
    6016 
    6017 > isolde stepto
    6018 
    6019 > isolde stepto
    6020 
    6021 > isolde stepto
    6022 
    6023 > isolde stepto
    6024 
    6025 > isolde stepto
    6026 
    6027 > isolde stepto
    6028 
    6029 > select clear
    6030 
    6031 > isolde stepto
    6032 
    6033 > isolde stepto
    6034 
    6035 > isolde stepto
    6036 
    6037 > isolde stepto
    6038 
    6039 > isolde stepto
    6040 
    6041 > isolde stepto
    6042 
    6043 > isolde stepto
    6044 
    6045 > isolde stepto
    6046 
    6047 > isolde stepto
    6048 
    6049 > isolde stepto
    6050 
    6051 > isolde stepto
    6052 
    6053 > isolde stepto
    6054 
    6055 > isolde stepto
    6056 
    6057 > isolde stepto
    6058 
    6059 > isolde stepto
    6060 
    6061 > isolde stepto
    6062 
    6063 > isolde stepto
    6064 
    6065 > isolde stepto
    6066 
    6067 > isolde stepto
    6068 
    6069 > isolde stepto
    6070 
    6071 > select clear
    6072 
    6073 > isolde stepto
    6074 
    6075 > isolde stepto
    6076 
    6077 > isolde stepto
    6078 
    6079 > isolde stepto
    6080 
    6081 > select /AM
    6082 
    6083 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6084 
    6085 > select clear
    6086 
    6087 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6088 bonded heavy atom. 
    6089 
    6090 > select clear
    6091 
    6092 > select /AM
    6093 
    6094 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6095 
    6096 > select clear
    6097 
    6098 > isolde stepto
    6099 
    6100 > isolde stepto
    6101 
    6102 > isolde stepto
    6103 
    6104 > isolde stepto
    6105 
    6106 > isolde stepto
    6107 
    6108 > isolde stepto
    6109 
    6110 > isolde stepto
    6111 
    6112 > isolde stepto
    6113 
    6114 > isolde stepto
    6115 
    6116 > isolde stepto
    6117 
    6118 > isolde stepto
    6119 
    6120 > isolde stepto
    6121 
    6122 > isolde stepto
    6123 
    6124 > isolde stepto
    6125 
    6126 > isolde stepto
    6127 
    6128 > isolde stepto
    6129 
    6130 > isolde stepto
    6131 
    6132 > isolde stepto
    6133 
    6134 > isolde stepto
    6135 
    6136 > isolde stepto
    6137 
    6138 > isolde stepto
    6139 
    6140 > isolde stepto
    6141 
    6142 > isolde stepto
    6143 
    6144 > isolde stepto
    6145 
    6146 > isolde stepto
    6147 
    6148 > isolde stepto
    6149 
    6150 > isolde stepto
    6151 
    6152 > isolde stepto
    6153 
    6154 > isolde stepto
    6155 
    6156 > isolde stepto
    6157 
    6158 > isolde stepto
    6159 
    6160 > isolde stepto
    6161 
    6162 > isolde stepto
    6163 
    6164 > isolde stepto
    6165 
    6166 > isolde stepto
    6167 
    6168 > isolde stepto
    6169 
    6170 > isolde stepto
    6171 
    6172 > isolde stepto
    6173 
    6174 > isolde stepto
    6175 
    6176 > isolde stepto
    6177 
    6178 > isolde stepto
    6179 
    6180 > isolde stepto
    6181 
    6182 > isolde stepto
    6183 
    6184 > isolde stepto
    6185 
    6186 > isolde stepto
    6187 
    6188 > isolde stepto
    6189 
    6190 > isolde stepto
    6191 
    6192 > isolde stepto
    6193 
    6194 > select /AN
    6195 
    6196 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6197 
    6198 > select clear
    6199 
    6200 > isolde stepto
    6201 
    6202 > isolde stepto
    6203 
    6204 > isolde stepto
    6205 
    6206 > isolde stepto
    6207 
    6208 > isolde stepto
    6209 
    6210 > isolde stepto
    6211 
    6212 > isolde stepto
    6213 
    6214 > isolde stepto
    6215 
    6216 > isolde stepto
    6217 
    6218 > isolde stepto
    6219 
    6220 > isolde stepto
    6221 
    6222 > isolde stepto
    6223 
    6224 > isolde stepto
    6225 
    6226 > isolde stepto
    6227 
    6228 > isolde stepto
    6229 
    6230 > isolde stepto
    6231 
    6232 > isolde stepto
    6233 
    6234 > isolde stepto
    6235 
    6236 > isolde stepto
    6237 
    6238 > isolde stepto
    6239 
    6240 > isolde stepto
    6241 
    6242 > isolde stepto
    6243 
    6244 > isolde stepto
    6245 
    6246 > isolde stepto
    6247 
    6248 > isolde stepto
    6249 
    6250 > isolde stepto
    6251 
    6252 > isolde stepto
    6253 
    6254 > isolde stepto
    6255 
    6256 > isolde stepto
    6257 
    6258 > isolde stepto
    6259 
    6260 > isolde stepto
    6261 
    6262 > isolde stepto
    6263 
    6264 > isolde stepto
    6265 
    6266 > isolde stepto
    6267 
    6268 > isolde stepto
    6269 
    6270 > isolde stepto
    6271 
    6272 > isolde stepto
    6273 
    6274 > isolde stepto
    6275 
    6276 > isolde stepto
    6277 
    6278 > isolde stepto
    6279 
    6280 > isolde stepto
    6281 
    6282 > isolde stepto
    6283 
    6284 > isolde stepto
    6285 
    6286 > isolde stepto
    6287 
    6288 > isolde ignore sel
    6289 
    6290 ISOLDE: currently ignoring 2 residues in model 8.2 
    6291 
    6292 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6293 bonded heavy atom. 
    6294 
    6295 > select clear
    6296 
    6297 > isolde ~ignore
    6298 
    6299 > isolde stepto
    6300 
    6301 > isolde stepto
    6302 
    6303 > isolde stepto
    6304 
    6305 > isolde stepto
    6306 
    6307 > select /AO
    6308 
    6309 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6310 
    6311 > select clear
    6312 
    6313 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6314 bonded heavy atom. 
    6315 
    6316 > isolde stepto
    6317 
    6318 > isolde stepto
    6319 
    6320 > isolde stepto
    6321 
    6322 > isolde stepto
    6323 
    6324 > isolde stepto
    6325 
    6326 > isolde stepto
    6327 
    6328 > isolde stepto
    6329 
    6330 > isolde stepto
    6331 
    6332 > isolde stepto
    6333 
    6334 > isolde stepto
    6335 
    6336 > isolde stepto
    6337 
    6338 > isolde stepto
    6339 
    6340 > isolde stepto
    6341 
    6342 > isolde stepto
    6343 
    6344 > isolde stepto
    6345 
    6346 > isolde stepto
    6347 
    6348 > isolde stepto
    6349 
    6350 > isolde stepto
    6351 
    6352 > isolde stepto
    6353 
    6354 > isolde stepto
    6355 
    6356 > isolde stepto
    6357 
    6358 > isolde stepto
    6359 
    6360 > isolde stepto
    6361 
    6362 > isolde stepto
    6363 
    6364 > isolde stepto
    6365 
    6366 > isolde stepto
    6367 
    6368 > isolde stepto
    6369 
    6370 > isolde stepto
    6371 
    6372 > isolde stepto
    6373 
    6374 > isolde stepto
    6375 
    6376 > isolde stepto
    6377 
    6378 > isolde stepto
    6379 
    6380 > isolde stepto
    6381 
    6382 > isolde stepto
    6383 
    6384 > isolde stepto
    6385 
    6386 > isolde stepto
    6387 
    6388 > isolde stepto
    6389 
    6390 > isolde stepto
    6391 
    6392 > isolde stepto
    6393 
    6394 > isolde stepto
    6395 
    6396 > isolde stepto
    6397 
    6398 > isolde stepto
    6399 
    6400 > isolde stepto
    6401 
    6402 > select clear
    6403 
    6404 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6405 bonded heavy atom. 
    6406 
    6407 > select clear
    6408 
    6409 > isolde stepto
    6410 
    6411 > isolde stepto
    6412 
    6413 > isolde stepto
    6414 
    6415 > isolde stepto
    6416 
    6417 > isolde stepto
    6418 
    6419 > select /AP
    6420 
    6421 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6422 
    6423 > select clear
    6424 
    6425 > select clear
    6426 
    6427 > isolde stepto
    6428 
    6429 > isolde stepto
    6430 
    6431 > isolde stepto
    6432 
    6433 > isolde stepto
    6434 
    6435 > isolde stepto
    6436 
    6437 > isolde stepto
    6438 
    6439 > isolde stepto
    6440 
    6441 > isolde stepto
    6442 
    6443 > isolde stepto
    6444 
    6445 > isolde stepto
    6446 
    6447 > isolde stepto
    6448 
    6449 > isolde stepto
    6450 
    6451 > isolde stepto
    6452 
    6453 > isolde stepto
    6454 
    6455 > isolde stepto
    6456 
    6457 > isolde stepto
    6458 
    6459 > isolde stepto
    6460 
    6461 > isolde stepto
    6462 
    6463 > isolde stepto
    6464 
    6465 > isolde stepto
    6466 
    6467 > isolde stepto
    6468 
    6469 > isolde stepto
    6470 
    6471 > isolde stepto
    6472 
    6473 > isolde stepto
    6474 
    6475 > isolde stepto
    6476 
    6477 > isolde stepto
    6478 
    6479 > isolde stepto
    6480 
    6481 > isolde stepto
    6482 
    6483 > isolde stepto
    6484 
    6485 > isolde stepto
    6486 
    6487 > isolde stepto
    6488 
    6489 > isolde stepto
    6490 
    6491 > isolde stepto
    6492 
    6493 > isolde stepto
    6494 
    6495 > isolde stepto
    6496 
    6497 > isolde stepto
    6498 
    6499 > isolde stepto
    6500 
    6501 > isolde stepto
    6502 
    6503 > isolde stepto
    6504 
    6505 > isolde stepto
    6506 
    6507 > isolde stepto
    6508 
    6509 > isolde stepto
    6510 
    6511 > isolde stepto
    6512 
    6513 > isolde stepto
    6514 
    6515 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6516 bonded heavy atom. 
    6517 
    6518 > select clear
    6519 
    6520 > isolde stepto
    6521 
    6522 > isolde stepto
    6523 
    6524 > isolde stepto
    6525 
    6526 > isolde stepto
    6527 
    6528 > select /AQ
    6529 
    6530 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6531 
    6532 > select clear
    6533 
    6534 > select clear
    6535 
    6536 > isolde stepto
    6537 
    6538 > isolde stepto
    6539 
    6540 > isolde stepto
    6541 
    6542 > isolde stepto
    6543 
    6544 > isolde stepto
    6545 
    6546 > isolde stepto
    6547 
    6548 > isolde stepto
    6549 
    6550 > isolde stepto
    6551 
    6552 > isolde stepto
    6553 
    6554 > isolde stepto
    6555 
    6556 > isolde stepto
    6557 
    6558 > isolde stepto
    6559 
    6560 > isolde stepto
    6561 
    6562 > isolde stepto
    6563 
    6564 > isolde stepto
    6565 
    6566 > isolde stepto
    6567 
    6568 > isolde stepto
    6569 
    6570 > isolde stepto
    6571 
    6572 > isolde stepto
    6573 
    6574 > isolde stepto
    6575 
    6576 > isolde stepto
    6577 
    6578 > isolde stepto
    6579 
    6580 > isolde stepto
    6581 
    6582 > isolde stepto
    6583 
    6584 > isolde stepto
    6585 
    6586 > isolde stepto
    6587 
    6588 > isolde stepto
    6589 
    6590 > isolde stepto
    6591 
    6592 > isolde stepto
    6593 
    6594 > isolde stepto
    6595 
    6596 > isolde stepto
    6597 
    6598 > isolde stepto
    6599 
    6600 > isolde stepto
    6601 
    6602 > isolde stepto
    6603 
    6604 > isolde stepto
    6605 
    6606 > isolde stepto
    6607 
    6608 > isolde stepto
    6609 
    6610 > isolde stepto
    6611 
    6612 > isolde stepto
    6613 
    6614 > isolde stepto
    6615 
    6616 > isolde stepto
    6617 
    6618 > isolde stepto
    6619 
    6620 > isolde stepto
    6621 
    6622 > isolde stepto
    6623 
    6624 > select clear
    6625 
    6626 > isolde stepto
    6627 
    6628 > isolde stepto
    6629 
    6630 > isolde stepto
    6631 
    6632 > isolde stepto
    6633 
    6634 > select /AR
    6635 
    6636 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6637 
    6638 > select clear
    6639 
    6640 > isolde stepto
    6641 
    6642 > isolde stepto
    6643 
    6644 > isolde stepto
    6645 
    6646 > isolde stepto
    6647 
    6648 > isolde stepto
    6649 
    6650 > isolde stepto
    6651 
    6652 > isolde stepto
    6653 
    6654 > isolde stepto
    6655 
    6656 > isolde stepto
    6657 
    6658 > isolde stepto
    6659 
    6660 > isolde stepto
    6661 
    6662 > isolde stepto
    6663 
    6664 > isolde stepto
    6665 
    6666 > isolde stepto
    6667 
    6668 > isolde stepto
    6669 
    6670 > isolde stepto
    6671 
    6672 > isolde stepto
    6673 
    6674 > isolde stepto
    6675 
    6676 > isolde stepto
    6677 
    6678 > isolde stepto
    6679 
    6680 > isolde stepto
    6681 
    6682 > isolde stepto
    6683 
    6684 > isolde stepto
    6685 
    6686 > isolde stepto
    6687 
    6688 > isolde stepto
    6689 
    6690 > isolde stepto
    6691 
    6692 > isolde stepto
    6693 
    6694 > isolde stepto
    6695 
    6696 > isolde stepto
    6697 
    6698 > isolde stepto
    6699 
    6700 > isolde stepto
    6701 
    6702 > isolde stepto
    6703 
    6704 > isolde stepto
    6705 
    6706 > isolde stepto
    6707 
    6708 > isolde stepto
    6709 
    6710 > isolde stepto
    6711 
    6712 > isolde stepto
    6713 
    6714 > isolde stepto
    6715 
    6716 > isolde stepto
    6717 
    6718 > isolde stepto
    6719 
    6720 > isolde stepto
    6721 
    6722 > isolde stepto
    6723 
    6724 > isolde stepto
    6725 
    6726 > isolde stepto
    6727 
    6728 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6729 bonded heavy atom. 
    6730 
    6731 > select clear
    6732 
    6733 > isolde stepto
    6734 
    6735 > isolde stepto
    6736 
    6737 > isolde stepto
    6738 
    6739 > isolde stepto
    6740 
    6741 > select /AS
    6742 
    6743 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6744 
    6745 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6746 bonded heavy atom. 
    6747 
    6748 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6749 bonded heavy atom. 
    6750 
    6751 > isolde stepto
    6752 
    6753 > isolde stepto
    6754 
    6755 > select clear
    6756 
    6757 > isolde stepto
    6758 
    6759 > isolde stepto
    6760 
    6761 > isolde stepto
    6762 
    6763 > isolde stepto
    6764 
    6765 > isolde stepto
    6766 
    6767 > isolde stepto
    6768 
    6769 > isolde stepto
    6770 
    6771 > isolde stepto
    6772 
    6773 > isolde stepto
    6774 
    6775 > isolde stepto
    6776 
    6777 > isolde stepto
    6778 
    6779 > isolde stepto
    6780 
    6781 > isolde stepto
    6782 
    6783 > isolde stepto
    6784 
    6785 > isolde stepto
    6786 
    6787 > isolde stepto
    6788 
    6789 > isolde stepto
    6790 
    6791 > isolde stepto
    6792 
    6793 > isolde stepto
    6794 
    6795 > isolde stepto
    6796 
    6797 > isolde stepto
    6798 
    6799 > isolde stepto
    6800 
    6801 > isolde stepto
    6802 
    6803 > isolde stepto
    6804 
    6805 > isolde stepto
    6806 
    6807 > isolde stepto
    6808 
    6809 > select clear
    6810 
    6811 > isolde stepto
    6812 
    6813 > isolde stepto
    6814 
    6815 > isolde stepto
    6816 
    6817 > isolde stepto
    6818 
    6819 > isolde stepto
    6820 
    6821 > isolde stepto
    6822 
    6823 > isolde stepto
    6824 
    6825 > isolde stepto
    6826 
    6827 > isolde stepto
    6828 
    6829 > isolde stepto
    6830 
    6831 > isolde stepto
    6832 
    6833 > isolde stepto
    6834 
    6835 > isolde stepto
    6836 
    6837 > isolde stepto
    6838 
    6839 > isolde stepto
    6840 
    6841 > isolde stepto
    6842 
    6843 > select clear
    6844 
    6845 > isolde stepto
    6846 
    6847 > isolde stepto
    6848 
    6849 > isolde stepto
    6850 
    6851 > isolde stepto
    6852 
    6853 > select /AT
    6854 
    6855 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6856 
    6857 > select clear
    6858 
    6859 > select clear
    6860 
    6861 > isolde stepto
    6862 
    6863 > isolde stepto
    6864 
    6865 > isolde stepto
    6866 
    6867 > isolde stepto
    6868 
    6869 > isolde stepto
    6870 
    6871 > isolde stepto
    6872 
    6873 > isolde stepto
    6874 
    6875 > isolde stepto
    6876 
    6877 > isolde stepto
    6878 
    6879 > isolde stepto
    6880 
    6881 > isolde stepto
    6882 
    6883 > isolde stepto
    6884 
    6885 > isolde stepto
    6886 
    6887 > isolde stepto
    6888 
    6889 > isolde stepto
    6890 
    6891 > isolde stepto
    6892 
    6893 > isolde stepto
    6894 
    6895 > isolde stepto
    6896 
    6897 > isolde stepto
    6898 
    6899 > isolde stepto
    6900 
    6901 > isolde stepto
    6902 
    6903 > isolde stepto
    6904 
    6905 > isolde stepto
    6906 
    6907 > isolde stepto
    6908 
    6909 > isolde stepto
    6910 
    6911 > isolde stepto
    6912 
    6913 > isolde stepto
    6914 
    6915 > isolde stepto
    6916 
    6917 > isolde stepto
    6918 
    6919 > isolde stepto
    6920 
    6921 > isolde stepto
    6922 
    6923 > isolde stepto
    6924 
    6925 > isolde stepto
    6926 
    6927 > isolde stepto
    6928 
    6929 > isolde stepto
    6930 
    6931 > isolde stepto
    6932 
    6933 > isolde stepto
    6934 
    6935 > isolde stepto
    6936 
    6937 > isolde stepto
    6938 
    6939 > isolde stepto
    6940 
    6941 > isolde stepto
    6942 
    6943 > isolde stepto
    6944 
    6945 > isolde stepto
    6946 
    6947 > isolde stepto
    6948 
    6949 > select clear
    6950 
    6951 > select clear
    6952 
    6953 > isolde stepto
    6954 
    6955 > isolde stepto
    6956 
    6957 > isolde stepto
    6958 
    6959 > isolde stepto
    6960 
    6961 > select /AU
    6962 
    6963 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6964 
    6965 > select clear
    6966 
    6967 > isolde stepto
    6968 
    6969 > isolde stepto
    6970 
    6971 > isolde stepto
    6972 
    6973 > isolde stepto
    6974 
    6975 > isolde stepto
    6976 
    6977 > isolde stepto
    6978 
    6979 > isolde stepto
    6980 
    6981 > isolde stepto
    6982 
    6983 > isolde stepto
    6984 
    6985 > isolde stepto
    6986 
    6987 > isolde stepto
    6988 
    6989 > select clear
    6990 
    6991 > isolde stepto
    6992 
    6993 > isolde stepto
    6994 
    6995 > isolde stepto
    6996 
    6997 > isolde stepto
    6998 
    6999 > isolde stepto
    7000 
    7001 > isolde stepto
    7002 
    7003 > isolde stepto
    7004 
    7005 > isolde stepto
    7006 
    7007 > isolde stepto
    7008 
    7009 > isolde stepto
    7010 
    7011 > isolde stepto
    7012 
    7013 > isolde stepto
    7014 
    7015 > isolde stepto
    7016 
    7017 > isolde stepto
    7018 
    7019 > isolde stepto
    7020 
    7021 > isolde stepto
    7022 
    7023 > isolde stepto
    7024 
    7025 > isolde stepto
    7026 
    7027 > isolde stepto
    7028 
    7029 > isolde stepto
    7030 
    7031 > isolde stepto
    7032 
    7033 > isolde stepto
    7034 
    7035 > isolde stepto
    7036 
    7037 > isolde stepto
    7038 
    7039 > isolde stepto
    7040 
    7041 > isolde stepto
    7042 
    7043 > isolde stepto
    7044 
    7045 > isolde stepto
    7046 
    7047 > isolde stepto
    7048 
    7049 > isolde stepto
    7050 
    7051 > isolde stepto
    7052 
    7053 > isolde stepto
    7054 
    7055 > isolde stepto
    7056 
    7057 > isolde stepto
    7058 
    7059 > isolde stepto prev
    7060 
    7061 > select clear
    7062 
    7063 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7064 bonded heavy atom. 
    7065 
    7066 > isolde stepto
    7067 
    7068 > isolde stepto
    7069 
    7070 > isolde stepto
    7071 
    7072 > isolde stepto
    7073 
    7074 > select /AV
    7075 
    7076 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    7077 
    7078 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7079 bonded heavy atom. 
    7080 
    7081 > isolde stepto
    7082 
    7083 > isolde stepto
    7084 
    7085 > isolde stepto
    7086 
    7087 > isolde stepto
    7088 
    7089 > isolde stepto
    7090 
    7091 > isolde stepto
    7092 
    7093 > isolde stepto
    7094 
    7095 > isolde stepto
    7096 
    7097 > isolde stepto
    7098 
    7099 > isolde stepto
    7100 
    7101 > isolde stepto
    7102 
    7103 > isolde stepto
    7104 
    7105 > select clear
    7106 
    7107 > isolde stepto
    7108 
    7109 > isolde stepto
    7110 
    7111 > isolde stepto
    7112 
    7113 > isolde stepto
    7114 
    7115 > isolde stepto
    7116 
    7117 > isolde stepto
    7118 
    7119 > isolde stepto
    7120 
    7121 > isolde stepto
    7122 
    7123 > isolde stepto
    7124 
    7125 > isolde stepto
    7126 
    7127 > isolde stepto
    7128 
    7129 > isolde stepto
    7130 
    7131 > isolde stepto
    7132 
    7133 > isolde stepto
    7134 
    7135 > isolde stepto
    7136 
    7137 > isolde stepto
    7138 
    7139 > isolde stepto
    7140 
    7141 > isolde stepto
    7142 
    7143 > isolde stepto
    7144 
    7145 > isolde stepto
    7146 
    7147 > isolde stepto
    7148 
    7149 > isolde stepto
    7150 
    7151 > isolde stepto
    7152 
    7153 > isolde stepto
    7154 
    7155 > isolde stepto
    7156 
    7157 > isolde stepto
    7158 
    7159 > isolde stepto
    7160 
    7161 > isolde stepto
    7162 
    7163 > isolde stepto
    7164 
    7165 > isolde stepto
    7166 
    7167 > isolde stepto
    7168 
    7169 > isolde stepto
    7170 
    7171 > select clear
    7172 
    7173 > select clear
    7174 
    7175 > isolde stepto
    7176 
    7177 > isolde stepto
    7178 
    7179 > isolde stepto
    7180 
    7181 > isolde stepto
    7182 
    7183 > select /AW
    7184 
    7185 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    7186 
    7187 > select clear
    7188 
    7189 > isolde stepto
    7190 
    7191 > isolde stepto
    7192 
    7193 > isolde stepto
    7194 
    7195 > isolde stepto
    7196 
    7197 > isolde stepto
    7198 
    7199 > isolde stepto
    7200 
    7201 > select clear
    7202 
    7203 > isolde stepto
    7204 
    7205 > isolde stepto
    7206 
    7207 > isolde stepto
    7208 
    7209 > isolde stepto
    7210 
    7211 > isolde stepto
    7212 
    7213 > isolde stepto
    7214 
    7215 > isolde stepto
    7216 
    7217 > isolde stepto
    7218 
    7219 > isolde stepto
    7220 
    7221 > isolde stepto
    7222 
    7223 > isolde stepto
    7224 
    7225 > isolde stepto
    7226 
    7227 > isolde stepto
    7228 
    7229 > isolde stepto
    7230 
    7231 > isolde stepto
    7232 
    7233 > isolde stepto
    7234 
    7235 > isolde stepto
    7236 
    7237 > isolde stepto
    7238 
    7239 > isolde stepto
    7240 
    7241 > isolde stepto
    7242 
    7243 > isolde stepto
    7244 
    7245 > isolde stepto
    7246 
    7247 > isolde stepto
    7248 
    7249 > isolde stepto
    7250 
    7251 > isolde stepto
    7252 
    7253 > isolde stepto
    7254 
    7255 > isolde stepto
    7256 
    7257 > isolde stepto
    7258 
    7259 > isolde stepto
    7260 
    7261 > isolde stepto
    7262 
    7263 > isolde stepto
    7264 
    7265 > isolde stepto
    7266 
    7267 > isolde stepto
    7268 
    7269 > isolde stepto
    7270 
    7271 > isolde stepto
    7272 
    7273 > isolde stepto
    7274 
    7275 > isolde stepto
    7276 
    7277 > isolde stepto
    7278 
    7279 > isolde stepto
    7280 
    7281 > isolde stepto
    7282 
    7283 > isolde stepto
    7284 
    7285 > isolde stepto
    7286 
    7287 > select /AX
    7288 
    7289 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    7290 
    7291 > select clear
    7292 
    7293 > isolde stepto
    7294 
    7295 > isolde stepto
    7296 
    7297 > isolde stepto
    7298 
    7299 > isolde stepto
    7300 
    7301 > isolde stepto
    7302 
    7303 > isolde stepto
    7304 
    7305 > isolde stepto
    7306 
    7307 > isolde stepto
    7308 
    7309 > isolde stepto
    7310 
    7311 > isolde stepto
    7312 
    7313 > isolde stepto
    7314 
    7315 > isolde stepto
    7316 
    7317 > isolde stepto
    7318 
    7319 > isolde stepto
    7320 
    7321 > isolde stepto
    7322 
    7323 > isolde stepto
    7324 
    7325 > isolde stepto
    7326 
    7327 > isolde stepto
    7328 
    7329 > isolde stepto
    7330 
    7331 > isolde stepto
    7332 
    7333 > isolde stepto
    7334 
    7335 > isolde stepto
    7336 
    7337 > isolde stepto
    7338 
    7339 > isolde stepto
    7340 
    7341 > isolde stepto
    7342 
    7343 > isolde stepto
    7344 
    7345 > isolde stepto
    7346 
    7347 > isolde stepto
    7348 
    7349 > isolde stepto
    7350 
    7351 > isolde stepto
    7352 
    7353 > isolde stepto
    7354 
    7355 > isolde stepto
    7356 
    7357 > isolde stepto
    7358 
    7359 > isolde stepto
    7360 
    7361 > isolde stepto
    7362 
    7363 > isolde stepto
    7364 
    7365 > isolde stepto
    7366 
    7367 > isolde stepto
    7368 
    7369 > isolde stepto
    7370 
    7371 > isolde stepto
    7372 
    7373 > isolde stepto
    7374 
    7375 > isolde stepto
    7376 
    7377 > isolde stepto
    7378 
    7379 > isolde stepto
    7380 
    7381 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7382 bonded heavy atom. 
    7383 
    7384 > select clear
    7385 
    7386 > select /AA
    7387 
    7388 981 atoms, 1002 bonds, 48 residues, 1 model selected 
    7389 
    7390 > select clear
    7391 
    7392 > save working.cxs
    7393 
    7394 Taking snapshot of stepper: working_2.pdb 
    7395 
    7396 > isolde stepto
    7397 
    7398 > isolde stepto
    7399 
    7400 > isolde stepto
    7401 
    7402 > isolde stepto
    7403 
    7404 > isolde stepto
    7405 
    7406 > select /BA
    7407 
    7408 766 atoms, 787 bonds, 40 residues, 1 model selected 
    7409 
    7410 > select clear
    7411 
    7412 > isolde stepto
    7413 
    7414 > isolde stepto
    7415 
    7416 > isolde stepto
    7417 
    7418 > isolde stepto
    7419 
    7420 > isolde stepto
    7421 
    7422 > isolde stepto
    7423 
    7424 > isolde stepto
    7425 
    7426 > isolde stepto
    7427 
    7428 > isolde stepto
    7429 
    7430 > isolde stepto
    7431 
    7432 > isolde stepto
    7433 
    7434 > isolde stepto
    7435 
    7436 > isolde stepto
    7437 
    7438 > isolde stepto
    7439 
    7440 > isolde stepto
    7441 
    7442 > isolde stepto
    7443 
    7444 > isolde stepto
    7445 
    7446 > isolde stepto
    7447 
    7448 > isolde stepto
    7449 
    7450 > isolde stepto
    7451 
    7452 > isolde stepto
    7453 
    7454 > isolde stepto
    7455 
    7456 > isolde stepto
    7457 
    7458 > isolde stepto
    7459 
    7460 > isolde stepto
    7461 
    7462 > isolde stepto
    7463 
    7464 > isolde stepto
    7465 
    7466 > isolde stepto
    7467 
    7468 > isolde stepto
    7469 
    7470 > isolde stepto
    7471 
    7472 > isolde stepto
    7473 
    7474 > isolde stepto
    7475 
    7476 > isolde stepto
    7477 
    7478 > isolde stepto
    7479 
    7480 > isolde stepto
    7481 
    7482 > isolde stepto
    7483 
    7484 > isolde stepto
    7485 
    7486 > isolde stepto
    7487 
    7488 > select /BB
    7489 
    7490 773 atoms, 794 bonds, 41 residues, 1 model selected 
    7491 
    7492 > select clear
    7493 
    7494 > isolde stepto
    7495 
    7496 > isolde stepto
    7497 
    7498 > isolde stepto
    7499 
    7500 > isolde stepto
    7501 
    7502 > isolde stepto
    7503 
    7504 > isolde stepto
    7505 
    7506 > isolde stepto
    7507 
    7508 > isolde stepto
    7509 
    7510 > isolde stepto
    7511 
    7512 > isolde stepto
    7513 
    7514 > isolde stepto
    7515 
    7516 > isolde stepto
    7517 
    7518 > isolde stepto
    7519 
    7520 > isolde stepto
    7521 
    7522 > isolde stepto
    7523 
    7524 > isolde stepto
    7525 
    7526 > isolde stepto
    7527 
    7528 > isolde stepto
    7529 
    7530 > isolde stepto
    7531 
    7532 > isolde stepto
    7533 
    7534 > isolde stepto
    7535 
    7536 > isolde stepto
    7537 
    7538 > isolde stepto
    7539 
    7540 > isolde stepto
    7541 
    7542 > isolde stepto
    7543 
    7544 > isolde stepto
    7545 
    7546 > isolde stepto
    7547 
    7548 > isolde stepto
    7549 
    7550 > isolde stepto
    7551 
    7552 > isolde stepto
    7553 
    7554 > isolde stepto
    7555 
    7556 > isolde stepto
    7557 
    7558 > isolde stepto
    7559 
    7560 > isolde stepto
    7561 
    7562 > isolde stepto
    7563 
    7564 > isolde stepto
    7565 
    7566 > isolde stepto
    7567 
    7568 > isolde stepto
    7569 
    7570 > isolde stepto
    7571 
    7572 > isolde stepto
    7573 
    7574 > select up
    7575 
    7576 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7577 
    7578 > select up
    7579 
    7580 40 atoms, 39 bonds, 3 residues, 1 model selected 
    7581 
    7582 > select up
    7583 
    7584 766 atoms, 787 bonds, 40 residues, 1 model selected 
    7585 
    7586 > select clear
    7587 
    7588 > select clear
    7589 
    7590 > isolde stepto
    7591 
    7592 > isolde stepto
    7593 
    7594 > isolde stepto
    7595 
    7596 > isolde stepto
    7597 
    7598 > isolde stepto
    7599 
    7600 > isolde stepto
    7601 
    7602 > isolde stepto
    7603 
    7604 > isolde stepto
    7605 
    7606 > isolde stepto
    7607 
    7608 > isolde stepto
    7609 
    7610 > isolde stepto
    7611 
    7612 > isolde stepto
    7613 
    7614 > isolde stepto
    7615 
    7616 > isolde stepto
    7617 
    7618 > isolde stepto
    7619 
    7620 > isolde stepto
    7621 
    7622 > isolde stepto
    7623 
    7624 > isolde stepto
    7625 
    7626 > isolde stepto
    7627 
    7628 > isolde stepto
    7629 
    7630 > isolde stepto
    7631 
    7632 > isolde stepto
    7633 
    7634 > isolde stepto
    7635 
    7636 > isolde stepto
    7637 
    7638 > isolde stepto
    7639 
    7640 > isolde stepto
    7641 
    7642 > isolde stepto
    7643 
    7644 > isolde stepto
    7645 
    7646 > isolde stepto
    7647 
    7648 > isolde stepto
    7649 
    7650 > isolde stepto
    7651 
    7652 > isolde stepto
    7653 
    7654 > isolde stepto
    7655 
    7656 > isolde stepto
    7657 
    7658 > isolde stepto
    7659 
    7660 > isolde stepto
    7661 
    7662 > isolde stepto
    7663 
    7664 > isolde stepto
    7665 
    7666 > isolde stepto
    7667 
    7668 > select clear
    7669 
    7670 > isolde stepto
    7671 
    7672 > isolde stepto
    7673 
    7674 > clipper spotlight radius 13.00
    7675 
    7676 > clipper spotlight radius 14.00
    7677 
    7678 > clipper spotlight radius 15.00
    7679 
    7680 > isolde stepto
    7681 
    7682 > isolde stepto
    7683 
    7684 > save working.cxs
    7685 
    7686 Taking snapshot of stepper: working_2.pdb 
    7687 
    7688 > isolde add ligand LMT
    7689 
    7690 place_ligand() was called with use_md_template=True, but no suitable template
    7691 was found. This command has been ignored. 
    7692 
    7693 Chain ak, residue 67 specifies more than one residue! The simulation can still
    7694 run, but this will probably cause problems later if not rectified by
    7695 renumbering. 
    7696 
    7697 Chain ak, residue 67 specifies more than one residue! The simulation can still
    7698 run, but this will probably cause problems later if not rectified by
    7699 renumbering. 
    7700 
    7701 > select up
    7702 
    7703 140 atoms, 148 bonds, 1 residue, 1 model selected 
    7704 
    7705 > isolde ignore sel
    7706 
    7707 ISOLDE: currently ignoring 1 residues in model 8.2 
    7708 
    7709 > isolde ~ignore
    7710 
    7711 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7712 bonded heavy atom. 
    7713 
    7714 > select clear
    7715 
    7716 > select up
    7717 
    7718 81 atoms, 82 bonds, 1 residue, 1 model selected 
    7719 
    7720 > delete sel
    7721 
    7722 > save working.cxs
    7723 
    7724 Taking snapshot of stepper: working_2.pdb 
    7725 opened ChimeraX session 
    7726 
    7727 > isolde start
    7728 
    7729 > set selectionWidth 4
    7730 
    7731 Done loading forcefield 
    7732 
    7733 > isolde stepto
    7734 
    7735 > clipper set contourSensitivity 0.25
    7736 
    7737 > select /AA
    7738 
    7739 1019 atoms, 1041 bonds, 51 residues, 1 model selected 
    7740 
    7741 > show #!1 models
    7742 
    7743 > select #1
    7744 
    7745 158 atoms, 160 bonds, 11 residues, 8 models selected 
    7746 
    7747 > select #1
    7748 
    7749 158 atoms, 160 bonds, 11 residues, 8 models selected 
    7750 
    7751 > close #1
    7752 
    7753 > isolde stepto /BA
    7754 
    7755 Multiple residues selected! Going to the first... 
    7756 
    7757 > isolde stepto /BB
    7758 
    7759 Multiple residues selected! Going to the first... 
    7760 
    7761 > select clear
    7762 
    7763 > select /BB
    7764 
    7765 773 atoms, 794 bonds, 41 residues, 1 model selected 
    7766 
    7767 > select clear
    7768 
    7769 > select clear
    7770 
    7771 > isolde stepto
    7772 
    7773 > isolde stepto
    7774 
    7775 > isolde stepto
    7776 
    7777 > isolde stepto
    7778 
    7779 > isolde stepto
    7780 
    7781 > isolde stepto
    7782 
    7783 > isolde stepto
    7784 
    7785 > isolde stepto
    7786 
    7787 > isolde stepto
    7788 
    7789 > isolde stepto
    7790 
    7791 > isolde stepto
    7792 
    7793 > isolde stepto
    7794 
    7795 > isolde stepto
    7796 
    7797 > isolde stepto
    7798 
    7799 > isolde stepto
    7800 
    7801 > isolde stepto
    7802 
    7803 > isolde stepto
    7804 
    7805 > isolde stepto
    7806 
    7807 > isolde stepto
    7808 
    7809 > isolde stepto
    7810 
    7811 > isolde stepto
    7812 
    7813 > isolde stepto
    7814 
    7815 > isolde stepto
    7816 
    7817 > isolde stepto
    7818 
    7819 > isolde stepto
    7820 
    7821 > isolde stepto
    7822 
    7823 > isolde stepto
    7824 
    7825 > isolde stepto
    7826 
    7827 > isolde stepto
    7828 
    7829 > isolde stepto
    7830 
    7831 > isolde stepto
    7832 
    7833 > isolde stepto
    7834 
    7835 > isolde stepto
    7836 
    7837 > isolde stepto
    7838 
    7839 > isolde stepto
    7840 
    7841 > isolde stepto
    7842 
    7843 > isolde stepto
    7844 
    7845 > isolde stepto
    7846 
    7847 > isolde stepto
    7848 
    7849 > isolde stepto
    7850 
    7851 > select up
    7852 
    7853 17 atoms, 16 bonds, 1 residue, 1 model selected 
    7854 
    7855 > select up
    7856 
    7857 40 atoms, 39 bonds, 3 residues, 1 model selected 
    7858 
    7859 > select up
    7860 
    7861 766 atoms, 787 bonds, 40 residues, 1 model selected 
    7862 
    7863 > select clear
    7864 
    7865 > isolde stepto
    7866 
    7867 > isolde stepto
    7868 
    7869 > isolde stepto
    7870 
    7871 > isolde stepto
    7872 
    7873 > isolde stepto
    7874 
    7875 > isolde stepto
    7876 
    7877 > isolde stepto
    7878 
    7879 > isolde stepto
    7880 
    7881 > isolde stepto
    7882 
    7883 > isolde stepto
    7884 
    7885 > isolde stepto
    7886 
    7887 > isolde stepto
    7888 
    7889 > isolde stepto
    7890 
    7891 > isolde stepto
    7892 
    7893 > isolde stepto
    7894 
    7895 > isolde stepto
    7896 
    7897 > isolde stepto
    7898 
    7899 > isolde stepto
    7900 
    7901 > isolde stepto
    7902 
    7903 > isolde stepto
    7904 
    7905 > isolde stepto
    7906 
    7907 > isolde stepto
    7908 
    7909 > isolde stepto
    7910 
    7911 > isolde stepto
    7912 
    7913 > isolde stepto
    7914 
    7915 > isolde stepto
    7916 
    7917 > isolde stepto
    7918 
    7919 > isolde stepto
    7920 
    7921 > isolde stepto
    7922 
    7923 > isolde stepto
    7924 
    7925 > isolde stepto
    7926 
    7927 > isolde stepto
    7928 
    7929 > isolde stepto
    7930 
    7931 > isolde stepto
    7932 
    7933 > isolde stepto
    7934 
    7935 > isolde stepto
    7936 
    7937 > isolde stepto
    7938 
    7939 > isolde stepto
    7940 
    7941 > isolde stepto
    7942 
    7943 > select clear
    7944 
    7945 > select up
    7946 
    7947 14 atoms, 13 bonds, 1 residue, 1 model selected 
    7948 
    7949 > select up
    7950 
    7951 47 atoms, 46 bonds, 4 residues, 1 model selected 
    7952 
    7953 > select up
    7954 
    7955 773 atoms, 794 bonds, 41 residues, 1 model selected 
    7956 
    7957 > select clear
    7958 
    7959 > isolde stepto
    7960 
    7961 > isolde stepto
    7962 
    7963 > isolde stepto
    7964 
    7965 > isolde stepto
    7966 
    7967 > isolde stepto
    7968 
    7969 > isolde stepto
    7970 
    7971 > isolde stepto
    7972 
    7973 > isolde stepto
    7974 
    7975 > isolde stepto
    7976 
    7977 > isolde stepto
    7978 
    7979 > isolde stepto
    7980 
    7981 > isolde stepto
    7982 
    7983 > isolde stepto
    7984 
    7985 > isolde stepto
    7986 
    7987 > isolde stepto
    7988 
    7989 > isolde stepto
    7990 
    7991 > isolde stepto
    7992 
    7993 > isolde stepto
    7994 
    7995 > isolde stepto
    7996 
    7997 > isolde stepto
    7998 
    7999 > isolde stepto
    8000 
    8001 > isolde stepto
    8002 
    8003 > isolde stepto
    8004 
    8005 > isolde stepto
    8006 
    8007 > isolde stepto
    8008 
    8009 > isolde stepto
    8010 
    8011 > isolde stepto
    8012 
    8013 > isolde stepto
    8014 
    8015 > isolde stepto
    8016 
    8017 > isolde stepto
    8018 
    8019 > isolde stepto
    8020 
    8021 > isolde stepto
    8022 
    8023 > isolde stepto
    8024 
    8025 > isolde stepto
    8026 
    8027 > isolde stepto
    8028 
    8029 > isolde stepto
    8030 
    8031 > isolde stepto
    8032 
    8033 > isolde stepto
    8034 
    8035 > isolde stepto
    8036 
    8037 > isolde stepto
    8038 
    8039 > select up
    8040 
    8041 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8042 
    8043 > select up
    8044 
    8045 47 atoms, 46 bonds, 4 residues, 1 model selected 
    8046 
    8047 > select up
    8048 
    8049 773 atoms, 794 bonds, 41 residues, 1 model selected 
    8050 
    8051 > select clear
    8052 
    8053 > isolde stepto
    8054 
    8055 > isolde stepto
    8056 
    8057 > isolde stepto
    8058 
    8059 > isolde stepto
    8060 
    8061 > isolde stepto
    8062 
    8063 > isolde stepto
    8064 
    8065 > isolde stepto
    8066 
    8067 > isolde stepto
    8068 
    8069 > isolde stepto
    8070 
    8071 > isolde stepto
    8072 
    8073 > isolde stepto
    8074 
    8075 > isolde stepto
    8076 
    8077 > isolde stepto
    8078 
    8079 > isolde stepto
    8080 
    8081 > isolde stepto
    8082 
    8083 > isolde stepto
    8084 
    8085 > isolde stepto
    8086 
    8087 > isolde stepto
    8088 
    8089 > isolde stepto
    8090 
    8091 > isolde stepto
    8092 
    8093 > isolde stepto
    8094 
    8095 > isolde stepto
    8096 
    8097 > isolde stepto
    8098 
    8099 > isolde stepto
    8100 
    8101 > isolde stepto
    8102 
    8103 > isolde stepto
    8104 
    8105 > isolde stepto
    8106 
    8107 > isolde stepto
    8108 
    8109 > isolde stepto
    8110 
    8111 > isolde stepto
    8112 
    8113 > isolde stepto
    8114 
    8115 > isolde stepto
    8116 
    8117 > isolde stepto
    8118 
    8119 > isolde stepto
    8120 
    8121 > isolde stepto
    8122 
    8123 > isolde stepto
    8124 
    8125 > isolde stepto
    8126 
    8127 > isolde stepto
    8128 
    8129 > isolde stepto
    8130 
    8131 > isolde stepto
    8132 
    8133 > select up
    8134 
    8135 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8136 
    8137 > select up
    8138 
    8139 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8140 
    8141 > select up
    8142 
    8143 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8144 
    8145 > select clear
    8146 
    8147 > isolde stepto
    8148 
    8149 > isolde stepto
    8150 
    8151 > isolde stepto
    8152 
    8153 > isolde stepto
    8154 
    8155 > isolde stepto
    8156 
    8157 > select clear
    8158 
    8159 > isolde stepto
    8160 
    8161 > isolde stepto
    8162 
    8163 > isolde stepto
    8164 
    8165 > isolde stepto
    8166 
    8167 > isolde stepto
    8168 
    8169 > isolde stepto
    8170 
    8171 > isolde stepto
    8172 
    8173 > isolde stepto
    8174 
    8175 > isolde stepto
    8176 
    8177 > isolde stepto
    8178 
    8179 > isolde stepto
    8180 
    8181 > isolde stepto
    8182 
    8183 > isolde stepto
    8184 
    8185 > isolde stepto
    8186 
    8187 > isolde stepto
    8188 
    8189 > isolde stepto
    8190 
    8191 > isolde stepto
    8192 
    8193 > isolde stepto
    8194 
    8195 > isolde stepto
    8196 
    8197 > isolde stepto
    8198 
    8199 > isolde stepto
    8200 
    8201 > isolde stepto
    8202 
    8203 > isolde stepto
    8204 
    8205 > isolde stepto
    8206 
    8207 > isolde stepto
    8208 
    8209 > isolde stepto
    8210 
    8211 > isolde stepto
    8212 
    8213 > isolde stepto
    8214 
    8215 > isolde stepto
    8216 
    8217 > isolde stepto
    8218 
    8219 > select clear
    8220 
    8221 > isolde stepto
    8222 
    8223 > isolde stepto
    8224 
    8225 > isolde stepto
    8226 
    8227 > isolde stepto
    8228 
    8229 > select up
    8230 
    8231 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8232 
    8233 > select up
    8234 
    8235 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8236 
    8237 > select up
    8238 
    8239 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8240 
    8241 > select up
    8242 
    8243 96639 atoms, 98747 bonds, 5194 residues, 1 model selected 
    8244 
    8245 Chain ak, residue 67 specifies more than one residue! The simulation can still
    8246 run, but this will probably cause problems later if not rectified by
    8247 renumbering. 
    8248 
    8249 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    8250 more memory-efficient implementation. 
    8251 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    8252 more memory-efficient implementation. 
    8253 
    8254 > select clear
    8255 
    8256 > select clear
    8257 
    8258 > select up
    8259 
    8260 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8261 
    8262 > select up
    8263 
    8264 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8265 
    8266 > select up
    8267 
    8268 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8269 
    8270 > select up
    8271 
    8272 96639 atoms, 98747 bonds, 5194 residues, 1 model selected 
    8273 
    8274 > select down
    8275 
    8276 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8277 
    8278 > select clear
    8279 
    8280 > isolde stepto
    8281 
    8282 > isolde stepto
    8283 
    8284 > isolde stepto
    8285 
    8286 > isolde stepto
    8287 
    8288 > isolde stepto
    8289 
    8290 > isolde stepto
    8291 
    8292 > isolde stepto
    8293 
    8294 > isolde stepto
    8295 
    8296 > isolde stepto
    8297 
    8298 > isolde stepto
    8299 
    8300 > isolde stepto
    8301 
    8302 > isolde stepto
    8303 
    8304 > isolde stepto
    8305 
    8306 > isolde stepto
    8307 
    8308 > isolde stepto
    8309 
    8310 > isolde stepto
    8311 
    8312 > isolde stepto
    8313 
    8314 > isolde stepto
    8315 
    8316 > isolde stepto
    8317 
    8318 > isolde stepto
    8319 
    8320 > isolde stepto
    8321 
    8322 > isolde stepto
    8323 
    8324 > isolde stepto
    8325 
    8326 > isolde stepto
    8327 
    8328 > isolde stepto
    8329 
    8330 > isolde stepto
    8331 
    8332 > isolde stepto
    8333 
    8334 > isolde stepto
    8335 
    8336 > isolde stepto
    8337 
    8338 > isolde stepto
    8339 
    8340 > isolde stepto
    8341 
    8342 > isolde stepto
    8343 
    8344 > isolde stepto
    8345 
    8346 > isolde stepto
    8347 
    8348 > isolde stepto
    8349 
    8350 > isolde stepto
    8351 
    8352 > isolde stepto
    8353 
    8354 > isolde stepto
    8355 
    8356 > isolde stepto
    8357 
    8358 > select up
    8359 
    8360 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8361 
    8362 > select up
    8363 
    8364 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8365 
    8366 > select up
    8367 
    8368 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8369 
    8370 > select clear
    8371 
    8372 > isolde stepto
    8373 
    8374 > isolde stepto
    8375 
    8376 > isolde stepto
    8377 
    8378 > isolde stepto
    8379 
    8380 > isolde stepto
    8381 
    8382 > isolde stepto
    8383 
    8384 > isolde stepto
    8385 
    8386 > isolde stepto
    8387 
    8388 > isolde stepto
    8389 
    8390 > isolde stepto
    8391 
    8392 > isolde stepto
    8393 
    8394 > isolde stepto
    8395 
    8396 > isolde stepto
    8397 
    8398 > isolde stepto
    8399 
    8400 > isolde stepto
    8401 
    8402 > isolde stepto
    8403 
    8404 > isolde stepto
    8405 
    8406 > isolde stepto
    8407 
    8408 > isolde stepto
    8409 
    8410 > isolde stepto
    8411 
    8412 > isolde stepto
    8413 
    8414 > isolde stepto
    8415 
    8416 > isolde stepto
    8417 
    8418 > isolde stepto
    8419 
    8420 > isolde stepto
    8421 
    8422 > isolde stepto
    8423 
    8424 > isolde stepto
    8425 
    8426 > isolde stepto
    8427 
    8428 > isolde stepto
    8429 
    8430 > isolde stepto
    8431 
    8432 > isolde stepto
    8433 
    8434 > isolde stepto
    8435 
    8436 > isolde stepto
    8437 
    8438 > isolde stepto
    8439 
    8440 > isolde stepto
    8441 
    8442 > isolde stepto
    8443 
    8444 > isolde stepto
    8445 
    8446 > isolde stepto
    8447 
    8448 > isolde stepto
    8449 
    8450 > select up
    8451 
    8452 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8453 
    8454 > select up
    8455 
    8456 47 atoms, 46 bonds, 4 residues, 1 model selected 
    8457 
    8458 > select up
    8459 
    8460 773 atoms, 794 bonds, 41 residues, 1 model selected 
    8461 
    8462 > select clear
    8463 
    8464 > isolde stepto
    8465 
    8466 > isolde stepto
    8467 
    8468 > isolde stepto
    8469 
    8470 > isolde stepto
    8471 
    8472 > isolde stepto
    8473 
    8474 > isolde stepto
    8475 
    8476 > isolde stepto
    8477 
    8478 > isolde stepto
    8479 
    8480 > isolde stepto
    8481 
    8482 > isolde stepto
    8483 
    8484 > isolde stepto
    8485 
    8486 > isolde stepto
    8487 
    8488 > isolde stepto
    8489 
    8490 > isolde stepto
    8491 
    8492 > isolde stepto
    8493 
    8494 > isolde stepto
    8495 
    8496 > isolde stepto
    8497 
    8498 > isolde stepto
    8499 
    8500 > isolde stepto
    8501 
    8502 > isolde stepto
    8503 
    8504 > isolde stepto
    8505 
    8506 > isolde stepto
    8507 
    8508 > isolde stepto
    8509 
    8510 > isolde stepto
    8511 
    8512 > isolde stepto
    8513 
    8514 > isolde stepto
    8515 
    8516 > isolde stepto
    8517 
    8518 > isolde stepto
    8519 
    8520 > isolde stepto
    8521 
    8522 > isolde stepto
    8523 
    8524 > isolde stepto
    8525 
    8526 > isolde stepto
    8527 
    8528 > isolde stepto
    8529 
    8530 > isolde stepto
    8531 
    8532 > isolde stepto
    8533 
    8534 > isolde stepto
    8535 
    8536 > isolde stepto
    8537 
    8538 > isolde stepto
    8539 
    8540 > isolde stepto
    8541 
    8542 > isolde stepto
    8543 
    8544 > select up
    8545 
    8546 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8547 
    8548 > select up
    8549 
    8550 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8551 
    8552 > select up
    8553 
    8554 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8555 
    8556 > select clear
    8557 
    8558 > isolde stepto
    8559 
    8560 > isolde stepto
    8561 
    8562 > isolde stepto
    8563 
    8564 > isolde stepto
    8565 
    8566 > isolde stepto
    8567 
    8568 > isolde stepto
    8569 
    8570 > isolde stepto
    8571 
    8572 > isolde stepto
    8573 
    8574 > isolde stepto
    8575 
    8576 > isolde stepto
    8577 
    8578 > isolde stepto
    8579 
    8580 > isolde stepto
    8581 
    8582 > isolde stepto
    8583 
    8584 > isolde stepto
    8585 
    8586 > isolde stepto
    8587 
    8588 > isolde stepto
    8589 
    8590 > isolde stepto
    8591 
    8592 > isolde stepto
    8593 
    8594 > isolde stepto
    8595 
    8596 > isolde stepto
    8597 
    8598 > isolde stepto
    8599 
    8600 > isolde stepto
    8601 
    8602 > isolde stepto
    8603 
    8604 > isolde stepto
    8605 
    8606 > isolde stepto
    8607 
    8608 > isolde stepto
    8609 
    8610 > isolde stepto
    8611 
    8612 > isolde stepto
    8613 
    8614 > isolde stepto
    8615 
    8616 > isolde stepto
    8617 
    8618 > isolde stepto
    8619 
    8620 > isolde stepto
    8621 
    8622 > isolde stepto
    8623 
    8624 > isolde stepto
    8625 
    8626 > isolde stepto
    8627 
    8628 > isolde stepto
    8629 
    8630 > isolde stepto
    8631 
    8632 > isolde stepto
    8633 
    8634 > isolde stepto
    8635 
    8636 > select up
    8637 
    8638 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8639 
    8640 > select up
    8641 
    8642 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8643 
    8644 > select up
    8645 
    8646 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8647 
    8648 > select clear
    8649 
    8650 > isolde stepto
    8651 
    8652 > isolde stepto
    8653 
    8654 > isolde stepto
    8655 
    8656 > isolde stepto
    8657 
    8658 > isolde stepto
    8659 
    8660 > isolde stepto
    8661 
    8662 > isolde stepto
    8663 
    8664 > isolde stepto
    8665 
    8666 > isolde stepto
    8667 
    8668 > isolde stepto
    8669 
    8670 > isolde stepto
    8671 
    8672 > isolde stepto
    8673 
    8674 > isolde stepto
    8675 
    8676 > isolde stepto
    8677 
    8678 > isolde stepto
    8679 
    8680 > isolde stepto
    8681 
    8682 > isolde stepto
    8683 
    8684 > isolde stepto
    8685 
    8686 > isolde stepto
    8687 
    8688 > isolde stepto
    8689 
    8690 > isolde stepto
    8691 
    8692 > isolde stepto
    8693 
    8694 > isolde stepto
    8695 
    8696 > isolde stepto
    8697 
    8698 > isolde stepto
    8699 
    8700 > isolde stepto
    8701 
    8702 > isolde stepto
    8703 
    8704 > isolde stepto
    8705 
    8706 > isolde stepto
    8707 
    8708 > isolde stepto
    8709 
    8710 > isolde stepto
    8711 
    8712 > isolde stepto
    8713 
    8714 > isolde stepto
    8715 
    8716 > isolde stepto
    8717 
    8718 > isolde stepto
    8719 
    8720 > isolde stepto
    8721 
    8722 > isolde stepto
    8723 
    8724 > isolde stepto
    8725 
    8726 > isolde stepto
    8727 
    8728 > select up
    8729 
    8730 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8731 
    8732 > select up
    8733 
    8734 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8735 
    8736 > select up
    8737 
    8738 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8739 
    8740 > select clear
    8741 
    8742 > isolde stepto
    8743 
    8744 > isolde stepto
    8745 
    8746 > isolde stepto
    8747 
    8748 > isolde stepto
    8749 
    8750 > isolde stepto
    8751 
    8752 > isolde stepto
    8753 
    8754 > isolde stepto
    8755 
    8756 > isolde stepto
    8757 
    8758 > isolde stepto
    8759 
    8760 > isolde stepto
    8761 
    8762 > isolde stepto
    8763 
    8764 > isolde stepto
    8765 
    8766 > isolde stepto
    8767 
    8768 > isolde stepto
    8769 
    8770 > isolde stepto
    8771 
    8772 > isolde stepto
    8773 
    8774 > isolde stepto
    8775 
    8776 > isolde stepto
    8777 
    8778 > select clear
    8779 
    8780 > isolde stepto
    8781 
    8782 > isolde stepto
    8783 
    8784 > isolde stepto
    8785 
    8786 > isolde stepto
    8787 
    8788 > isolde stepto
    8789 
    8790 > isolde stepto
    8791 
    8792 > isolde stepto
    8793 
    8794 > isolde stepto
    8795 
    8796 > isolde stepto
    8797 
    8798 > isolde stepto
    8799 
    8800 > isolde stepto
    8801 
    8802 > isolde stepto
    8803 
    8804 > isolde stepto
    8805 
    8806 > isolde stepto
    8807 
    8808 > isolde stepto
    8809 
    8810 > isolde stepto
    8811 
    8812 > isolde stepto
    8813 
    8814 > isolde stepto
    8815 
    8816 > isolde stepto
    8817 
    8818 > isolde stepto
    8819 
    8820 > isolde stepto
    8821 
    8822 > select up
    8823 
    8824 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8825 
    8826 > select up
    8827 
    8828 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8829 
    8830 > select up
    8831 
    8832 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8833 
    8834 > select clear
    8835 
    8836 > isolde stepto
    8837 
    8838 > isolde stepto
    8839 
    8840 > isolde stepto
    8841 
    8842 > isolde stepto
    8843 
    8844 > isolde stepto
    8845 
    8846 > isolde stepto
    8847 
    8848 > isolde stepto
    8849 
    8850 > isolde stepto
    8851 
    8852 > isolde stepto
    8853 
    8854 > isolde stepto
    8855 
    8856 > isolde stepto
    8857 
    8858 > isolde stepto
    8859 
    8860 > isolde stepto
    8861 
    8862 > isolde stepto
    8863 
    8864 > isolde stepto
    8865 
    8866 > isolde stepto
    8867 
    8868 > isolde stepto
    8869 
    8870 > isolde stepto
    8871 
    8872 > isolde stepto
    8873 
    8874 > isolde stepto
    8875 
    8876 > isolde stepto
    8877 
    8878 > isolde stepto
    8879 
    8880 > isolde stepto
    8881 
    8882 > isolde stepto
    8883 
    8884 > isolde stepto
    8885 
    8886 > isolde stepto
    8887 
    8888 > isolde stepto
    8889 
    8890 > isolde stepto
    8891 
    8892 > isolde stepto
    8893 
    8894 > isolde stepto
    8895 
    8896 > isolde stepto
    8897 
    8898 > isolde stepto
    8899 
    8900 > isolde stepto
    8901 
    8902 > isolde stepto
    8903 
    8904 > isolde stepto
    8905 
    8906 > isolde stepto
    8907 
    8908 > isolde stepto
    8909 
    8910 > isolde stepto
    8911 
    8912 > isolde stepto
    8913 
    8914 > select up
    8915 
    8916 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8917 
    8918 > select up
    8919 
    8920 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8921 
    8922 > select up
    8923 
    8924 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8925 
    8926 > select clear
    8927 
    8928 > isolde stepto
    8929 
    8930 > isolde stepto
    8931 
    8932 > isolde stepto
    8933 
    8934 > isolde stepto
    8935 
    8936 > isolde stepto
    8937 
    8938 > isolde stepto
    8939 
    8940 > isolde stepto
    8941 
    8942 > isolde stepto
    8943 
    8944 > select up
    8945 
    8946 100 atoms, 99 bonds, 1 residue, 1 model selected 
    8947 
    8948 > show sel
    8949 
    8950 > select clear
    8951 
    8952 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    8953 bonded heavy atom. 
    8954 
    8955 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    8956 bonded heavy atom. 
    8957 
    8958 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    8959 bonded heavy atom. 
    8960 
    8961 > select clear
    8962 
    8963 > isolde stepto
    8964 
    8965 > isolde stepto
    8966 
    8967 > isolde stepto
    8968 
    8969 > isolde stepto
    8970 
    8971 > isolde stepto
    8972 
    8973 > isolde stepto
    8974 
    8975 > isolde stepto
    8976 
    8977 > isolde stepto
    8978 
    8979 > isolde stepto
    8980 
    8981 > isolde stepto
    8982 
    8983 > isolde stepto
    8984 
    8985 > isolde stepto
    8986 
    8987 > isolde stepto
    8988 
    8989 > isolde stepto
    8990 
    8991 > isolde stepto
    8992 
    8993 > isolde stepto
    8994 
    8995 > isolde stepto
    8996 
    8997 > isolde stepto
    8998 
    8999 > isolde stepto
    9000 
    9001 > isolde stepto
    9002 
    9003 > isolde stepto
    9004 
    9005 > isolde stepto
    9006 
    9007 > isolde stepto
    9008 
    9009 > isolde stepto
    9010 
    9011 > isolde stepto
    9012 
    9013 > isolde stepto
    9014 
    9015 > isolde stepto
    9016 
    9017 > isolde stepto
    9018 
    9019 > isolde stepto
    9020 
    9021 > isolde stepto
    9022 
    9023 > isolde stepto
    9024 
    9025 > select up
    9026 
    9027 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9028 
    9029 > select up
    9030 
    9031 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9032 
    9033 > select up
    9034 
    9035 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9036 
    9037 > select clear
    9038 
    9039 > isolde stepto
    9040 
    9041 > isolde stepto
    9042 
    9043 > isolde stepto
    9044 
    9045 > isolde stepto
    9046 
    9047 > isolde stepto
    9048 
    9049 > isolde stepto
    9050 
    9051 > isolde stepto
    9052 
    9053 > isolde stepto
    9054 
    9055 > isolde stepto
    9056 
    9057 > isolde stepto
    9058 
    9059 > isolde stepto
    9060 
    9061 > isolde stepto
    9062 
    9063 > isolde stepto
    9064 
    9065 > isolde stepto
    9066 
    9067 > isolde stepto
    9068 
    9069 > isolde stepto
    9070 
    9071 > isolde stepto
    9072 
    9073 > isolde stepto
    9074 
    9075 > isolde stepto
    9076 
    9077 > isolde stepto
    9078 
    9079 > isolde stepto
    9080 
    9081 > isolde stepto
    9082 
    9083 > isolde stepto
    9084 
    9085 > isolde stepto
    9086 
    9087 > isolde stepto
    9088 
    9089 > isolde stepto
    9090 
    9091 > isolde stepto
    9092 
    9093 > isolde stepto
    9094 
    9095 > isolde stepto
    9096 
    9097 > isolde stepto
    9098 
    9099 > isolde stepto
    9100 
    9101 > isolde stepto
    9102 
    9103 > isolde stepto
    9104 
    9105 > isolde stepto
    9106 
    9107 > isolde stepto
    9108 
    9109 > isolde stepto
    9110 
    9111 > isolde stepto
    9112 
    9113 > isolde stepto
    9114 
    9115 > isolde stepto
    9116 
    9117 > select up
    9118 
    9119 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9120 
    9121 > select up
    9122 
    9123 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9124 
    9125 > select clear
    9126 
    9127 > isolde stepto
    9128 
    9129 > isolde stepto
    9130 
    9131 > isolde stepto
    9132 
    9133 > isolde stepto
    9134 
    9135 > isolde stepto
    9136 
    9137 > isolde stepto
    9138 
    9139 > isolde stepto
    9140 
    9141 > isolde stepto
    9142 
    9143 > isolde stepto
    9144 
    9145 > isolde stepto
    9146 
    9147 > isolde stepto
    9148 
    9149 > isolde stepto
    9150 
    9151 > isolde stepto
    9152 
    9153 > isolde stepto
    9154 
    9155 > select up
    9156 
    9157 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9158 
    9159 > select up
    9160 
    9161 503 atoms, 512 bonds, 32 residues, 1 model selected 
    9162 
    9163 > select up
    9164 
    9165 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9166 
    9167 > select clear
    9168 
    9169 > isolde stepto
    9170 
    9171 > isolde stepto
    9172 
    9173 > isolde stepto
    9174 
    9175 > isolde stepto
    9176 
    9177 > isolde stepto
    9178 
    9179 > isolde stepto
    9180 
    9181 > isolde stepto
    9182 
    9183 > isolde stepto
    9184 
    9185 > isolde stepto
    9186 
    9187 > isolde stepto
    9188 
    9189 > isolde stepto
    9190 
    9191 > isolde stepto
    9192 
    9193 > isolde stepto
    9194 
    9195 > isolde stepto
    9196 
    9197 > isolde stepto
    9198 
    9199 > isolde stepto
    9200 
    9201 > isolde stepto
    9202 
    9203 > isolde stepto
    9204 
    9205 > isolde stepto
    9206 
    9207 > isolde stepto
    9208 
    9209 > isolde stepto
    9210 
    9211 > isolde stepto
    9212 
    9213 > isolde stepto
    9214 
    9215 > isolde stepto
    9216 
    9217 > isolde stepto
    9218 
    9219 > select up
    9220 
    9221 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9222 
    9223 > select up
    9224 
    9225 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9226 
    9227 > select up
    9228 
    9229 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9230 
    9231 > ui tool show Shell
    9232 
    9233 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    9234 UserWarning: IPython History requires SQLite, your history will not be saved 
    9235 warn("IPython History requires SQLite, your history will not be saved") 
    9236 
    9237 > select up
    9238 
    9239 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9240 
    9241 > select up
    9242 
    9243 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9244 
    9245 > select up
    9246 
    9247 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9248 
    9249 > select clear
    9250 
    9251 > select clear
    9252 
    9253 > isolde stepto
    9254 
    9255 > isolde stepto
    9256 
    9257 > isolde stepto
    9258 
    9259 > isolde stepto
    9260 
    9261 > isolde stepto
    9262 
    9263 > isolde stepto
    9264 
    9265 > isolde stepto
    9266 
    9267 > isolde stepto
    9268 
    9269 > isolde stepto
    9270 
    9271 > isolde stepto
    9272 
    9273 > isolde stepto
    9274 
    9275 > isolde stepto
    9276 
    9277 > isolde stepto
    9278 
    9279 > isolde stepto
    9280 
    9281 > isolde stepto
    9282 
    9283 > isolde stepto
    9284 
    9285 > isolde stepto
    9286 
    9287 > isolde stepto
    9288 
    9289 > isolde stepto
    9290 
    9291 > isolde stepto
    9292 
    9293 > isolde stepto
    9294 
    9295 > isolde stepto
    9296 
    9297 > isolde stepto
    9298 
    9299 > isolde stepto
    9300 
    9301 > isolde stepto
    9302 
    9303 > isolde stepto
    9304 
    9305 > isolde stepto
    9306 
    9307 > isolde stepto
    9308 
    9309 > isolde stepto
    9310 
    9311 > isolde stepto
    9312 
    9313 > isolde stepto
    9314 
    9315 > isolde stepto
    9316 
    9317 > isolde stepto
    9318 
    9319 > isolde stepto
    9320 
    9321 > isolde stepto
    9322 
    9323 > isolde stepto
    9324 
    9325 > isolde stepto
    9326 
    9327 > isolde stepto
    9328 
    9329 > isolde stepto
    9330 
    9331 > select up
    9332 
    9333 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9334 
    9335 > select up
    9336 
    9337 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9338 
    9339 > select clear
    9340 
    9341 > isolde stepto
    9342 
    9343 > isolde stepto
    9344 
    9345 > isolde stepto
    9346 
    9347 > isolde stepto
    9348 
    9349 > isolde stepto
    9350 
    9351 > isolde stepto
    9352 
    9353 > isolde stepto
    9354 
    9355 > isolde stepto
    9356 
    9357 > isolde stepto
    9358 
    9359 > isolde stepto
    9360 
    9361 > isolde stepto
    9362 
    9363 > select up
    9364 
    9365 503 atoms, 512 bonds, 32 residues, 1 model selected 
    9366 
    9367 > select up
    9368 
    9369 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9370 
    9371 > select down
    9372 
    9373 503 atoms, 512 bonds, 32 residues, 1 model selected 
    9374 
    9375 > select up
    9376 
    9377 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9378 
    9379 > select clear
    9380 
    9381 > isolde stepto
    9382 
    9383 > isolde stepto
    9384 
    9385 > isolde stepto
    9386 
    9387 > isolde stepto
    9388 
    9389 > isolde stepto
    9390 
    9391 > isolde stepto
    9392 
    9393 > isolde stepto
    9394 
    9395 > isolde stepto
    9396 
    9397 > isolde stepto
    9398 
    9399 > isolde stepto
    9400 
    9401 > isolde stepto
    9402 
    9403 > isolde stepto
    9404 
    9405 > isolde stepto
    9406 
    9407 > isolde stepto
    9408 
    9409 > isolde stepto
    9410 
    9411 > isolde stepto
    9412 
    9413 > isolde stepto
    9414 
    9415 > isolde stepto
    9416 
    9417 > isolde stepto
    9418 
    9419 > isolde stepto
    9420 
    9421 > isolde stepto
    9422 
    9423 > isolde stepto
    9424 
    9425 > isolde stepto
    9426 
    9427 > isolde stepto
    9428 
    9429 > isolde stepto
    9430 
    9431 > isolde stepto
    9432 
    9433 > isolde stepto
    9434 
    9435 > isolde stepto
    9436 
    9437 > select up
    9438 
    9439 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9440 
    9441 > select up
    9442 
    9443 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9444 
    9445 > select up
    9446 
    9447 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9448 
    9449 > select clear
    9450 
    9451 > isolde stepto
    9452 
    9453 > isolde stepto
    9454 
    9455 > isolde stepto
    9456 
    9457 > isolde stepto
    9458 
    9459 > isolde stepto
    9460 
    9461 > isolde stepto
    9462 
    9463 > isolde stepto
    9464 
    9465 > isolde stepto
    9466 
    9467 > isolde stepto
    9468 
    9469 > isolde stepto
    9470 
    9471 > isolde stepto
    9472 
    9473 > isolde stepto
    9474 
    9475 > isolde stepto
    9476 
    9477 > isolde stepto
    9478 
    9479 > isolde stepto
    9480 
    9481 > isolde stepto
    9482 
    9483 > isolde stepto
    9484 
    9485 > isolde stepto
    9486 
    9487 > isolde stepto
    9488 
    9489 > isolde stepto
    9490 
    9491 > isolde stepto
    9492 
    9493 > isolde stepto
    9494 
    9495 > isolde stepto
    9496 
    9497 > isolde stepto
    9498 
    9499 > isolde stepto
    9500 
    9501 > isolde stepto
    9502 
    9503 > isolde stepto
    9504 
    9505 > isolde stepto
    9506 
    9507 > isolde stepto
    9508 
    9509 > isolde stepto
    9510 
    9511 > isolde stepto
    9512 
    9513 > isolde stepto
    9514 
    9515 > isolde stepto
    9516 
    9517 > isolde stepto
    9518 
    9519 > isolde stepto
    9520 
    9521 > isolde stepto
    9522 
    9523 > isolde stepto
    9524 
    9525 > isolde stepto
    9526 
    9527 > isolde stepto
    9528 
    9529 > select up
    9530 
    9531 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9532 
    9533 > select up
    9534 
    9535 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9536 
    9537 > select up
    9538 
    9539 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9540 
    9541 > select clear
    9542 
    9543 > isolde stepto
    9544 
    9545 > isolde stepto
    9546 
    9547 > isolde stepto
    9548 
    9549 > isolde stepto
    9550 
    9551 > isolde stepto
    9552 
    9553 > select up
    9554 
    9555 63 atoms, 60 bonds, 3 residues, 1 model selected 
    9556 
    9557 > select up
    9558 
    9559 1073 atoms, 1092 bonds, 67 residues, 1 model selected 
    9560 
    9561 > select clear
    9562 
    9563 > select clear
    9564 
    9565 > isolde stepto
    9566 
    9567 > isolde stepto
    9568 
    9569 > isolde stepto
    9570 
    9571 > isolde stepto
    9572 
    9573 > isolde stepto
    9574 
    9575 > isolde stepto
    9576 
    9577 > isolde stepto
    9578 
    9579 > isolde stepto
    9580 
    9581 > isolde stepto
    9582 
    9583 > isolde stepto
    9584 
    9585 > isolde stepto
    9586 
    9587 > isolde stepto
    9588 
    9589 > isolde stepto
    9590 
    9591 > isolde stepto
    9592 
    9593 > isolde stepto
    9594 
    9595 > isolde stepto
    9596 
    9597 > isolde stepto
    9598 
    9599 > isolde stepto
    9600 
    9601 > isolde stepto
    9602 
    9603 > isolde stepto
    9604 
    9605 > isolde stepto
    9606 
    9607 > isolde stepto
    9608 
    9609 > isolde stepto
    9610 
    9611 > isolde stepto
    9612 
    9613 > isolde stepto
    9614 
    9615 > isolde stepto
    9616 
    9617 > isolde stepto
    9618 
    9619 > isolde stepto
    9620 
    9621 > isolde stepto
    9622 
    9623 > isolde stepto
    9624 
    9625 > isolde stepto
    9626 
    9627 > isolde stepto
    9628 
    9629 > isolde stepto
    9630 
    9631 > isolde stepto
    9632 
    9633 > select up
    9634 
    9635 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9636 
    9637 > select up
    9638 
    9639 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9640 
    9641 > select up
    9642 
    9643 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9644 
    9645 > select clear
    9646 
    9647 > select clear
    9648 
    9649 > isolde stepto
    9650 
    9651 > isolde stepto
    9652 
    9653 > isolde stepto
    9654 
    9655 > isolde stepto
    9656 
    9657 > isolde stepto
    9658 
    9659 > isolde stepto
    9660 
    9661 > isolde stepto
    9662 
    9663 > isolde stepto
    9664 
    9665 > isolde stepto
    9666 
    9667 > isolde stepto
    9668 
    9669 > isolde stepto
    9670 
    9671 > isolde stepto
    9672 
    9673 > isolde stepto
    9674 
    9675 > isolde stepto
    9676 
    9677 > isolde stepto
    9678 
    9679 > isolde stepto
    9680 
    9681 > isolde stepto
    9682 
    9683 > isolde stepto
    9684 
    9685 > isolde stepto
    9686 
    9687 > isolde stepto
    9688 
    9689 > isolde stepto
    9690 
    9691 > isolde stepto
    9692 
    9693 > isolde stepto
    9694 
    9695 > isolde stepto
    9696 
    9697 > isolde stepto
    9698 
    9699 > isolde stepto
    9700 
    9701 > isolde stepto
    9702 
    9703 > isolde stepto
    9704 
    9705 > isolde stepto
    9706 
    9707 > isolde stepto
    9708 
    9709 > isolde stepto
    9710 
    9711 > isolde stepto
    9712 
    9713 > isolde stepto
    9714 
    9715 > isolde stepto
    9716 
    9717 > isolde stepto
    9718 
    9719 > isolde stepto
    9720 
    9721 > isolde stepto
    9722 
    9723 > isolde stepto
    9724 
    9725 > isolde stepto
    9726 
    9727 > select up
    9728 
    9729 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9730 
    9731 > select up
    9732 
    9733 47 atoms, 46 bonds, 4 residues, 1 model selected 
    9734 
    9735 > select up
    9736 
    9737 773 atoms, 794 bonds, 41 residues, 1 model selected 
    9738 
    9739 > select clear
    9740 
    9741 > isolde stepto
    9742 
    9743 > isolde stepto
    9744 
    9745 > isolde stepto
    9746 
    9747 > isolde stepto
    9748 
    9749 > isolde stepto
    9750 
    9751 > isolde stepto
    9752 
    9753 > isolde stepto
    9754 
    9755 > isolde stepto
    9756 
    9757 > isolde stepto
    9758 
    9759 > isolde stepto
    9760 
    9761 > isolde stepto
    9762 
    9763 > isolde stepto
    9764 
    9765 > isolde stepto
    9766 
    9767 > isolde stepto
    9768 
    9769 > isolde stepto
    9770 
    9771 > isolde stepto
    9772 
    9773 > isolde stepto
    9774 
    9775 > isolde stepto
    9776 
    9777 > isolde stepto
    9778 
    9779 > isolde stepto
    9780 
    9781 > isolde stepto
    9782 
    9783 > isolde stepto
    9784 
    9785 > isolde stepto
    9786 
    9787 > isolde stepto
    9788 
    9789 > isolde stepto
    9790 
    9791 > isolde stepto
    9792 
    9793 > isolde stepto
    9794 
    9795 > isolde stepto
    9796 
    9797 > isolde stepto
    9798 
    9799 > isolde stepto
    9800 
    9801 > isolde stepto
    9802 
    9803 > isolde stepto
    9804 
    9805 > isolde stepto
    9806 
    9807 > isolde stepto
    9808 
    9809 > isolde stepto
    9810 
    9811 > isolde stepto
    9812 
    9813 > isolde stepto
    9814 
    9815 > isolde stepto
    9816 
    9817 > isolde stepto
    9818 
    9819 > isolde stepto
    9820 
    9821 > select up
    9822 
    9823 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9824 
    9825 > select up
    9826 
    9827 47 atoms, 46 bonds, 4 residues, 1 model selected 
    9828 
    9829 > select up
    9830 
    9831 773 atoms, 794 bonds, 41 residues, 1 model selected 
    9832 
    9833 > select clear
    9834 
    9835 > select clear
    9836 
    9837 > select clear
    9838 
    9839 > isolde stepto
    9840 
    9841 > isolde stepto
    9842 
    9843 > isolde stepto
    9844 
    9845 > isolde stepto
    9846 
    9847 > isolde stepto
    9848 
    9849 > isolde stepto
    9850 
    9851 > isolde stepto
    9852 
    9853 > isolde stepto
    9854 
    9855 > isolde stepto
    9856 
    9857 > isolde stepto
    9858 
    9859 > isolde stepto
    9860 
    9861 > isolde stepto
    9862 
    9863 > isolde stepto
    9864 
    9865 > isolde stepto
    9866 
    9867 > isolde stepto
    9868 
    9869 > isolde stepto
    9870 
    9871 > isolde stepto
    9872 
    9873 > isolde stepto
    9874 
    9875 > isolde stepto
    9876 
    9877 > select clear
    9878 
    9879 > isolde stepto
    9880 
    9881 > isolde stepto
    9882 
    9883 > isolde stepto
    9884 
    9885 > isolde stepto
    9886 
    9887 > isolde stepto
    9888 
    9889 > isolde stepto
    9890 
    9891 > isolde stepto
    9892 
    9893 > isolde stepto
    9894 
    9895 > isolde stepto
    9896 
    9897 > isolde stepto
    9898 
    9899 > isolde stepto
    9900 
    9901 > isolde stepto
    9902 
    9903 > isolde stepto
    9904 
    9905 > isolde stepto
    9906 
    9907 > isolde stepto
    9908 
    9909 > isolde stepto
    9910 
    9911 > isolde stepto
    9912 
    9913 > isolde stepto
    9914 
    9915 > isolde stepto
    9916 
    9917 > isolde stepto
    9918 
    9919 > select clear
    9920 
    9921 > save working.cxs
    9922 
    9923 Taking snapshot of stepper: working_2.pdb 
    9924 
    9925 > isolde stepto
    9926 
    9927 > select up
    9928 
    9929 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9930 
    9931 > select up
    9932 
    9933 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9934 
    9935 > select up
    9936 
    9937 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9938 
    9939 > select clear
    9940 
    9941 > isolde stepto
    9942 
    9943 > isolde stepto
    9944 
    9945 > isolde stepto
    9946 
    9947 > isolde stepto
    9948 
    9949 > isolde stepto
    9950 
    9951 > isolde stepto
    9952 
    9953 > isolde stepto
    9954 
    9955 > isolde stepto
    9956 
    9957 > isolde stepto
    9958 
    9959 > isolde stepto
    9960 
    9961 > isolde stepto
    9962 
    9963 > isolde stepto
    9964 
    9965 > isolde stepto
    9966 
    9967 > isolde stepto
    9968 
    9969 > isolde stepto
    9970 
    9971 > isolde stepto
    9972 
    9973 > isolde stepto
    9974 
    9975 > isolde stepto
    9976 
    9977 > isolde stepto
    9978 
    9979 > isolde stepto
    9980 
    9981 > isolde stepto
    9982 
    9983 > isolde stepto
    9984 
    9985 > isolde stepto
    9986 
    9987 > isolde stepto
    9988 
    9989 > isolde stepto
    9990 
    9991 > isolde stepto
    9992 
    9993 > isolde stepto
    9994 
    9995 > isolde stepto
    9996 
    9997 > isolde stepto
    9998 
    9999 > isolde stepto
    10000 
    10001 > isolde stepto
    10002 
    10003 > isolde stepto
    10004 
    10005 > isolde stepto
    10006 
    10007 > isolde stepto
    10008 
    10009 > isolde stepto
    10010 
    10011 > isolde stepto
    10012 
    10013 > isolde stepto
    10014 
    10015 > isolde stepto
    10016 
    10017 > isolde stepto
    10018 
    10019 > select clear
    10020 
    10021 > select clear
    10022 
    10023 > isolde stepto /aa
    10024 
    10025 Multiple residues selected! Going to the first... 
    10026 
    10027 > select up
    10028 
    10029 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10030 
    10031 > select up
    10032 
    10033 86 atoms, 87 bonds, 4 residues, 1 model selected 
    10034 
    10035 > select up
    10036 
    10037 1062 atoms, 1082 bonds, 60 residues, 1 model selected 
    10038 
    10039 > select clear
    10040 
    10041 > isolde stepto
    10042 
    10043 > select clear
    10044 
    10045 > isolde stepto
    10046 
    10047 > isolde stepto
    10048 
    10049 > isolde stepto
    10050 
    10051 > isolde stepto
    10052 
    10053 > isolde stepto
    10054 
    10055 > isolde stepto
    10056 
    10057 > isolde stepto
    10058 
    10059 > isolde stepto
    10060 
    10061 > isolde stepto
    10062 
    10063 > isolde stepto
    10064 
    10065 > isolde stepto
    10066 
    10067 > isolde stepto
    10068 
    10069 > select clear
    10070 
    10071 > isolde stepto
    10072 
    10073 > isolde stepto
    10074 
    10075 > isolde stepto
    10076 
    10077 > isolde stepto
    10078 
    10079 > isolde stepto
    10080 
    10081 > isolde stepto
    10082 
    10083 > isolde stepto
    10084 
    10085 > isolde stepto
    10086 
    10087 > isolde stepto
    10088 
    10089 > isolde stepto
    10090 
    10091 > isolde stepto
    10092 
    10093 > isolde stepto
    10094 
    10095 > isolde stepto
    10096 
    10097 > isolde stepto
    10098 
    10099 > isolde stepto
    10100 
    10101 > isolde stepto
    10102 
    10103 > isolde stepto
    10104 
    10105 > isolde stepto
    10106 
    10107 > isolde stepto
    10108 
    10109 > isolde stepto
    10110 
    10111 > isolde stepto
    10112 
    10113 > isolde stepto
    10114 
    10115 > isolde stepto
    10116 
    10117 > isolde stepto
    10118 
    10119 > isolde stepto
    10120 
    10121 > isolde stepto
    10122 
    10123 > isolde stepto
    10124 
    10125 > isolde stepto
    10126 
    10127 > isolde stepto
    10128 
    10129 > isolde stepto
    10130 
    10131 > isolde stepto
    10132 
    10133 > isolde stepto
    10134 
    10135 > isolde stepto
    10136 
    10137 > isolde stepto
    10138 
    10139 > isolde stepto
    10140 
    10141 > isolde stepto
    10142 
    10143 > isolde stepto
    10144 
    10145 > isolde stepto
    10146 
    10147 > isolde stepto
    10148 
    10149 > isolde stepto
    10150 
    10151 > isolde stepto
    10152 
    10153 > isolde stepto
    10154 
    10155 > isolde stepto
    10156 
    10157 > isolde stepto
    10158 
    10159 > isolde stepto
    10160 
    10161 > isolde stepto
    10162 
    10163 > select up
    10164 
    10165 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10166 
    10167 > select up
    10168 
    10169 84 atoms, 86 bonds, 4 residues, 1 model selected 
    10170 
    10171 > select up
    10172 
    10173 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10174 
    10175 > select up
    10176 
    10177 96659 atoms, 98767 bonds, 5198 residues, 1 model selected 
    10178 
    10179 > select down
    10180 
    10181 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10182 
    10183 > select clear
    10184 
    10185 > select clear
    10186 
    10187 > isolde stepto
    10188 
    10189 > isolde stepto
    10190 
    10191 > isolde stepto
    10192 
    10193 > isolde stepto
    10194 
    10195 > isolde stepto
    10196 
    10197 > isolde stepto
    10198 
    10199 > isolde stepto
    10200 
    10201 > isolde stepto
    10202 
    10203 > isolde stepto
    10204 
    10205 > isolde stepto
    10206 
    10207 > isolde stepto
    10208 
    10209 > isolde stepto
    10210 
    10211 > isolde stepto
    10212 
    10213 > isolde stepto
    10214 
    10215 > isolde stepto
    10216 
    10217 > isolde stepto
    10218 
    10219 > isolde stepto
    10220 
    10221 > isolde stepto
    10222 
    10223 > isolde stepto
    10224 
    10225 > isolde stepto
    10226 
    10227 > isolde stepto
    10228 
    10229 > isolde stepto
    10230 
    10231 > isolde stepto
    10232 
    10233 > isolde stepto
    10234 
    10235 > isolde stepto
    10236 
    10237 > select clear
    10238 
    10239 > isolde stepto
    10240 
    10241 > isolde stepto
    10242 
    10243 > isolde stepto
    10244 
    10245 > isolde stepto
    10246 
    10247 > isolde stepto
    10248 
    10249 > isolde stepto
    10250 
    10251 > select clear
    10252 
    10253 > isolde stepto
    10254 
    10255 > isolde stepto
    10256 
    10257 > isolde stepto
    10258 
    10259 > isolde stepto
    10260 
    10261 > isolde stepto
    10262 
    10263 > isolde stepto
    10264 
    10265 > isolde stepto
    10266 
    10267 > isolde stepto
    10268 
    10269 > isolde stepto
    10270 
    10271 > isolde stepto
    10272 
    10273 > isolde stepto
    10274 
    10275 > isolde stepto
    10276 
    10277 > isolde stepto
    10278 
    10279 > isolde stepto
    10280 
    10281 > isolde stepto
    10282 
    10283 > isolde stepto
    10284 
    10285 > isolde stepto
    10286 
    10287 > isolde stepto
    10288 
    10289 > isolde stepto
    10290 
    10291 > isolde stepto
    10292 
    10293 > isolde stepto
    10294 
    10295 > isolde stepto
    10296 
    10297 > isolde stepto
    10298 
    10299 > isolde stepto
    10300 
    10301 > select clear
    10302 
    10303 > isolde stepto
    10304 
    10305 > isolde stepto
    10306 
    10307 > isolde stepto
    10308 
    10309 > isolde stepto
    10310 
    10311 > isolde stepto
    10312 
    10313 > view /ab:2
    10314 
    10315 > select clear
    10316 
    10317 > isolde stepto
    10318 
    10319 > view /ab:2
    10320 
    10321 > select clear
    10322 
    10323 > select clear
    10324 
    10325 > isolde stepto
    10326 
    10327 > select up
    10328 
    10329 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10330 
    10331 > select up
    10332 
    10333 84 atoms, 86 bonds, 4 residues, 1 model selected 
    10334 
    10335 > select up
    10336 
    10337 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10338 
    10339 > select clear
    10340 
    10341 > isolde stepto
    10342 
    10343 > isolde stepto
    10344 
    10345 > isolde stepto
    10346 
    10347 > isolde stepto
    10348 
    10349 > select clear
    10350 
    10351 > isolde stepto
    10352 
    10353 > isolde stepto
    10354 
    10355 > isolde stepto
    10356 
    10357 > isolde stepto
    10358 
    10359 > select clear
    10360 
    10361 > isolde stepto
    10362 
    10363 > isolde stepto
    10364 
    10365 > isolde stepto
    10366 
    10367 > isolde stepto
    10368 
    10369 > isolde stepto
    10370 
    10371 > isolde stepto
    10372 
    10373 > isolde stepto
    10374 
    10375 > isolde stepto
    10376 
    10377 > isolde stepto
    10378 
    10379 > isolde stepto
    10380 
    10381 > isolde stepto
    10382 
    10383 > isolde stepto
    10384 
    10385 > isolde stepto
    10386 
    10387 > isolde stepto
    10388 
    10389 > isolde stepto
    10390 
    10391 > isolde stepto
    10392 
    10393 > isolde stepto
    10394 
    10395 > isolde stepto
    10396 
    10397 > isolde stepto
    10398 
    10399 > select clear
    10400 
    10401 > isolde stepto
    10402 
    10403 > isolde stepto
    10404 
    10405 > isolde stepto
    10406 
    10407 > isolde stepto
    10408 
    10409 > isolde stepto
    10410 
    10411 > isolde stepto
    10412 
    10413 > isolde stepto
    10414 
    10415 > isolde stepto
    10416 
    10417 > isolde stepto
    10418 
    10419 > isolde stepto
    10420 
    10421 > isolde stepto
    10422 
    10423 > isolde stepto
    10424 
    10425 > isolde stepto
    10426 
    10427 > isolde stepto
    10428 
    10429 > isolde stepto
    10430 
    10431 > isolde stepto
    10432 
    10433 > isolde stepto
    10434 
    10435 > isolde stepto
    10436 
    10437 > isolde stepto
    10438 
    10439 > isolde stepto
    10440 
    10441 > isolde stepto
    10442 
    10443 > isolde stepto
    10444 
    10445 > isolde stepto
    10446 
    10447 > isolde stepto
    10448 
    10449 > select clear
    10450 
    10451 > delete sel
    10452 
    10453 > select clear
    10454 
    10455 > isolde stepto
    10456 
    10457 > isolde stepto
    10458 
    10459 > isolde stepto
    10460 
    10461 > select up
    10462 
    10463 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10464 
    10465 > select up
    10466 
    10467 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10468 
    10469 > save working.cxs
    10470 
    10471 Taking snapshot of stepper: working_2.pdb 
    10472 
    10473 > select clear
    10474 
    10475 > select up
    10476 
    10477 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10478 
    10479 > select up
    10480 
    10481 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10482 
    10483 > select up
    10484 
    10485 96615 atoms, 98722 bonds, 5194 residues, 1 model selected 
    10486 
    10487 > select down
    10488 
    10489 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10490 
    10491 > select clear
    10492 
    10493 > select clear
    10494 
    10495 > save working.cxs
    10496 
    10497 Taking snapshot of stepper: working_2.pdb 
    10498 
    10499 > select up
    10500 
    10501 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10502 
    10503 > select up
    10504 
    10505 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10506 
    10507 > select clear
    10508 
    10509 > isolde stepto
    10510 
    10511 > isolde stepto
    10512 
    10513 > isolde stepto
    10514 
    10515 > isolde stepto
    10516 
    10517 > isolde stepto
    10518 
    10519 > isolde stepto
    10520 
    10521 > isolde stepto
    10522 
    10523 > isolde stepto
    10524 
    10525 > isolde stepto
    10526 
    10527 > isolde stepto
    10528 
    10529 > isolde stepto
    10530 
    10531 > isolde add ligand CDL
    10532 
    10533 place_ligand() was called with use_md_template=True, but no suitable template
    10534 was found. This command has been ignored. 
    10535 
    10536 > select up
    10537 
    10538 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10539 
    10540 > isolde ignore ~sel
    10541 
    10542 ISOLDE: currently ignoring 5194 residues in model 8.2 
    10543 
    10544 > select up
    10545 
    10546 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10547 
    10548 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10549 bonded heavy atom. 
    10550 
    10551 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10552 bonded heavy atom. 
    10553 
    10554 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10555 bonded heavy atom. 
    10556 
    10557 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10558 bonded heavy atom. 
    10559 
    10560 > isolde ~ignore
    10561 
    10562 > select up
    10563 
    10564 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10565 
    10566 > select up
    10567 
    10568 140 atoms, 148 bonds, 1 residue, 1 model selected 
    10569 
    10570 > isolde ignore sel
    10571 
    10572 ISOLDE: currently ignoring 1 residues in model 8.2 
    10573 
    10574 > select up
    10575 
    10576 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10577 
    10578 > select down
    10579 
    10580 2 atoms, 1 bond, 1 residue, 1 model selected 
    10581 
    10582 > isolde ~ignore
    10583 
    10584 > select up
    10585 
    10586 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10587 
    10588 > isolde ignore sel
    10589 
    10590 ISOLDE: currently ignoring 1 residues in model 8.2 
    10591 
    10592 > isolde ~ignore
    10593 
    10594 Chain ak, residue 67 specifies more than one residue! The simulation can still
    10595 run, but this will probably cause problems later if not rectified by
    10596 renumbering. 
    10597 
    10598 > select clear
    10599 
    10600 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10601 bonded heavy atom. 
    10602 
    10603 > select up
    10604 
    10605 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10606 
    10607 > clipper isolate sel contextDistance 0 maskRadius 3
    10608 
    10609 > select clear
    10610 
    10611 > ~cartoon
    10612 
    10613 > hide HC
    10614 
    10615 > hide #!8.1.1.2 models
    10616 
    10617 > show #!8.1.1.2 models
    10618 
    10619 > select clear
    10620 
    10621 > save resolved_cdl.jpg
    10622 
    10623 > cartoon
    10624 
    10625 > select /ae:CDL
    10626 
    10627 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10628 
    10629 > select /ae:11-30@CA
    10630 
    10631 20 atoms, 20 residues, 1 model selected 
    10632 
    10633 > select /af:11-30@CA
    10634 
    10635 20 atoms, 20 residues, 1 model selected 
    10636 
    10637 > save working_cdl.cxs
    10638 
    10639 Taking snapshot of stepper: working_2.pdb 
    10640 
    10641 > select up
    10642 
    10643 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10644 
    10645 > isolde ignore ~sel
    10646 
    10647 ISOLDE: currently ignoring 5195 residues in model 8.2 
    10648 
    10649 > select up
    10650 
    10651 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10652 
    10653 > isolde ignore sel
    10654 
    10655 ISOLDE: currently ignoring 5196 residues in model 8.2 
    10656 Traceback (most recent call last): 
    10657 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10658 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    10659 self.start_sim() 
    10660 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10661 packages/chimerax/isolde/isolde.py", line 2727, in start_sim 
    10662 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    10663 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10664 packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__ 
    10665 self._prepare_mdff_managers() 
    10666 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10667 packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    10668 _prepare_mdff_managers 
    10669 focus = False) 
    10670 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10671 packages/chimerax/clipper/symmetry.py", line 982, in
    10672 isolate_and_cover_selection 
    10673 extra_padding=extra_padding) 
    10674 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10675 packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms 
    10676 zm.set_symmetry_map(atoms, transforms, transform_indices) 
    10677 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10678 packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map 
    10679 self.structure = self._unique_structure(atoms) 
    10680 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10681 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    10682 _unique_structure 
    10683 raise TypeError('All atoms for zone mask must be from a single model!') 
    10684 TypeError: All atoms for zone mask must be from a single model! 
    10685  
    10686 TypeError: All atoms for zone mask must be from a single model! 
    10687  
    10688 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10689 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    10690 _unique_structure 
    10691 raise TypeError('All atoms for zone mask must be from a single model!') 
    10692  
    10693 See log for complete Python traceback. 
    10694  
    10695 
    10696 > isolde ~ignore
    10697 
    10698 > color bychain
    10699 
    10700 > color byhetero
    10701 
    10702 > select up
    10703 
    10704 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10705 
    10706 > isolde ignore sel
    10707 
    10708 ISOLDE: currently ignoring 1 residues in model 8.2 
    10709 
    10710 > select up
    10711 
    10712 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10713 
    10714 > isolde ~ignore
    10715 
    10716 > isolde ignore ~sel
    10717 
    10718 ISOLDE: currently ignoring 5195 residues in model 8.2 
    10719 
    10720 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10721 bonded heavy atom. 
    10722 
    10723 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10724 bonded heavy atom. 
    10725 
    10726 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10727 bonded heavy atom. 
    10728 
    10729 > select up
    10730 
    10731 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10732 
    10733 > isolde ~ignore
    10734 
    10735 > select clear
    10736 
    10737 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10738 bonded heavy atom. 
    10739 
    10740 > select /ag:11-30@CA
    10741 
    10742 20 atoms, 20 residues, 1 model selected 
    10743 
    10744 > select up
    10745 
    10746 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10747 
    10748 > isolde ignore ~sel
    10749 
    10750 ISOLDE: currently ignoring 5196 residues in model 8.2 
    10751 
    10752 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10753 bonded heavy atom. 
    10754 
    10755 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10756 bonded heavy atom. 
    10757 
    10758 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10759 bonded heavy atom. 
    10760 
    10761 > select up
    10762 
    10763 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10764 
    10765 > isolde ~ignore
    10766 
    10767 > select up
    10768 
    10769 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10770 
    10771 > isolde ignore sel
    10772 
    10773 ISOLDE: currently ignoring 1 residues in model 8.2 
    10774 
    10775 > select clear
    10776 
    10777 > isolde ~ignore
    10778 
    10779 > select clear
    10780 
    10781 > save working_cdl.cxs
    10782 
    10783 Taking snapshot of stepper: working_2.pdb 
    10784 
    10785 > select /ah:11-30@CA
    10786 
    10787 20 atoms, 20 residues, 1 model selected 
    10788 
    10789 > select /AH
    10790 
    10791 1018 atoms, 1040 bonds, 51 residues, 1 model selected 
    10792 
    10793 > cartoon
    10794 
    10795 > select :CDL
    10796 
    10797 768 atoms, 765 bonds, 3 residues, 1 model selected 
    10798 
    10799 > select /ae, af, ag
    10800 
    10801 4005 atoms, 4062 bonds, 186 residues, 1 model selected 
    10802 
    10803 > select /ae, af, ag,ah
    10804 
    10805 5084 atoms, 5161 bonds, 247 residues, 1 model selected 
    10806 
    10807 > select clear
    10808 
    10809 > select /ah:11-30@CA
    10810 
    10811 20 atoms, 20 residues, 1 model selected 
    10812 
    10813 > select up
    10814 
    10815 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10816 
    10817 > delete sel
    10818 
    10819 > select /ad
    10820 
    10821 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10822 
    10823 > select /ad,ae
    10824 
    10825 2414 atoms, 2453 bonds, 123 residues, 1 model selected 
    10826 
    10827 > select /ad:11-30@CA
    10828 
    10829 20 atoms, 20 residues, 1 model selected 
    10830 
    10831 > select up
    10832 
    10833 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10834 
    10835 > delete sel
    10836 
    10837 > select clear
    10838 
    10839 > isolde stepto
    10840 
    10841 > select clear
    10842 
    10843 > select up
    10844 
    10845 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10846 
    10847 > select up
    10848 
    10849 84 atoms, 86 bonds, 4 residues, 1 model selected 
    10850 
    10851 > select up
    10852 
    10853 184 atoms, 185 bonds, 5 residues, 1 model selected 
    10854 
    10855 > select up
    10856 
    10857 2037 atoms, 2081 bonds, 102 residues, 1 model selected 
    10858 
    10859 > select down
    10860 
    10861 184 atoms, 185 bonds, 5 residues, 1 model selected 
    10862 
    10863 > select up
    10864 
    10865 2037 atoms, 2081 bonds, 102 residues, 1 model selected 
    10866 
    10867 > select down
    10868 
    10869 184 atoms, 185 bonds, 5 residues, 1 model selected 
    10870 
    10871 > select up
    10872 
    10873 2037 atoms, 2081 bonds, 102 residues, 1 model selected 
    10874 
    10875 > select clear
    10876 
    10877 > isolde stepto
    10878 
    10879 > isolde stepto
    10880 
    10881 > isolde stepto
    10882 
    10883 > isolde stepto
    10884 
    10885 > isolde stepto
    10886 
    10887 > isolde stepto
    10888 
    10889 > isolde stepto
    10890 
    10891 > isolde stepto
    10892 
    10893 > isolde stepto
    10894 
    10895 > isolde stepto
    10896 
    10897 > isolde stepto
    10898 
    10899 > isolde stepto
    10900 
    10901 > select clear
    10902 
    10903 > isolde stepto
    10904 
    10905 > isolde stepto
    10906 
    10907 > isolde stepto
    10908 
    10909 > isolde stepto
    10910 
    10911 > isolde stepto
    10912 
    10913 > isolde stepto
    10914 
    10915 > isolde stepto
    10916 
    10917 > isolde stepto
    10918 
    10919 > isolde stepto
    10920 
    10921 > isolde stepto
    10922 
    10923 > isolde stepto
    10924 
    10925 > isolde stepto
    10926 
    10927 > isolde stepto
    10928 
    10929 > isolde stepto
    10930 
    10931 > isolde stepto
    10932 
    10933 > isolde stepto
    10934 
    10935 > isolde stepto
    10936 
    10937 > isolde stepto
    10938 
    10939 > isolde stepto
    10940 
    10941 > isolde stepto
    10942 
    10943 > isolde stepto
    10944 
    10945 > isolde stepto
    10946 
    10947 > isolde stepto
    10948 
    10949 > isolde stepto
    10950 
    10951 > isolde stepto
    10952 
    10953 > isolde stepto
    10954 
    10955 > isolde stepto
    10956 
    10957 > isolde stepto
    10958 
    10959 > isolde stepto
    10960 
    10961 > isolde stepto
    10962 
    10963 > select clear
    10964 
    10965 > isolde stepto
    10966 
    10967 > isolde stepto
    10968 
    10969 > isolde stepto
    10970 
    10971 > isolde stepto
    10972 
    10973 > isolde stepto
    10974 
    10975 > isolde stepto
    10976 
    10977 > isolde stepto
    10978 
    10979 > select up
    10980 
    10981 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10982 
    10983 > select up
    10984 
    10985 1018 atoms, 1040 bonds, 51 residues, 1 model selected 
    10986 
    10987 > select clear
    10988 
    10989 > select clear
    10990 
    10991 > select clear
    10992 
    10993 > isolde stepto
    10994 
    10995 > isolde stepto
    10996 
    10997 > isolde stepto
    10998 
    10999 > isolde stepto
    11000 
    11001 > isolde stepto
    11002 
    11003 > isolde stepto
    11004 
    11005 > isolde stepto
    11006 
    11007 > isolde stepto
    11008 
    11009 > isolde stepto
    11010 
    11011 > isolde stepto
    11012 
    11013 > isolde stepto
    11014 
    11015 > isolde stepto
    11016 
    11017 > isolde stepto
    11018 
    11019 > isolde stepto
    11020 
    11021 > isolde stepto
    11022 
    11023 > isolde stepto
    11024 
    11025 > isolde stepto
    11026 
    11027 > isolde stepto
    11028 
    11029 > isolde stepto
    11030 
    11031 > isolde stepto
    11032 
    11033 > isolde stepto
    11034 
    11035 > isolde stepto
    11036 
    11037 > isolde stepto
    11038 
    11039 > isolde stepto
    11040 
    11041 > isolde stepto
    11042 
    11043 > isolde stepto
    11044 
    11045 > isolde stepto
    11046 
    11047 > isolde stepto
    11048 
    11049 > isolde stepto
    11050 
    11051 > isolde stepto
    11052 
    11053 > isolde stepto
    11054 
    11055 > isolde stepto
    11056 
    11057 > isolde stepto
    11058 
    11059 > isolde stepto
    11060 
    11061 > isolde stepto
    11062 
    11063 > isolde stepto
    11064 
    11065 > isolde stepto
    11066 
    11067 > isolde stepto
    11068 
    11069 > isolde stepto
    11070 
    11071 > isolde stepto
    11072 
    11073 > isolde stepto
    11074 
    11075 > isolde stepto
    11076 
    11077 > isolde stepto
    11078 
    11079 > isolde stepto
    11080 
    11081 > isolde stepto
    11082 
    11083 > isolde stepto
    11084 
    11085 > isolde stepto
    11086 
    11087 > isolde stepto
    11088 
    11089 > isolde stepto
    11090 
    11091 > select up
    11092 
    11093 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11094 
    11095 > select up
    11096 
    11097 1004 atoms, 1025 bonds, 50 residues, 1 model selected 
    11098 
    11099 > select clear
    11100 
    11101 > isolde stepto
    11102 
    11103 > isolde stepto
    11104 
    11105 > isolde stepto
    11106 
    11107 > isolde stepto
    11108 
    11109 > isolde stepto
    11110 
    11111 > isolde stepto
    11112 
    11113 > isolde stepto
    11114 
    11115 > isolde stepto
    11116 
    11117 > isolde stepto
    11118 
    11119 > isolde stepto
    11120 
    11121 > isolde stepto
    11122 
    11123 > isolde stepto
    11124 
    11125 > isolde stepto
    11126 
    11127 > isolde stepto
    11128 
    11129 > isolde stepto
    11130 
    11131 > isolde stepto
    11132 
    11133 > isolde stepto
    11134 
    11135 > isolde stepto
    11136 
    11137 > isolde stepto
    11138 
    11139 > isolde stepto
    11140 
    11141 > isolde stepto
    11142 
    11143 > isolde stepto
    11144 
    11145 > isolde stepto
    11146 
    11147 > isolde stepto
    11148 
    11149 > isolde stepto
    11150 
    11151 > isolde stepto
    11152 
    11153 > isolde stepto
    11154 
    11155 > isolde stepto
    11156 
    11157 > isolde stepto
    11158 
    11159 > isolde stepto
    11160 
    11161 > isolde stepto
    11162 
    11163 > isolde stepto
    11164 
    11165 > isolde stepto
    11166 
    11167 > isolde stepto
    11168 
    11169 > isolde stepto
    11170 
    11171 > isolde stepto
    11172 
    11173 > isolde stepto
    11174 
    11175 > isolde stepto
    11176 
    11177 > isolde stepto
    11178 
    11179 > isolde stepto
    11180 
    11181 > isolde stepto
    11182 
    11183 > isolde stepto
    11184 
    11185 > select clear
    11186 
    11187 > isolde stepto
    11188 
    11189 > isolde stepto
    11190 
    11191 > isolde stepto
    11192 
    11193 > isolde stepto
    11194 
    11195 > isolde stepto
    11196 
    11197 > select clear
    11198 
    11199 > isolde stepto
    11200 
    11201 > select up
    11202 
    11203 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11204 
    11205 > select up
    11206 
    11207 1004 atoms, 1025 bonds, 50 residues, 1 model selected 
    11208 
    11209 > select clear
    11210 
    11211 > usage isolde jupm
    11212 
    11213 Subcommands are:
    11214 
    11215   * isolde add ligand
    11216   * isolde add water
    11217   * isolde adjust distances
    11218   * isolde adjust torsions
    11219   * isolde cisflip
    11220   * isolde demo
    11221   * isolde ignore
    11222   * isolde ~ignore
    11223   * isolde jumpto
    11224   * isolde pepflip
    11225   * isolde release distances
    11226   * isolde release torsions
    11227   * isolde remote rest info
    11228   * isolde remote rest start
    11229   * isolde remote rest stop
    11230   * isolde remote xmlrpc
    11231   * isolde replace ligand
    11232   * isolde report
    11233   * isolde reset forcefield
    11234   * isolde restrain distances
    11235   * isolde restrain ligands
    11236   * isolde restrain single distance
    11237   * isolde restrain torsions
    11238   * isolde set
    11239   * isolde sim
    11240   * isolde start
    11241   * isolde stepto
    11242   * isolde tutorial
    11243 
    11244  
    11245 
    11246 > usage isolde jump
    11247 
    11248 isolde jumpto [direction] 
    11249 — Jump the view to the first residue of the next chain or the last residue of
    11250 the previous chain. 
    11251 direction: one of next or prev 
    11252 
    11253 > isolde jumpto prev
    11254 
    11255 > isolde jumpto prev
    11256 
    11257 > isolde jumpto prev
    11258 
    11259 > isolde jumpto prev
    11260 
    11261 > save working.cxs
    11262 
    11263 Taking snapshot of stepper: working_2.pdb 
    11264 Restoring stepper: working_2.pdb 
    11265 opened ChimeraX session 
    11266 
    11267 > usage volume mask
    11268 
    11269 volume mask volumes surfaces a surfaces specifier [pad a number] [extend an
    11270 integer] [fullMap true or false] [slab slab] [invertMask true or false] [axis
    11271 an axis vector] [sandwich true or false] [fillOverlap true or false] [modelId
    11272 modelId] 
    11273 — Mask a map to a surface 
    11274 slab: a number or some numbers 
    11275 modelId: a model id 
    11276 
    11277 > usage volume zone
    11278 
    11279 volume zone volumes nearAtoms an atoms specifier [range a number]
    11280 [bondPointSpacing a number] [minimalBounds true or false] [newMap true or
    11281 false] [invert true or false] [subregion map region] [step map step] [modelId
    11282 modelId] 
    11283 — Zero map values beyond a distance range from atoms 
    11284 modelId: a model id 
    11285 
    11286 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    11287 
    11288 > close #1
    11289 
    11290 > select #1
    11291 
    11292 Nothing selected 
    11293 
    11294 > select #8
    11295 
    11296 97383 atoms, 99487 bonds, 14 pseudobonds, 5197 residues, 21 models selected 
    11297 
    11298 > select clear
    11299 
    11300 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    11301 
    11302 > usage volume subtr
    11303 
    11304 volume subtract volumes [onGrid a density maps specifier] [boundingGrid true
    11305 or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3
    11306 floats] [valueType numeric value type] [hideMaps true or false] [subregion map
    11307 region] [step map step] [modelId modelId] [inPlace true or false]
    11308 [scaleFactors scaleFactors] [minRms true or false] 
    11309 — Subtract maps pointwise 
    11310 modelId: a model id 
    11311 scaleFactors: some numbers 
    11312 
    11313 > volume subtract #8.1.1.1 #1 inPlace false
    11314 
    11315 > close #1
    11316 
    11317 > volume #2 level 0.03352
    11318 
    11319 > volume #2 level 0.03748
    11320 
    11321 > select :CDL
    11322 
    11323 768 atoms, 765 bonds, 3 residues, 1 model selected 
    11324 
    11325 > select /C1
    11326 
    11327 1472 atoms, 1487 bonds, 92 residues, 1 model selected 
    11328 
    11329 > select clear
    11330 
    11331 > delete sel
    11332 
    11333 > select up
    11334 
    11335 12 atoms, 11 bonds, 1 residue, 1 model selected 
    11336 
    11337 > select up
    11338 
    11339 125 atoms, 128 bonds, 9 residues, 1 model selected 
    11340 
    11341 > hide #!2 models
    11342 
    11343 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11344 bonded heavy atom. 
    11345 
    11346 > show #!2 models
    11347 
    11348 > select clear
    11349 
    11350 > hide #!2 models
    11351 
    11352 > show #!2 models
    11353 
    11354 > hide #!2 models
    11355 
    11356 > ui tool show "Build Structure"
    11357 
    11358 > build start peptide "custom built" AAAAAAAAAAAAAA -139.0,135.0 -139.0,135.0
    11359 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    11360 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    11361 > -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    11362 
    11363 Chain information for custom built #1 
    11364 --- 
    11365 Chain | Description 
    11366 A | No description available 
    11367  
    11368 
    11369 > select #1
    11370 
    11371 71 atoms, 70 bonds, 14 residues, 1 model selected 
    11372 
    11373 > ui mousemode right "translate selected models"
    11374 
    11375 > ui mousemode right "rotate selected models"
    11376 
    11377 > ui mousemode right "translate selected models"
    11378 
    11379 > delete /C1:1-14
    11380 
    11381 > addh #1
    11382 
    11383 Summary of feedback from adding hydrogens to custom built #1 
    11384 --- 
    11385 notes | No usable SEQRES records for custom built (#1) chain A; guessing
    11386 termini instead 
    11387 Chain-initial residues that are actual N termini: custom built #1/A ALA 1 
    11388 Chain-initial residues that are not actual N termini: 
    11389 Chain-final residues that are actual C termini: custom built #1/A ALA 14 
    11390 Chain-final residues that are not actual C termini: 
    11391 0 hydrogen bonds 
    11392 72 hydrogens added 
    11393  
    11394 
    11395 > hide #1 models
    11396 
    11397 > select /C1:1-14
    11398 
    11399 143 atoms, 142 bonds, 14 residues, 1 model selected 
    11400 
    11401 > select /C1:1-14
    11402 
    11403 143 atoms, 142 bonds, 14 residues, 1 model selected 
    11404 
    11405 > swapaa mousemode sel PRO
    11406 
    11407 > select clear
    11408 
    11409 > swapaa mousemode sel PRO
    11410 
    11411 > swapaa mousemode sel GLN
    11412 
    11413 > swapaa mousemode sel THR
    11414 
    11415 > swapaa mousemode sel GLY
    11416 
    11417 > open
    11418 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1a_24A.mrc
    11419 
    11420 Opened class1a_24A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    11421 0.0212, step 2, values float32 
    11422 
    11423 > ui tool show "Volume Viewer"
    11424 
    11425 > volume #3 step 1
    11426 
    11427 > volume #3 level 0.04119
    11428 
    11429 > volume #3 level 0.03163
    11430 
    11431 > open
    11432 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class2a_26A.mrc
    11433 
    11434 Opened class2a_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    11435 0.0249, step 2, values float32 
    11436 
    11437 > volume #4 step 1
    11438 
    11439 > volume #4 level 0.05455
    11440 
    11441 > fitmap #4 inMap #8.1.1.1
    11442 
    11443 Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points 
    11444 correlation = 0.0582, correlation about mean = 0.003368, overlap = 2.152 
    11445 steps = 964, shift = 6.3, angle = 5.34 degrees 
    11446  
    11447 Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
    11448 coordinates: 
    11449 Matrix rotation and translation 
    11450 0.99577666 -0.02365016 -0.08871027 25.10161578 
    11451 0.02499610 0.99958822 0.01409207 -14.07791580 
    11452 0.08834046 -0.01624996 0.99595778 -13.06451755 
    11453 Axis -0.16303956 -0.95136249 0.26139533 
    11454 Axis point 178.35759174 0.00000000 285.28764281 
    11455 Rotation angle (degrees) 5.33916146 
    11456 Shift along axis 5.88564083 
    11457  
    11458 
    11459 > fitmap #4 inMap #8.1.1.1
    11460 
    11461 Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points 
    11462 correlation = 0.1152, correlation about mean = 0.06419, overlap = 9.627 
    11463 steps = 672, shift = 6.89, angle = 21.3 degrees 
    11464  
    11465 Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
    11466 coordinates: 
    11467 Matrix rotation and translation 
    11468 0.92701975 -0.37501178 0.00074524 89.89128138 
    11469 0.37500543 0.92701261 0.00430577 -61.35976247 
    11470 -0.00230557 -0.00371206 0.99999045 1.56396515 
    11471 Axis -0.01068950 0.00406739 0.99993459 
    11472 Axis point 202.60869093 200.28337525 0.00000000 
    11473 Rotation angle (degrees) 22.02636092 
    11474 Shift along axis 0.35339585 
    11475  
    11476 
    11477 > select /C1:1-14
    11478 
    11479 159 atoms, 160 bonds, 14 residues, 1 model selected 
    11480 
    11481 > select /C1
    11482 
    11483 1784 atoms, 1805 bonds, 117 residues, 1 model selected 
    11484 
    11485 > volume #4 level 0.04206
    11486 
    11487 > swapaa mousemode sel GLN
    11488 
    11489 > select up
    11490 
    11491 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11492 
    11493 > select up
    11494 
    11495 166 atoms, 167 bonds, 14 residues, 1 model selected 
    11496 
    11497 > swapaa mousemode sel ASSP
    11498 
    11499 Missing or invalid "restype" argument: Should be one of 'ALA', 'ARG', 'ASN',
    11500 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE',
    11501 'PRO', 'SER', 'THR', 'TRP', 'TYR', or 'VAL' 
    11502 
    11503 > swapaa mousemode sel ASP
    11504 
    11505 > swapaa mousemode sel ARG
    11506 
    11507 > swapaa mousemode sel GLY
    11508 
    11509 > swapaa mousemode sel VAL
    11510 
    11511 > swapaa mousemode sel PRO
    11512 
    11513 > select up
    11514 
    11515 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11516 
    11517 > select up
    11518 
    11519 190 atoms, 193 bonds, 14 residues, 1 model selected 
    11520 
    11521 > select clear
    11522 
    11523 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11524 bonded heavy atom. 
    11525 
    11526 Unable to flip peptide bond after 50 rounds. Giving up. 
    11527 
    11528 > select /C1:1-14
    11529 
    11530 190 atoms, 193 bonds, 14 residues, 1 model selected 
    11531 
    11532 > select clear
    11533 
    11534 > save working.cxs
    11535 
    11536 Taking snapshot of stepper: working_2.pdb 
    11537 
    11538 > select /C1
    11539 
    11540 1815 atoms, 1838 bonds, 117 residues, 1 model selected 
    11541 
    11542 > select clear
    11543 
    11544 > select /ak
    11545 
    11546 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    11547 
    11548 > isolde stepto /c
    11549 
    11550 Selection contains no residues! 
    11551 
    11552 > isolde stepto /ac
    11553 
    11554 Multiple residues selected! Going to the first... 
    11555 
    11556 > select up
    11557 
    11558 17 atoms, 17 bonds, 1 residue, 1 model selected 
    11559 
    11560 > select up
    11561 
    11562 84 atoms, 86 bonds, 4 residues, 1 model selected 
    11563 
    11564 > select up
    11565 
    11566 1035 atoms, 1054 bonds, 57 residues, 1 model selected 
    11567 
    11568 > select clear
    11569 
    11570 > isolde stepto
    11571 
    11572 > isolde stepto
    11573 
    11574 > isolde stepto
    11575 
    11576 > isolde stepto
    11577 
    11578 > isolde stepto
    11579 
    11580 > isolde stepto
    11581 
    11582 > isolde stepto
    11583 
    11584 > isolde stepto
    11585 
    11586 > isolde stepto
    11587 
    11588 > isolde stepto
    11589 
    11590 > isolde stepto
    11591 
    11592 > isolde stepto
    11593 
    11594 > isolde stepto
    11595 
    11596 > isolde stepto
    11597 
    11598 > isolde stepto
    11599 
    11600 > isolde stepto
    11601 
    11602 > isolde stepto
    11603 
    11604 > isolde stepto
    11605 
    11606 > isolde stepto
    11607 
    11608 > isolde stepto
    11609 
    11610 > isolde stepto
    11611 
    11612 > isolde stepto
    11613 
    11614 > isolde stepto
    11615 
    11616 > isolde stepto
    11617 
    11618 > isolde stepto
    11619 
    11620 > isolde stepto
    11621 
    11622 > isolde stepto
    11623 
    11624 > isolde stepto
    11625 
    11626 > isolde stepto
    11627 
    11628 > isolde stepto
    11629 
    11630 > isolde stepto
    11631 
    11632 > isolde stepto
    11633 
    11634 > isolde stepto
    11635 
    11636 > isolde stepto
    11637 
    11638 > isolde stepto
    11639 
    11640 > isolde stepto
    11641 
    11642 > isolde stepto
    11643 
    11644 > isolde stepto
    11645 
    11646 > isolde stepto
    11647 
    11648 > isolde stepto
    11649 
    11650 > isolde stepto
    11651 
    11652 > isolde stepto
    11653 
    11654 > isolde stepto
    11655 
    11656 > isolde stepto
    11657 
    11658 > isolde stepto
    11659 
    11660 > isolde stepto
    11661 
    11662 > isolde stepto
    11663 
    11664 > isolde stepto
    11665 
    11666 > isolde stepto
    11667 
    11668 > isolde stepto
    11669 
    11670 > close #1
    11671 
    11672 > show #!2 models
    11673 
    11674 > select :CDL
    11675 
    11676 768 atoms, 765 bonds, 3 residues, 1 model selected 
    11677 
    11678 > hide #!2 models
    11679 
    11680 > clipper set contourSensitivity o.25
    11681 
    11682 Missing or invalid "sensitivity" argument: Expected a number 
    11683 
    11684 > clipper set contourSensitivity 0.25
    11685 
    11686 > show #!2 models
    11687 
    11688 > select :BCL
    11689 
    11690 11760 atoms, 12432 bonds, 84 residues, 1 model selected 
    11691 
    11692 > hide #!2 models
    11693 
    11694 > show #!2 models
    11695 
    11696 > select clear
    11697 
    11698 > hide #!2 models
    11699 
    11700 > select /af
    11701 
    11702 1335 atoms, 1354 bonds, 62 residues, 1 model selected 
    11703 
    11704 > select /ag
    11705 
    11706 1335 atoms, 1354 bonds, 62 residues, 1 model selected 
    11707 
    11708 > select /ae
    11709 
    11710 1335 atoms, 1354 bonds, 62 residues, 1 model selected 
    11711 
    11712 > select down
    11713 
    11714 2 atoms, 1 bond, 1 residue, 1 model selected 
    11715 
    11716 > select up
    11717 
    11718 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11719 
    11720 > save working.cxs
    11721 
    11722 Taking snapshot of stepper: working_2.pdb 
    11723 
    11724 > isolde add ligand CDL
    11725 
    11726 place_ligand() was called with use_md_template=True, but no suitable template
    11727 was found. This command has been ignored. 
    11728 
    11729 > show #!2 models
    11730 
    11731 > hide #!2 models
    11732 
    11733 > select up
    11734 
    11735 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11736 
    11737 > hide ~sel
    11738 
    11739 > isolde ignore ~sel
    11740 
    11741 ISOLDE: currently ignoring 5222 residues in model 8.2 
    11742 
    11743 > show #!2 models
    11744 
    11745 > show ~HC
    11746 
    11747 > hide protein&~@CA
    11748 
    11749 > select up
    11750 
    11751 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11752 
    11753 > select up
    11754 
    11755 1282 atoms, 1300 bonds, 63 residues, 1 model selected 
    11756 
    11757 > select down
    11758 
    11759 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11760 
    11761 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11762 bonded heavy atom. 
    11763 
    11764 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11765 bonded heavy atom. 
    11766 
    11767 > select clear
    11768 
    11769 > select clear
    11770 
    11771 > isolde ~ignore
    11772 
    11773 > select up
    11774 
    11775 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11776 
    11777 > show ~HC
    11778 
    11779 > isolde ignore sel
    11780 
    11781 ISOLDE: currently ignoring 1 residues in model 8.2 
    11782 
    11783 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11784 bonded heavy atom. 
    11785 
    11786 > select up
    11787 
    11788 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11789 
    11790 > isolde ~ignore
    11791 
    11792 > select clear
    11793 
    11794 > save working.cxs
    11795 
    11796 Taking snapshot of stepper: working_2.pdb 
    11797 
    11798 > hide
    11799 
    11800 > hide #!8 models
    11801 
    11802 > volume #2 level 0.03016
    11803 
    11804 > volume #2 level 0.03131
    11805 
    11806 > show #!8 models
    11807 
    11808 > show ~HC
    11809 
    11810 > hide #!8 models
    11811 
    11812 > show #!8 models
    11813 
    11814 > select :CDL
    11815 
    11816 1024 atoms, 1020 bonds, 4 residues, 1 model selected 
    11817 
    11818 > hide #!2 models
    11819 
    11820 > show #!2 models
    11821 
    11822 > hide #!2 models
    11823 
    11824 > select clear
    11825 
    11826 > select :CDL
    11827 
    11828 1024 atoms, 1020 bonds, 4 residues, 1 model selected 
    11829 
    11830 > select up
    11831 
    11832 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11833 
    11834 > save cdl_ref.pdb #8 selectedOnly true
    11835 
    11836 > open cdl_ref.pdb
    11837 
    11838 Summary of feedback from opening cdl_ref.pdb 
    11839 --- 
    11840 warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
    11841 TRP A 5 1 4 
    11842 Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
    11843 26 
    11844 Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
    11845 6 
    11846 Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3 
    11847 Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
    11848 27 
    11849 267 messages similar to the above omitted 
    11850 Cannot find LINK/SSBOND residue CYS (95 ) 
    11851 Cannot find LINK/SSBOND residue CYS (98 ) 
    11852 Cannot find LINK/SSBOND residue THR (108 ) 
    11853 Cannot find LINK/SSBOND residue CYS (146 ) 
    11854 Cannot find LINK/SSBOND residue CYS (149 ) 
    11855 25 messages similar to the above omitted 
    11856  
    11857 
    11858 > select #1
    11859 
    11860 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11861 
    11862 > ui mousemode right "translate selected models"
    11863 
    11864 > hide #1 models
    11865 
    11866 > select up
    11867 
    11868 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11869 
    11870 > isolde ~ignore
    11871 
    11872 > isolde ignore ~sel
    11873 
    11874 ISOLDE: currently ignoring 5223 residues in model 8.2 
    11875 ISOLDE: currently ignoring 1 residues in model 1 
    11876 
    11877 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11878 bonded heavy atom. 
    11879 
    11880 > isolde ~ignore
    11881 
    11882 > save working.cxs
    11883 
    11884 Taking snapshot of stepper: working_2.pdb 
    11885 
    11886 > show #!2 models
    11887 
    11888 > close #2
    11889 
    11890 > select #8
    11891 
    11892 98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models selected 
    11893 
    11894 > select clear
    11895 
    11896 > volume zone #8.1.1.1 nearAtoms #8 dist 1.5 newMap true
    11897 
    11898 Expected a keyword 
    11899 
    11900 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    11901 
    11902 > volume subtract #8.1.1.1 #2 inPlace false
    11903 
    11904 > close #2
    11905 
    11906 > volume #5 level 0.03153
    11907 
    11908 > volume #5 color #73d216
    11909 
    11910 > select clear
    11911 
    11912 > hide #!5 models
    11913 
    11914 > show #!5 models
    11915 
    11916 > volume #5 level 0.03261
    11917 
    11918 > select :CDL
    11919 
    11920 1536 atoms, 1530 bonds, 6 residues, 2 models selected 
    11921 
    11922 > volume #3 level 0.03461
    11923 
    11924 > volume #5 level 0.03526
    11925 
    11926 > volume #5 level 0.0345
    11927 
    11928 > hide #!5 models
    11929 
    11930 > select :MAN
    11931 
    11932 40 atoms, 40 bonds, 2 residues, 1 model selected 
    11933 
    11934 > show #!5 models
    11935 
    11936 > select ~CDL
    11937 
    11938 Expected an objects specifier or a keyword 
    11939 
    11940 > select :CDL
    11941 
    11942 1536 atoms, 1530 bonds, 6 residues, 2 models selected 
    11943 
    11944 > hide #!5 models
    11945 
    11946 > select :GPC
    11947 
    11948 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    11949 
    11950 > select clear
    11951 
    11952 > select ~protein
    11953 
    11954 18265 atoms, 18944 bonds, 14 pseudobonds, 147 residues, 35 models selected 
    11955 
    11956 > select clear
    11957 
    11958 > select clear
    11959 
    11960 > select up
    11961 
    11962 140 atoms, 148 bonds, 1 residue, 1 model selected 
    11963 
    11964 > show sel
    11965 
    11966 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11967 bonded heavy atom. 
    11968 
    11969 > select clear
    11970 
    11971 > select clear
    11972 
    11973 > select clear
    11974 
    11975 > show sel
    11976 
    11977 > show sel
    11978 
    11979 > select clear
    11980 
    11981 > select clear
    11982 
    11983 > select clear
    11984 
    11985 > select clear
    11986 
    11987 > select clear
    11988 
    11989 > select clear
    11990 
    11991 > select clear
    11992 
    11993 > select clear
    11994 
    11995 > select clear
    11996 
    11997 > select clear
    11998 
    11999 > select clear
    12000 
    12001 > select clear
    12002 
    12003 > select clear
    12004 
    12005 > select clear
    12006 
    12007 > select clear
    12008 
    12009 > select clear
    12010 
    12011 > show sel
    12012 
    12013 > select clear
    12014 
    12015 > select up
    12016 
    12017 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12018 
    12019 > select clear
    12020 
    12021 > select clear
    12022 
    12023 > select clear
    12024 
    12025 > select clear
    12026 
    12027 > show sel
    12028 
    12029 > select clear
    12030 
    12031 > select clear
    12032 
    12033 > select clear
    12034 
    12035 > select clear
    12036 
    12037 > select clear
    12038 
    12039 > select clear
    12040 
    12041 > select clear
    12042 
    12043 > select clear
    12044 
    12045 > select clear
    12046 
    12047 > select clear
    12048 
    12049 > select clear
    12050 
    12051 > select clear
    12052 
    12053 > select clear
    12054 
    12055 > select clear
    12056 
    12057 > select clear
    12058 
    12059 > select clear
    12060 
    12061 > select clear
    12062 
    12063 > select clear
    12064 
    12065 > select clear
    12066 
    12067 > select clear
    12068 
    12069 > select clear
    12070 
    12071 > select clear
    12072 
    12073 > select clear
    12074 
    12075 > select clear
    12076 
    12077 > select clear
    12078 
    12079 > select clear
    12080 
    12081 > select clear
    12082 
    12083 > select clear
    12084 
    12085 > select clear
    12086 
    12087 > select clear
    12088 
    12089 > select clear
    12090 
    12091 > select up
    12092 
    12093 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12094 
    12095 > select clear
    12096 
    12097 > select clear
    12098 
    12099 > select clear
    12100 
    12101 > save working.cxs
    12102 
    12103 Taking snapshot of stepper: working_2.pdb 
    12104 
    12105 > select clear
    12106 
    12107 > select clear
    12108 
    12109 > select clear
    12110 
    12111 > select clear
    12112 
    12113 > select clear
    12114 
    12115 > select clear
    12116 
    12117 > select clear
    12118 
    12119 > select clear
    12120 
    12121 > select clear
    12122 
    12123 > select clear
    12124 
    12125 > select clear
    12126 
    12127 > select clear
    12128 
    12129 Chain L, residue 68 specifies more than one residue! The simulation can still
    12130 run, but this will probably cause problems later if not rectified by
    12131 renumbering. 
    12132 
    12133 > select clear
    12134 
    12135 > select clear
    12136 
    12137 > select clear
    12138 
    12139 > select clear
    12140 
    12141 > select clear
    12142 
    12143 > select up
    12144 
    12145 138 atoms, 139 bonds, 1 residue, 1 model selected 
    12146 
    12147 > show sel
    12148 
    12149 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12150 bonded heavy atom. 
    12151 
    12152 Chain ak, residue 67 specifies more than one residue! The simulation can still
    12153 run, but this will probably cause problems later if not rectified by
    12154 renumbering. 
    12155 
    12156 > select clear
    12157 
    12158 > isolde ignore ~sel
    12159 
    12160 ISOLDE: currently ignoring 5223 residues in model 8.2 
    12161 ISOLDE: currently ignoring 1 residues in model 1 
    12162 
    12163 > isolde ~ignore
    12164 
    12165 > select clear
    12166 
    12167 > isolde ~ignore
    12168 
    12169 > select clear
    12170 
    12171 > select clear
    12172 
    12173 > select clear
    12174 
    12175 > select clear
    12176 
    12177 > select clear
    12178 
    12179 > select clear
    12180 
    12181 > select clear
    12182 
    12183 > select clear
    12184 
    12185 > view /C:234
    12186 
    12187 > swapaa mousemode sel GLN
    12188 
    12189 Traceback (most recent call last): 
    12190 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12191 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    12192 self.start_sim() 
    12193 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12194 packages/chimerax/isolde/isolde.py", line 2724, in start_sim 
    12195 main_sel = self._last_main_sel = self._get_main_sim_selection() 
    12196 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12197 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    12198 raise TypeError('You must select at least one atom from the current ' 
    12199 TypeError: You must select at least one atom from the current working model
    12200 prior to starting a simulation! 
    12201  
    12202 TypeError: You must select at least one atom from the current working model
    12203 prior to starting a simulation! 
    12204  
    12205 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12206 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    12207 raise TypeError('You must select at least one atom from the current ' 
    12208  
    12209 See log for complete Python traceback. 
    12210  
    12211 
    12212 > swapaa mousemode sel ALA
    12213 
    12214 > select clear
    12215 
    12216 > select clear
    12217 
    12218 > select clear
    12219 
    12220 > select clear
    12221 
    12222 > select clear
    12223 
    12224 > select clear
    12225 
    12226 > select clear
    12227 
    12228 > select clear
    12229 
    12230 > select clear
    12231 
    12232 > select clear
    12233 
    12234 > select clear
    12235 
    12236 > select clear
    12237 
    12238 > select clear
    12239 
    12240 > select clear
    12241 
    12242 > select clear
    12243 
    12244 > select clear
    12245 
    12246 > select clear
    12247 
    12248 > select clear
    12249 
    12250 > select clear
    12251 
    12252 > select clear
    12253 
    12254 > select clear
    12255 
    12256 > select up
    12257 
    12258 100 atoms, 99 bonds, 1 residue, 1 model selected 
    12259 
    12260 > select clear
    12261 
    12262 > select clear
    12263 
    12264 > select clear
    12265 
    12266 > select clear
    12267 
    12268 > select clear
    12269 
    12270 > select clear
    12271 
    12272 > select clear
    12273 
    12274 > select clear
    12275 
    12276 > select clear
    12277 
    12278 > select up
    12279 
    12280 98238 atoms, 100348 bonds, 5224 residues, 1 model selected 
    12281 
    12282 > select clear
    12283 
    12284 > select clear
    12285 
    12286 > select clear
    12287 
    12288 > select clear
    12289 
    12290 > select clear
    12291 
    12292 > select clear
    12293 
    12294 > select clear
    12295 
    12296 > select clear
    12297 
    12298 > select clear
    12299 
    12300 > select clear
    12301 
    12302 > select clear
    12303 
    12304 > select clear
    12305 
    12306 > select clear
    12307 
    12308 > select clear
    12309 
    12310 > select clear
    12311 
    12312 > save working.cxs
    12313 
    12314 Taking snapshot of stepper: working_2.pdb 
    12315 
    12316 > close #5
    12317 
    12318 > select #8
    12319 
    12320 98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models selected 
    12321 
    12322 > select clear
    12323 
    12324 > volume zone #8.1.1.1.1 nearAtoms #8 range 1.5 newMap true
    12325 
    12326 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    12327 
    12328 > volume subtract #8.1.1.1 #2 inPlace false
    12329 
    12330 > close #2
    12331 
    12332 > volume #5 level 0.04033
    12333 
    12334 > volume #5 level 0.03573
    12335 
    12336 > isolde add ligand LMT
    12337 
    12338 place_ligand() was called with use_md_template=True, but no suitable template
    12339 was found. This command has been ignored. 
    12340 
    12341 > select up
    12342 
    12343 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12344 
    12345 > ui mousemode right "translate selected atoms"
    12346 
    12347 > isolde ignore ~sel
    12348 
    12349 ISOLDE: currently ignoring 5224 residues in model 8.2 
    12350 ISOLDE: currently ignoring 1 residues in model 1 
    12351 
    12352 Chain L, residue 68 specifies more than one residue! The simulation can still
    12353 run, but this will probably cause problems later if not rectified by
    12354 renumbering. 
    12355 
    12356 Chain ak, residue 67 specifies more than one residue! The simulation can still
    12357 run, but this will probably cause problems later if not rectified by
    12358 renumbering. 
    12359 
    12360 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12361 bonded heavy atom. 
    12362 
    12363 > isolde ~ignore
    12364 
    12365 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12366 bonded heavy atom. 
    12367 
    12368 > select /AG:10-30@CA
    12369 
    12370 21 atoms, 21 residues, 1 model selected 
    12371 
    12372 > select /AH:10-30@CA
    12373 
    12374 21 atoms, 21 residues, 1 model selected 
    12375 
    12376 > select up
    12377 
    12378 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12379 
    12380 > delete sel
    12381 
    12382 > show #!5 models
    12383 
    12384 > select /AG,AH,AI,AJ
    12385 
    12386 4153 atoms, 4242 bonds, 205 residues, 1 model selected 
    12387 
    12388 > select /AI:10-30@CA
    12389 
    12390 21 atoms, 21 residues, 1 model selected 
    12391 
    12392 > select clear
    12393 
    12394 > select up
    12395 
    12396 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12397 
    12398 > ui mousemode right "translate selected atoms"
    12399 
    12400 > hide #!5 models
    12401 
    12402 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12403 bonded heavy atom. 
    12404 
    12405 > select /AG,AI:LMT
    12406 
    12407 162 atoms, 164 bonds, 2 residues, 1 model selected 
    12408 
    12409 > show #!5 models
    12410 
    12411 > select /AG,AJ
    12412 
    12413 2117 atoms, 2162 bonds, 103 residues, 1 model selected 
    12414 
    12415 > select /AJ:10-30@CA
    12416 
    12417 21 atoms, 21 residues, 1 model selected 
    12418 
    12419 > select /AG:LMT
    12420 
    12421 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12422 
    12423 > select /AI:LMT
    12424 
    12425 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12426 
    12427 > select /AJ:10-30@CA
    12428 
    12429 21 atoms, 21 residues, 1 model selected 
    12430 
    12431 > hide #!5 models
    12432 
    12433 > select up
    12434 
    12435 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12436 
    12437 > select clear
    12438 
    12439 > view /AL:LMT
    12440 
    12441 > select clear
    12442 
    12443 > select /AM:10-30@CA
    12444 
    12445 21 atoms, 21 residues, 1 model selected 
    12446 
    12447 > select up
    12448 
    12449 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12450 
    12451 > select /AM:10-30@CA
    12452 
    12453 21 atoms, 21 residues, 1 model selected 
    12454 
    12455 > view /AM:LMT
    12456 
    12457 > select up
    12458 
    12459 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12460 
    12461 > view /AO:LMT
    12462 
    12463 > select /AP:10-30@CA
    12464 
    12465 21 atoms, 21 residues, 1 model selected 
    12466 
    12467 > select up
    12468 
    12469 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12470 
    12471 > view /AP:LMT
    12472 
    12473 > select up
    12474 
    12475 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12476 
    12477 > view /AR:LMT
    12478 
    12479 > select clear
    12480 
    12481 > select /AS:10-30@CA
    12482 
    12483 21 atoms, 21 residues, 1 model selected 
    12484 
    12485 > select up
    12486 
    12487 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12488 
    12489 > view /AS:LMT
    12490 
    12491 > select up
    12492 
    12493 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12494 
    12495 > view /AU:LMT
    12496 
    12497 > select /AV:10-30@CA
    12498 
    12499 21 atoms, 21 residues, 1 model selected 
    12500 
    12501 > select up
    12502 
    12503 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12504 
    12505 > view /AV:LMT
    12506 
    12507 > view /AV:LMT
    12508 
    12509 > select up
    12510 
    12511 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12512 
    12513 > select clear
    12514 
    12515 > view /AX:LMT
    12516 
    12517 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12518 bonded heavy atom. 
    12519 
    12520 > select up
    12521 
    12522 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12523 
    12524 > select /AA:10-30@CA
    12525 
    12526 21 atoms, 21 residues, 1 model selected 
    12527 
    12528 > view /AA:LMT
    12529 
    12530 > select clear
    12531 
    12532 > select up
    12533 
    12534 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12535 
    12536 > view /AC:LMT
    12537 
    12538 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12539 bonded heavy atom. 
    12540 
    12541 > select up
    12542 
    12543 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12544 
    12545 > select /AD:10-30@CA
    12546 
    12547 21 atoms, 21 residues, 1 model selected 
    12548 
    12549 > select up
    12550 
    12551 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12552 
    12553 > view /AD:LMT
    12554 
    12555 > select up
    12556 
    12557 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12558 
    12559 > view /AF:LMT
    12560 
    12561 > save working.cxs
    12562 
    12563 Taking snapshot of stepper: working_2.pdb 
    12564 opened ChimeraX session 
    12565 
    12566 > open
    12567 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    12568 
    12569 Summary of feedback from opening
    12570 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb 
    12571 --- 
    12572 warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
    12573 TRP A 5 1 4 
    12574 Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
    12575 26 
    12576 Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
    12577 6 
    12578 Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3 
    12579 Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
    12580 27 
    12581 264 messages similar to the above omitted 
    12582 Cannot find LINK/SSBOND residue CYS (95 ) 
    12583 Cannot find LINK/SSBOND residue CYS (98 ) 
    12584 Cannot find LINK/SSBOND residue THR (108 ) 
    12585 Cannot find LINK/SSBOND residue CYS (146 ) 
    12586 Cannot find LINK/SSBOND residue CYS (149 ) 
    12587 25 messages similar to the above omitted 
    12588  
    12589 
    12590 > view #2
    12591 
    12592 > select #2/AJ:61@C5'
    12593 
    12594 1 atom, 1 residue, 1 model selected 
    12595 
    12596 > select #2:61
    12597 
    12598 162 atoms, 164 bonds, 2 residues, 1 model selected 
    12599 
    12600 > delete sel
    12601 
    12602 > close #2
    12603 
    12604 > open
    12605 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    12606 
    12607 Summary of feedback from opening
    12608 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb 
    12609 --- 
    12610 warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
    12611 TRP A 5 1 4 
    12612 Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
    12613 26 
    12614 Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
    12615 6 
    12616 Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3 
    12617 Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
    12618 27 
    12619 264 messages similar to the above omitted 
    12620 Cannot find LINK/SSBOND residue CYS (95 ) 
    12621 Cannot find LINK/SSBOND residue CYS (98 ) 
    12622 Cannot find LINK/SSBOND residue THR (108 ) 
    12623 Cannot find LINK/SSBOND residue CYS (146 ) 
    12624 Cannot find LINK/SSBOND residue CYS (149 ) 
    12625 25 messages similar to the above omitted 
    12626  
    12627 
    12628 > delete #2/AJ:61
    12629 
    12630 > isolde start
    12631 
    12632 > set selectionWidth 4
    12633 
    12634 Done loading forcefield 
    12635 
    12636 > ui tool show Shell
    12637 
    12638 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    12639 UserWarning: IPython History requires SQLite, your history will not be saved 
    12640 warn("IPython History requires SQLite, your history will not be saved") 
    12641 
    12642 > select #2
    12643 
    12644 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12645 
    12646 > hide #2 models
    12647 
    12648 > hide #!1 models
    12649 
    12650 > select clear
    12651 
    12652 > select clear
    12653 
    12654 > select /AK
    12655 
    12656 1406 atoms, 1428 bonds, 55 residues, 2 models selected 
    12657 
    12658 > select /AK:10-30@CA
    12659 
    12660 21 atoms, 21 residues, 1 model selected 
    12661 
    12662 > view /AA:PEX
    12663 
    12664 > select /AA:PEX
    12665 
    12666 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12667 
    12668 > select up
    12669 
    12670 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12671 
    12672 > delete sel
    12673 
    12674 > view /AC:PEX
    12675 
    12676 > select up
    12677 
    12678 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12679 
    12680 > select up
    12681 
    12682 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12683 
    12684 > delete sel
    12685 
    12686 > view /AE:PEX
    12687 
    12688 > select /AA, AC, AE,
    12689 
    12690 Expected an objects specifier or a keyword 
    12691 
    12692 > select /AA, AC, AE
    12693 
    12694 3397 atoms, 3464 bonds, 156 residues, 1 model selected 
    12695 
    12696 > select clear
    12697 
    12698 > view /AG:PEX
    12699 
    12700 > select /AG:PEX
    12701 
    12702 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12703 
    12704 > delete /AA,AC,AE,AG,AI,AM,AO,AQ,AS,AU,AW:61,62
    12705 
    12706 > view /AB:PEX
    12707 
    12708 > view /AE:PEX
    12709 
    12710 > view /AH:PEX
    12711 
    12712 > view /AB:PEX
    12713 
    12714 > select /AB:PEX,LMT
    12715 
    12716 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12717 
    12718 > select clear
    12719 
    12720 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12721 bonded heavy atom. 
    12722 
    12723 > select /AE:PEX,LMT
    12724 
    12725 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12726 
    12727 > view sel
    12728 
    12729 > select clear
    12730 
    12731 > select /AH:PEX,LMT
    12732 
    12733 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12734 
    12735 > view sel
    12736 
    12737 > select clear
    12738 
    12739 > isolde add ligand LMT
    12740 
    12741 > ui mousemode right "translate selected atoms"
    12742 
    12743 > isolde add ligand BCL
    12744 
    12745 > ui mousemode right "translate selected atoms"
    12746 
    12747 > isolde ignore ~sel
    12748 
    12749 ISOLDE: currently ignoring 2 residues in model 2 
    12750 ISOLDE: currently ignoring 5249 residues in model 8.2 
    12751 ISOLDE: currently ignoring 1 residues in model 1.2 
    12752 
    12753 > select up
    12754 
    12755 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12756 
    12757 > delete sel
    12758 
    12759 > isolde add ligand BPH
    12760 
    12761 > ui mousemode right "translate selected atoms"
    12762 
    12763 > isolde add ligand BCL
    12764 
    12765 > ui mousemode right "translate selected atoms"
    12766 
    12767 > select up
    12768 
    12769 141 atoms, 146 bonds, 1 residue, 1 model selected 
    12770 
    12771 > delete sel
    12772 
    12773 > select up
    12774 
    12775 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12776 
    12777 > isolde ~ignore
    12778 
    12779 > select clear
    12780 
    12781 > select up
    12782 
    12783 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12784 
    12785 > save extra_bcl.pdb #1 selectedOnly true
    12786 
    12787 > select /AN:PEX,LMT
    12788 
    12789 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12790 
    12791 > view sel
    12792 
    12793 > select clear
    12794 
    12795 > isolde add ligand LMT
    12796 
    12797 > ui mousemode right "translate selected atoms"
    12798 
    12799 > isolde ignore ~sel
    12800 
    12801 ISOLDE: currently ignoring 2 residues in model 2 
    12802 ISOLDE: currently ignoring 5250 residues in model 8.2 
    12803 ISOLDE: currently ignoring 1 residues in model 1.2 
    12804 
    12805 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12806 bonded heavy atom. 
    12807 
    12808 > isolde ~ignore
    12809 
    12810 > select up
    12811 
    12812 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12813 
    12814 > isolde ignore sel
    12815 
    12816 ISOLDE: currently ignoring 1 residues in model 8.2 
    12817 
    12818 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12819 bonded heavy atom. 
    12820 
    12821 > isolde ~ignore
    12822 
    12823 > select clear
    12824 
    12825 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12826 bonded heavy atom. 
    12827 
    12828 > select /AQ:PEX,LMT
    12829 
    12830 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12831 
    12832 > view sel
    12833 
    12834 > select clear
    12835 
    12836 > select /AT:PEX,LMT
    12837 
    12838 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12839 
    12840 > view sel
    12841 
    12842 > select clear
    12843 
    12844 > isolde add ligand LMT
    12845 
    12846 > ui mousemode right "translate selected atoms"
    12847 
    12848 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12849 bonded heavy atom. 
    12850 
    12851 > select clear
    12852 
    12853 > select /AW:PEX,LMT
    12854 
    12855 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12856 
    12857 > view sel
    12858 
    12859 > select clear
    12860 
    12861 > select clear
    12862 
    12863 > save working.cxs
    12864 
    12865 Taking snapshot of stepper: working_2.pdb 
    12866 
    12867 > close #5
    12868 
    12869 > select #8
    12870 
    12871 100821 atoms, 102950 bonds, 14 pseudobonds, 5252 residues, 22 models selected 
    12872 
    12873 > select clear
    12874 
    12875 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    12876 
    12877 > volume diff #8.1.1.1 #5 inpl f
    12878 
    12879 Expected a density maps specifier or a keyword 
    12880 
    12881 > volume subtract #8.1.1.1 #5 inPlace false
    12882 
    12883 > close #5
    12884 
    12885 > show #2 models
    12886 
    12887 > select #2
    12888 
    12889 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12890 
    12891 > select clear
    12892 
    12893 > select #2
    12894 
    12895 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12896 
    12897 > hide #!6 models
    12898 
    12899 > show #!6 models
    12900 
    12901 > ui mousemode right "translate selected models"
    12902 
    12903 > select #2:PEX
    12904 
    12905 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12906 
    12907 > select clear
    12908 
    12909 > volume #6 level 0.0417
    12910 
    12911 > hide #2 models
    12912 
    12913 > hide #!6 models
    12914 
    12915 > select up
    12916 
    12917 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12918 
    12919 > isolde ignore ~sel
    12920 
    12921 ISOLDE: currently ignoring 2 residues in model 2 
    12922 ISOLDE: currently ignoring 5252 residues in model 8.2 
    12923 ISOLDE: currently ignoring 1 residues in model 1.2 
    12924 
    12925 > select clear
    12926 
    12927 > select clear
    12928 
    12929 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12930 bonded heavy atom. 
    12931 
    12932 > isolde ~ignore
    12933 
    12934 > isolde add ligand LMT
    12935 
    12936 > ui mousemode right "translate selected atoms"
    12937 
    12938 > select up
    12939 
    12940 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12941 
    12942 > select /AX:10-30@CA
    12943 
    12944 21 atoms, 21 residues, 1 model selected 
    12945 
    12946 > select /AC:PEX,LMT
    12947 
    12948 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12949 
    12950 > view sel
    12951 
    12952 > select up
    12953 
    12954 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12955 
    12956 > ui mousemode right "translate selected atoms"
    12957 
    12958 > select /AF:PEX,LMT
    12959 
    12960 275 atoms, 276 bonds, 3 residues, 1 model selected 
    12961 
    12962 > view sel
    12963 
    12964 > select up
    12965 
    12966 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12967 
    12968 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12969 bonded heavy atom. 
    12970 
    12971 > select /AI:PEX,LMT
    12972 
    12973 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12974 
    12975 > view sel
    12976 
    12977 > isolde add ligand LMT
    12978 
    12979 > ui mousemode right "translate selected atoms"
    12980 
    12981 > select up
    12982 
    12983 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12984 
    12985 > isolde ignore sel
    12986 
    12987 ISOLDE: currently ignoring 1 residues in model 8.2 
    12988 
    12989 > select up
    12990 
    12991 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12992 
    12993 > isolde ~ignore
    12994 
    12995 > select /AL:PEX,LMT
    12996 
    12997 275 atoms, 276 bonds, 3 residues, 1 model selected 
    12998 
    12999 > view sel
    13000 
    13001 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13002 bonded heavy atom. 
    13003 
    13004 > select /AO:PEX,LMT
    13005 
    13006 194 atoms, 194 bonds, 2 residues, 1 model selected 
    13007 
    13008 > view sel
    13009 
    13010 > isolde add ligand LMT
    13011 
    13012 > ui mousemode right "translate selected atoms"
    13013 
    13014 > select up
    13015 
    13016 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13017 
    13018 > delete sel
    13019 
    13020 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13021 bonded heavy atom. 
    13022 
    13023 > select /AR:PEX,LMT
    13024 
    13025 275 atoms, 276 bonds, 3 residues, 1 model selected 
    13026 
    13027 > view sel
    13028 
    13029 > select up
    13030 
    13031 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13032 
    13033 > delete sel
    13034 
    13035 > select /AU:PEX,LMT
    13036 
    13037 194 atoms, 194 bonds, 2 residues, 1 model selected 
    13038 
    13039 > view sel
    13040 
    13041 > isolde add ligand LMT
    13042 
    13043 > ui mousemode right "translate selected atoms"
    13044 
    13045 > select clear
    13046 
    13047 > save working.cxs
    13048 
    13049 Taking snapshot of stepper: working_2.pdb 
    13050 
    13051 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13052 bonded heavy atom. 
    13053 
    13054 > select clear
    13055 
    13056 > close #6
    13057 
    13058 > select #8
    13059 
    13060 102454 atoms, 104584 bonds, 14 pseudobonds, 5269 residues, 22 models selected 
    13061 
    13062 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    13063 
    13064 > volume subtract #8.1.1.1 #5 inPlace false
    13065 
    13066 > close #5
    13067 
    13068 > select clear
    13069 
    13070 > select :LMT
    13071 
    13072 2349 atoms, 2378 bonds, 29 residues, 2 models selected 
    13073 
    13074 > isolde add ligand LMT
    13075 
    13076 > ui mousemode right "translate selected atoms"
    13077 
    13078 > delete sel
    13079 
    13080 > isolde add ligand LMT
    13081 
    13082 > ui mousemode right "translate selected atoms"
    13083 
    13084 > isolde add ligand LMT
    13085 
    13086 > ui mousemode right "translate selected atoms"
    13087 
    13088 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13089 bonded heavy atom. 
    13090 
    13091 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13092 bonded heavy atom. 
    13093 
    13094 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13095 bonded heavy atom. 
    13096 
    13097 > isolde add ligand LMT
    13098 
    13099 > ui mousemode right "translate selected atoms"
    13100 
    13101 > save working.cxs
    13102 
    13103 Taking snapshot of stepper: working_2.pdb 
    13104 opened ChimeraX session 
    13105 
    13106 > isolde start
    13107 
    13108 > set selectionWidth 4
    13109 
    13110 Done loading forcefield 
    13111 
    13112 > select up
    13113 
    13114 162 atoms, 164 bonds, 2 residues, 1 model selected 
    13115 
    13116 > ui tool show Shell
    13117 
    13118 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    13119 UserWarning: IPython History requires SQLite, your history will not be saved 
    13120 warn("IPython History requires SQLite, your history will not be saved") 
    13121 
    13122 > select /BH:10-30@CA
    13123 
    13124 21 atoms, 21 residues, 1 model selected 
    13125 
    13126 > select /BH:10-40@CA
    13127 
    13128 31 atoms, 31 residues, 1 model selected 
    13129 
    13130 > select up
    13131 
    13132 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13133 
    13134 > select /BG:10-40@CA
    13135 
    13136 31 atoms, 31 residues, 1 model selected 
    13137 Loading residue template for PEX from internal database 
    13138 
    13139 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13140 run, but this will probably cause problems later if not rectified by
    13141 renumbering. 
    13142 
    13143 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13144 run, but this will probably cause problems later if not rectified by
    13145 renumbering. 
    13146 
    13147 Chain BA, residue 60 specifies more than one residue! The simulation can still
    13148 run, but this will probably cause problems later if not rectified by
    13149 renumbering. 
    13150 
    13151 Chain BB, residue 60 specifies more than one residue! The simulation can still
    13152 run, but this will probably cause problems later if not rectified by
    13153 renumbering. 
    13154 
    13155 Chain BC, residue 60 specifies more than one residue! The simulation can still
    13156 run, but this will probably cause problems later if not rectified by
    13157 renumbering. 
    13158 
    13159 Chain BD, residue 60 specifies more than one residue! The simulation can still
    13160 run, but this will probably cause problems later if not rectified by
    13161 renumbering. 
    13162 
    13163 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13164 run, but this will probably cause problems later if not rectified by
    13165 renumbering. 
    13166 
    13167 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13168 run, but this will probably cause problems later if not rectified by
    13169 renumbering. 
    13170 
    13171 Chain BG, residue 60 specifies more than one residue! The simulation can still
    13172 run, but this will probably cause problems later if not rectified by
    13173 renumbering. 
    13174 
    13175 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13176 run, but this will probably cause problems later if not rectified by
    13177 renumbering. 
    13178 
    13179 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13180 run, but this will probably cause problems later if not rectified by
    13181 renumbering. 
    13182 
    13183 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13184 run, but this will probably cause problems later if not rectified by
    13185 renumbering. 
    13186 
    13187 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13188 run, but this will probably cause problems later if not rectified by
    13189 renumbering. 
    13190 
    13191 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13192 run, but this will probably cause problems later if not rectified by
    13193 renumbering. 
    13194 
    13195 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13196 run, but this will probably cause problems later if not rectified by
    13197 renumbering. 
    13198 
    13199 Chain BN, residue 60 specifies more than one residue! The simulation can still
    13200 run, but this will probably cause problems later if not rectified by
    13201 renumbering. 
    13202 
    13203 Chain BO, residue 60 specifies more than one residue! The simulation can still
    13204 run, but this will probably cause problems later if not rectified by
    13205 renumbering. 
    13206 
    13207 Chain BP, residue 60 specifies more than one residue! The simulation can still
    13208 run, but this will probably cause problems later if not rectified by
    13209 renumbering. 
    13210 
    13211 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    13212 run, but this will probably cause problems later if not rectified by
    13213 renumbering. 
    13214 
    13215 Chain BR, residue 60 specifies more than one residue! The simulation can still
    13216 run, but this will probably cause problems later if not rectified by
    13217 renumbering. 
    13218 
    13219 Chain BS, residue 60 specifies more than one residue! The simulation can still
    13220 run, but this will probably cause problems later if not rectified by
    13221 renumbering. 
    13222 
    13223 Chain BT, residue 60 specifies more than one residue! The simulation can still
    13224 run, but this will probably cause problems later if not rectified by
    13225 renumbering. 
    13226 
    13227 Chain BU, residue 60 specifies more than one residue! The simulation can still
    13228 run, but this will probably cause problems later if not rectified by
    13229 renumbering. 
    13230 
    13231 Chain BV, residue 60 specifies more than one residue! The simulation can still
    13232 run, but this will probably cause problems later if not rectified by
    13233 renumbering. 
    13234 
    13235 Chain BW, residue 60 specifies more than one residue! The simulation can still
    13236 run, but this will probably cause problems later if not rectified by
    13237 renumbering. 
    13238 
    13239 Chain BX, residue 60 specifies more than one residue! The simulation can still
    13240 run, but this will probably cause problems later if not rectified by
    13241 renumbering. 
    13242 
    13243 Chain L, residue 68 specifies more than one residue! The simulation can still
    13244 run, but this will probably cause problems later if not rectified by
    13245 renumbering. 
    13246 
    13247 Chain ak, residue 67 specifies more than one residue! The simulation can still
    13248 run, but this will probably cause problems later if not rectified by
    13249 renumbering. 
    13250 
    13251 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13252 run, but this will probably cause problems later if not rectified by
    13253 renumbering. 
    13254 
    13255 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13256 run, but this will probably cause problems later if not rectified by
    13257 renumbering. 
    13258 
    13259 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13260 run, but this will probably cause problems later if not rectified by
    13261 renumbering. 
    13262 
    13263 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13264 run, but this will probably cause problems later if not rectified by
    13265 renumbering. 
    13266 
    13267 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13268 run, but this will probably cause problems later if not rectified by
    13269 renumbering. 
    13270 
    13271 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13272 run, but this will probably cause problems later if not rectified by
    13273 renumbering. 
    13274 
    13275 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13276 run, but this will probably cause problems later if not rectified by
    13277 renumbering. 
    13278 
    13279 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13280 run, but this will probably cause problems later if not rectified by
    13281 renumbering. 
    13282 
    13283 > select ~protein
    13284 
    13285 28426 atoms, 29196 bonds, 14 pseudobonds, 265 residues, 39 models selected 
    13286 
    13287 > select clear
    13288 
    13289 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13290 run, but this will probably cause problems later if not rectified by
    13291 renumbering. 
    13292 
    13293 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13294 run, but this will probably cause problems later if not rectified by
    13295 renumbering. 
    13296 
    13297 > select clear
    13298 
    13299 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13300 run, but this will probably cause problems later if not rectified by
    13301 renumbering. 
    13302 
    13303 Chain BN, residue 60 specifies more than one residue! The simulation can still
    13304 run, but this will probably cause problems later if not rectified by
    13305 renumbering. 
    13306 
    13307 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13308 bonded heavy atom. 
    13309 
    13310 Chain BN, residue 60 specifies more than one residue! The simulation can still
    13311 run, but this will probably cause problems later if not rectified by
    13312 renumbering. 
    13313 
    13314 Chain BO, residue 60 specifies more than one residue! The simulation can still
    13315 run, but this will probably cause problems later if not rectified by
    13316 renumbering. 
    13317 
    13318 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13319 bonded heavy atom. 
    13320 
    13321 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13322 bonded heavy atom. 
    13323 
    13324 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13325 bonded heavy atom. 
    13326 
    13327 Chain BO, residue 60 specifies more than one residue! The simulation can still
    13328 run, but this will probably cause problems later if not rectified by
    13329 renumbering. 
    13330 
    13331 Chain BP, residue 60 specifies more than one residue! The simulation can still
    13332 run, but this will probably cause problems later if not rectified by
    13333 renumbering. 
    13334 
    13335 > select clear
    13336 
    13337 Chain BP, residue 60 specifies more than one residue! The simulation can still
    13338 run, but this will probably cause problems later if not rectified by
    13339 renumbering. 
    13340 
    13341 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    13342 run, but this will probably cause problems later if not rectified by
    13343 renumbering. 
    13344 
    13345 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13346 bonded heavy atom. 
    13347 
    13348 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    13349 run, but this will probably cause problems later if not rectified by
    13350 renumbering. 
    13351 
    13352 Chain BR, residue 60 specifies more than one residue! The simulation can still
    13353 run, but this will probably cause problems later if not rectified by
    13354 renumbering. 
    13355 
    13356 > select clear
    13357 
    13358 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13359 bonded heavy atom. 
    13360 
    13361 > hide #!6 models
    13362 
    13363 Chain BR, residue 60 specifies more than one residue! The simulation can still
    13364 run, but this will probably cause problems later if not rectified by
    13365 renumbering. 
    13366 
    13367 Chain BS, residue 60 specifies more than one residue! The simulation can still
    13368 run, but this will probably cause problems later if not rectified by
    13369 renumbering. 
    13370 
    13371 > select clear
    13372 
    13373 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13374 bonded heavy atom. 
    13375 
    13376 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13377 bonded heavy atom. 
    13378 
    13379 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13380 bonded heavy atom. 
    13381 
    13382 Chain BS, residue 60 specifies more than one residue! The simulation can still
    13383 run, but this will probably cause problems later if not rectified by
    13384 renumbering. 
    13385 
    13386 Chain BT, residue 60 specifies more than one residue! The simulation can still
    13387 run, but this will probably cause problems later if not rectified by
    13388 renumbering. 
    13389 
    13390 Chain BT, residue 60 specifies more than one residue! The simulation can still
    13391 run, but this will probably cause problems later if not rectified by
    13392 renumbering. 
    13393 
    13394 Chain BU, residue 60 specifies more than one residue! The simulation can still
    13395 run, but this will probably cause problems later if not rectified by
    13396 renumbering. 
    13397 
    13398 > select clear
    13399 
    13400 Chain BU, residue 60 specifies more than one residue! The simulation can still
    13401 run, but this will probably cause problems later if not rectified by
    13402 renumbering. 
    13403 
    13404 Chain BV, residue 60 specifies more than one residue! The simulation can still
    13405 run, but this will probably cause problems later if not rectified by
    13406 renumbering. 
    13407 
    13408 Chain BV, residue 60 specifies more than one residue! The simulation can still
    13409 run, but this will probably cause problems later if not rectified by
    13410 renumbering. 
    13411 
    13412 Chain BW, residue 60 specifies more than one residue! The simulation can still
    13413 run, but this will probably cause problems later if not rectified by
    13414 renumbering. 
    13415 
    13416 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13417 bonded heavy atom. 
    13418 
    13419 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13420 bonded heavy atom. 
    13421 
    13422 Chain BW, residue 60 specifies more than one residue! The simulation can still
    13423 run, but this will probably cause problems later if not rectified by
    13424 renumbering. 
    13425 
    13426 Chain BX, residue 60 specifies more than one residue! The simulation can still
    13427 run, but this will probably cause problems later if not rectified by
    13428 renumbering. 
    13429 
    13430 Chain BA, residue 60 specifies more than one residue! The simulation can still
    13431 run, but this will probably cause problems later if not rectified by
    13432 renumbering. 
    13433 
    13434 Chain BX, residue 60 specifies more than one residue! The simulation can still
    13435 run, but this will probably cause problems later if not rectified by
    13436 renumbering. 
    13437 
    13438 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13439 bonded heavy atom. 
    13440 
    13441 Chain BA, residue 60 specifies more than one residue! The simulation can still
    13442 run, but this will probably cause problems later if not rectified by
    13443 renumbering. 
    13444 
    13445 Chain BB, residue 60 specifies more than one residue! The simulation can still
    13446 run, but this will probably cause problems later if not rectified by
    13447 renumbering. 
    13448 
    13449 Chain BB, residue 60 specifies more than one residue! The simulation can still
    13450 run, but this will probably cause problems later if not rectified by
    13451 renumbering. 
    13452 
    13453 Chain BC, residue 60 specifies more than one residue! The simulation can still
    13454 run, but this will probably cause problems later if not rectified by
    13455 renumbering. 
    13456 
    13457 Chain BC, residue 60 specifies more than one residue! The simulation can still
    13458 run, but this will probably cause problems later if not rectified by
    13459 renumbering. 
    13460 
    13461 Chain BD, residue 60 specifies more than one residue! The simulation can still
    13462 run, but this will probably cause problems later if not rectified by
    13463 renumbering. 
    13464 
    13465 Chain BD, residue 60 specifies more than one residue! The simulation can still
    13466 run, but this will probably cause problems later if not rectified by
    13467 renumbering. 
    13468 
    13469 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13470 run, but this will probably cause problems later if not rectified by
    13471 renumbering. 
    13472 
    13473 > select clear
    13474 
    13475 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13476 bonded heavy atom. 
    13477 
    13478 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13479 run, but this will probably cause problems later if not rectified by
    13480 renumbering. 
    13481 
    13482 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13483 run, but this will probably cause problems later if not rectified by
    13484 renumbering. 
    13485 
    13486 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13487 bonded heavy atom. 
    13488 
    13489 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13490 run, but this will probably cause problems later if not rectified by
    13491 renumbering. 
    13492 
    13493 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13494 run, but this will probably cause problems later if not rectified by
    13495 renumbering. 
    13496 
    13497 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13498 run, but this will probably cause problems later if not rectified by
    13499 renumbering. 
    13500 
    13501 Chain BG, residue 60 specifies more than one residue! The simulation can still
    13502 run, but this will probably cause problems later if not rectified by
    13503 renumbering. 
    13504 
    13505 Chain BG, residue 60 specifies more than one residue! The simulation can still
    13506 run, but this will probably cause problems later if not rectified by
    13507 renumbering. 
    13508 
    13509 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13510 run, but this will probably cause problems later if not rectified by
    13511 renumbering. 
    13512 
    13513 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13514 run, but this will probably cause problems later if not rectified by
    13515 renumbering. 
    13516 
    13517 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13518 run, but this will probably cause problems later if not rectified by
    13519 renumbering. 
    13520 
    13521 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13522 run, but this will probably cause problems later if not rectified by
    13523 renumbering. 
    13524 
    13525 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13526 run, but this will probably cause problems later if not rectified by
    13527 renumbering. 
    13528 
    13529 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13530 bonded heavy atom. 
    13531 
    13532 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13533 run, but this will probably cause problems later if not rectified by
    13534 renumbering. 
    13535 
    13536 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13537 run, but this will probably cause problems later if not rectified by
    13538 renumbering. 
    13539 
    13540 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13541 bonded heavy atom. 
    13542 
    13543 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13544 run, but this will probably cause problems later if not rectified by
    13545 renumbering. 
    13546 
    13547 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13548 run, but this will probably cause problems later if not rectified by
    13549 renumbering. 
    13550 
    13551 > select clear
    13552 
    13553 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13554 bonded heavy atom. 
    13555 
    13556 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13557 run, but this will probably cause problems later if not rectified by
    13558 renumbering. 
    13559 
    13560 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13561 run, but this will probably cause problems later if not rectified by
    13562 renumbering. 
    13563 
    13564 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13565 run, but this will probably cause problems later if not rectified by
    13566 renumbering. 
    13567 
    13568 Chain BN, residue 60 specifies more than one residue! The simulation can still
    13569 run, but this will probably cause problems later if not rectified by
    13570 renumbering. 
    13571 
    13572 > save working.cxs
    13573 
    13574 Taking snapshot of stepper: working_2.pdb 
    13575 
    13576 > close #6
    13577 
    13578 > select #8
    13579 
    13580 108286 atoms, 110488 bonds, 14 pseudobonds, 5341 residues, 22 models selected 
    13581 
    13582 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    13583 
    13584 > volume subtract #8.1.1.1 #5 inPlace false
    13585 
    13586 > close #5
    13587 
    13588 > select clear
    13589 
    13590 > hide #!6 models
    13591 
    13592 > show #!6 models
    13593 
    13594 > isolde add ligand PC1
    13595 
    13596 > ui mousemode right "translate selected atoms"
    13597 
    13598 > isolde ignore ~sel
    13599 
    13600 ISOLDE: currently ignoring 5341 residues in model 8.2 
    13601 ISOLDE: currently ignoring 1 residues in model 2 
    13602 ISOLDE: currently ignoring 1 residues in model 1.2 
    13603 
    13604 > volume #6 level 0.04625
    13605 
    13606 > hide #!6 models
    13607 
    13608 > isolde ~ignore
    13609 
    13610 > select up
    13611 
    13612 142 atoms, 141 bonds, 1 residue, 1 model selected 
    13613 
    13614 > isolde ignore sel
    13615 
    13616 ISOLDE: currently ignoring 1 residues in model 8.2 
    13617 
    13618 > isolde ~ignore
    13619 
    13620 > select up
    13621 
    13622 256 atoms, 255 bonds, 1 residue, 1 model selected 
    13623 
    13624 > select clear
    13625 
    13626 Chain L, residue 68 specifies more than one residue! The simulation can still
    13627 run, but this will probably cause problems later if not rectified by
    13628 renumbering. 
    13629 
    13630 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13631 bonded heavy atom. 
    13632 
    13633 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13634 bonded heavy atom. 
    13635 
    13636 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13637 bonded heavy atom. 
    13638 
    13639 > select up
    13640 
    13641 142 atoms, 141 bonds, 1 residue, 1 model selected 
    13642 
    13643 > isolde replace ligand sel P5S
    13644 
    13645 Deleted the following atoms from residue PC1 H11001: H143, H151, H122, C14,
    13646 C15, H152, H131, H142, H141, H153, H132, C13, H133 
    13647 
    13648 126 atoms were automatically renamed to match the template: C12->CA, C11->CB,
    13649 O13->OG, P->P12, H111->HB, H112->HBA, H121->HA, O11->O16, C1->C3, C3->C1,
    13650 O21->O37, C21->C38, C22->C39, C23->C40, C24->C41, C25->C42, C26->C43,
    13651 C27->C44, C28->C45, C29->C46, C2A->C48, C2B->C49, C2C->C50, C2D->C51,
    13652 C2E->C52, C2F->C53, C2G->C54, C2H->C55, C2I->C56, O31->O19, C31->C17,
    13653 C32->C20, C33->C21, C34->C22, C35->C23, C36->C24, C37->C25, C38->C26,
    13654 C39->C27, C3A->C28, C3B->C29, C3C->C30, C3D->C31, C3E->C32, C3F->C33,
    13655 C3G->C34, C3H->C35, C3I->C36, O22->O47, O32->O18, H11->H3, H12->H3A,
    13656 H221->H39, H222->H39A, H231->H40, H232->H40A, H241->H41, H242->H41A,
    13657 H251->H42, H252->H42A, H261->H43, H262->H43A, H271->H44, H272->H44A,
    13658 H281->H45, H282->H45A, H291->H46, H292->H46A, H2A1->H48, H2A2->H48A,
    13659 H2B1->H49, H2B2->H49A, H2C1->H50, H2C2->H50A, H2D1->H51, H2D2->H51A,
    13660 H2E1->H52, H2E2->H52A, H2F1->H53, H2F2->H53A, H2G1->H54, H2G2->H54A,
    13661 H2H1->H55, H2H2->H55A, H31->H1, H32->H1A, H321->H20, H322->H20A, H331->H21,
    13662 H332->H21A, H341->H22, H342->H22A, H351->H23, H352->H23A, H361->H24,
    13663 H362->H24A, H371->H25, H372->H25A, H381->H26, H382->H26A, H391->H27,
    13664 H392->H27A, H3A1->H28, H3A2->H28A, H3B1->H29, H3B2->H29A, H3C1->H30,
    13665 H3C2->H30A, H3D1->H31, H3D2->H31A, H3E1->H32, H3E2->H32A, H3F1->H33,
    13666 H3F2->H33A, H3G1->H34, H3G2->H34A, H3H1->H35, H3H2->H35A, O12->O15, O14->O13,
    13667 H2I1->H56, H2I2->H56A, H2I3->H56B, H3I1->H36, H3I2->H36A, H3I3->H36B 
    13668 
    13669 Rebuilt ligand P5S has chiral centres at atoms CA,C2 (highlighted). Since the
    13670 current algorithm used to match topologies is not chirality aware, you should
    13671 check these sites carefully to ensure they are sensible. If in doubt, it is
    13672 best to delete with "del #8.2/H1:1001" and replace with "isolde add ligand
    13673 P5S". 
    13674 
    13675 > isolde replace ligand sel P5S
    13676 
    13677 Deleted the following atoms from residue P5S H11001: HXT, HO15 
    13678 Traceback (most recent call last): 
    13679 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13680 packages/chimerax/cmd_line/tool.py", line 275, in execute 
    13681 cmd.run(cmd_text) 
    13682 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13683 packages/chimerax/core/commands/cli.py", line 2805, in run 
    13684 result = ci.function(session, **kw_args) 
    13685 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    13686 packages/chimerax/isolde/atomic/building/cmd.py", line 44, in replace_residue 
    13687 chiral_centers = Atoms([a for a in residue.atoms if
    13688 residue.ideal_chirality(a.name) != 'N']) 
    13689 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    13690 packages/chimerax/isolde/atomic/building/cmd.py", line 44, in <listcomp> 
    13691 chiral_centers = Atoms([a for a in residue.atoms if
    13692 residue.ideal_chirality(a.name) != 'N']) 
    13693 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13694 packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality 
    13695 return f(self.name.encode('utf-8'), atom_name.encode('utf-8')) 
    13696 KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S' 
    13697  
    13698 KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S' 
    13699  
    13700 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13701 packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality 
    13702 return f(self.name.encode('utf-8'), atom_name.encode('utf-8')) 
    13703  
    13704 See log for complete Python traceback. 
    13705  
    13706 
    13707 Chain L, residue 68 specifies more than one residue! The simulation can still
    13708 run, but this will probably cause problems later if not rectified by
    13709 renumbering. 
    13710 
    13711 > select clear
    13712 
    13713 > isolde add ligand P5S
    13714 
    13715 Deleted the following atoms from residue P5S H11002: HO15, HXT 
    13716 
    13717 > ui mousemode right "translate selected atoms"
    13718 
    13719 > delete sel
    13720 
    13721 Chain L, residue 68 specifies more than one residue! The simulation can still
    13722 run, but this will probably cause problems later if not rectified by
    13723 renumbering. 
    13724 
    13725 > show #!6 models
    13726 
    13727 running convert_amber_files 
    13728 
    13729 > isolde add ligand 2Y5
    13730 
    13731 Fetching CCD 2Y5 from http://ligand-expo.rcsb.org/reports/2/2Y5/2Y5.cif 
    13732 Deleted the following atoms from residue 2Y5 L607: H81, H18, H78 
    13733 
    13734 > ui mousemode right "translate selected atoms"
    13735 
    13736 > isolde ignore ~sel
    13737 
    13738 ISOLDE: currently ignoring 5342 residues in model 8.2 
    13739 ISOLDE: currently ignoring 1 residues in model 2 
    13740 ISOLDE: currently ignoring 1 residues in model 1.2 
    13741 
    13742 > hide #!6 models
    13743 
    13744 > delete sel
    13745 
    13746 > isolde add ligand LMG
    13747 
    13748 Fetching CCD LMG from http://ligand-expo.rcsb.org/reports/L/LMG/LMG.cif 
    13749 
    13750 > ui mousemode right "translate selected atoms"
    13751 
    13752 > isolde ignore ~sel
    13753 
    13754 ISOLDE: currently ignoring 5342 residues in model 8.2 
    13755 ISOLDE: currently ignoring 1 residues in model 2 
    13756 ISOLDE: currently ignoring 1 residues in model 1.2 
    13757 
    13758 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13759 bonded heavy atom. 
    13760 
    13761 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13762 bonded heavy atom. 
    13763 
    13764 > select clear
    13765 
    13766 > delete sel
    13767 
    13768 > select up
    13769 
    13770 129 atoms, 129 bonds, 1 residue, 1 model selected 
    13771 
    13772 > save LMX.pdb #8 selectedOnly true
    13773 
    13774 running convert_amber_files 
    13775 
    13776 > isolde ~ignore
    13777 
    13778 > select clear
    13779 
    13780 Failed to add
    13781 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/PEE.xml:
    13782 Residue template USER_PEE with the same override level 0 already exists. 
    13783 
    13784 > isolde add ligand PEE
    13785 
    13786 Deleted the following atoms from residue PEE L608: H83 
    13787 
    13788 > ui mousemode right "translate selected atoms"
    13789 
    13790 > isolde ignore ~sel
    13791 
    13792 ISOLDE: currently ignoring 5343 residues in model 8.2 
    13793 ISOLDE: currently ignoring 1 residues in model 2 
    13794 ISOLDE: currently ignoring 1 residues in model 1.2 
    13795 
    13796 > isolde ~ignore
    13797 
    13798 > select up
    13799 
    13800 133 atoms, 132 bonds, 1 residue, 1 model selected 
    13801 
    13802 > isolde ignore sel
    13803 
    13804 ISOLDE: currently ignoring 1 residues in model 8.2 
    13805 
    13806 > select clear
    13807 
    13808 > select up
    13809 
    13810 256 atoms, 255 bonds, 1 residue, 1 model selected 
    13811 
    13812 > isolde ~ignore
    13813 
    13814 > select clear
    13815 
    13816 > select :PEE@H35
    13817 
    13818 1 atom, 1 residue, 1 model selected 
    13819 
    13820 > select up
    13821 
    13822 133 atoms, 132 bonds, 1 residue, 1 model selected 
    13823 
    13824 > isolde ignore sel
    13825 
    13826 ISOLDE: currently ignoring 1 residues in model 8.2 
    13827 
    13828 > isolde ~ignore
    13829 
    13830 > select clear
    13831 
    13832 > select clear
    13833 
    13834 > isolde add ligand LMT
    13835 
    13836 > ui mousemode right "translate selected atoms"
    13837 
    13838 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13839 bonded heavy atom. 
    13840 
    13841 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13842 bonded heavy atom. 
    13843 
    13844 > select clear
    13845 
    13846 > save working.cxs
    13847 
    13848 Taking snapshot of stepper: working_2.pdb 
    13849 
    13850 > isolde add ligand LMT
    13851 
    13852 > ui mousemode right "translate selected atoms"
    13853 
    13854 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13855 bonded heavy atom. 
    13856 
    13857 > isolde add ligand LMG
    13858 
    13859 > ui mousemode right "translate selected atoms"
    13860 
    13861 > isolde ignore sel
    13862 
    13863 ISOLDE: currently ignoring 1 residues in model 8.2 
    13864 
    13865 > isolde ~ignore
    13866 
    13867 > isolde ignore ~sel
    13868 
    13869 ISOLDE: currently ignoring 5346 residues in model 8.2 
    13870 ISOLDE: currently ignoring 1 residues in model 2 
    13871 ISOLDE: currently ignoring 1 residues in model 1.2 
    13872 
    13873 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13874 bonded heavy atom. 
    13875 
    13876 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13877 bonded heavy atom. 
    13878 
    13879 > isolde ~ignore
    13880 
    13881 > select clear
    13882 
    13883 > isolde add ligand PEE
    13884 
    13885 Deleted the following atoms from residue PEE H11002: H83 
    13886 
    13887 > ui mousemode right "translate selected atoms"
    13888 
    13889 > isolde ignore ~sel
    13890 
    13891 ISOLDE: currently ignoring 5347 residues in model 8.2 
    13892 ISOLDE: currently ignoring 1 residues in model 2 
    13893 ISOLDE: currently ignoring 1 residues in model 1.2 
    13894 
    13895 > isolde ~ignore
    13896 
    13897 > select up
    13898 
    13899 133 atoms, 132 bonds, 1 residue, 1 model selected 
    13900 
    13901 > select clear
    13902 
    13903 > show #!6 models
    13904 
    13905 > hide #!6 models
    13906 
    13907 > isolde add ligand PEE
    13908 
    13909 Deleted the following atoms from residue PEE M704: H83 
    13910 
    13911 > ui mousemode right "translate selected atoms"
    13912 
    13913 > isolde ignore ~sel
    13914 
    13915 ISOLDE: currently ignoring 5348 residues in model 8.2 
    13916 ISOLDE: currently ignoring 1 residues in model 2 
    13917 ISOLDE: currently ignoring 1 residues in model 1.2 
    13918 
    13919 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13920 bonded heavy atom. 
    13921 
    13922 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13923 bonded heavy atom. 
    13924 
    13925 > isolde ~ignore
    13926 
    13927 Chain ak, residue 67 specifies more than one residue! The simulation can still
    13928 run, but this will probably cause problems later if not rectified by
    13929 renumbering. 
    13930 
    13931 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13932 bonded heavy atom. 
    13933 
    13934 > select #8
    13935 
    13936 109253 atoms, 111453 bonds, 14 pseudobonds, 5349 residues, 22 models selected 
    13937 
    13938 > close #6
    13939 
    13940 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    13941 
    13942 > volume subtract #8.1.1.1 #5 new t
    13943 
    13944 Expected a keyword 
    13945 
    13946 > volume subtract #8.1.1.1 #5 inPlace true
    13947 
    13948 Can't modify volume in place: class1b_26A.mrc 
    13949 
    13950 > volume subtract #8.1.1.1 #5 inPlace false
    13951 
    13952 > close #5
    13953 
    13954 > select clear
    13955 
    13956 > save working.cxs
    13957 
    13958 Taking snapshot of stepper: working_2.pdb 
    13959 
    13960 > isolde add ligand LMT
    13961 
    13962 > hide #!6 models
    13963 
    13964 > ui mousemode right "translate selected atoms"
    13965 
    13966 > isolde add ligand LMT
    13967 
    13968 > ui mousemode right "rotate selected models"
    13969 
    13970 > ui mousemode right "translate selected atoms"
    13971 
    13972 > isolde add ligand LMT
    13973 
    13974 > ui mousemode right "translate selected atoms"
    13975 
    13976 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13977 bonded heavy atom. 
    13978 
    13979 > isolde add ligand LMT
    13980 
    13981 > ui mousemode right "translate selected atoms"
    13982 
    13983 > ui mousemode right "translate selected atoms"
    13984 
    13985 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13986 bonded heavy atom. 
    13987 
    13988 > show #!6 models
    13989 
    13990 > isolde add ligand LMT
    13991 
    13992 > ui mousemode right "translate selected atoms"
    13993 
    13994 > hide #!6 models
    13995 
    13996 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13997 bonded heavy atom. 
    13998 
    13999 > select clear
    14000 
    14001 > show #!6 models
    14002 
    14003 > isolde add ligand LMT
    14004 
    14005 > ui mousemode right "translate selected atoms"
    14006 
    14007 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14008 bonded heavy atom. 
    14009 
    14010 > close #6
    14011 
    14012 > select #8
    14013 
    14014 109739 atoms, 111945 bonds, 14 pseudobonds, 5355 residues, 22 models selected 
    14015 
    14016 > select clear
    14017 
    14018 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14019 
    14020 > volume subtract #8.1.1.1 #5 inPlace false
    14021 
    14022 > close #5
    14023 
    14024 > select ~BCL
    14025 
    14026 Expected an objects specifier or a keyword 
    14027 
    14028 > select :BCL
    14029 
    14030 11900 atoms, 12580 bonds, 85 residues, 1 model selected 
    14031 
    14032 > select down
    14033 
    14034 2 atoms, 1 bond, 1 residue, 1 model selected 
    14035 
    14036 > select up
    14037 
    14038 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14039 
    14040 > select /AG:10-40@CA
    14041 
    14042 31 atoms, 31 residues, 1 model selected 
    14043 
    14044 > select /AH:10-40@CA
    14045 
    14046 31 atoms, 31 residues, 1 model selected 
    14047 
    14048 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14049 run, but this will probably cause problems later if not rectified by
    14050 renumbering. 
    14051 
    14052 Chain BG, residue 60 specifies more than one residue! The simulation can still
    14053 run, but this will probably cause problems later if not rectified by
    14054 renumbering. 
    14055 
    14056 Chain BH, residue 60 specifies more than one residue! The simulation can still
    14057 run, but this will probably cause problems later if not rectified by
    14058 renumbering. 
    14059 
    14060 > isolde add ligand LMT
    14061 
    14062 > ui mousemode right "translate selected atoms"
    14063 
    14064 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14065 run, but this will probably cause problems later if not rectified by
    14066 renumbering. 
    14067 
    14068 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14069 bonded heavy atom. 
    14070 
    14071 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14072 bonded heavy atom. 
    14073 
    14074 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14075 bonded heavy atom. 
    14076 
    14077 > ui mousemode right "translate selected atoms"
    14078 
    14079 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14080 run, but this will probably cause problems later if not rectified by
    14081 renumbering. 
    14082 
    14083 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14084 bonded heavy atom. 
    14085 
    14086 > select /AJ:10-40@CA
    14087 
    14088 31 atoms, 31 residues, 1 model selected 
    14089 
    14090 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14091 run, but this will probably cause problems later if not rectified by
    14092 renumbering. 
    14093 
    14094 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14095 run, but this will probably cause problems later if not rectified by
    14096 renumbering. 
    14097 
    14098 > select /AK:10-40@CA
    14099 
    14100 31 atoms, 31 residues, 1 model selected 
    14101 
    14102 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14103 run, but this will probably cause problems later if not rectified by
    14104 renumbering. 
    14105 
    14106 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14107 run, but this will probably cause problems later if not rectified by
    14108 renumbering. 
    14109 
    14110 Chain BK, residue 60 specifies more than one residue! The simulation can still
    14111 run, but this will probably cause problems later if not rectified by
    14112 renumbering. 
    14113 
    14114 > select /AM:10-40@CA
    14115 
    14116 31 atoms, 31 residues, 1 model selected 
    14117 
    14118 Chain BL, residue 60 specifies more than one residue! The simulation can still
    14119 run, but this will probably cause problems later if not rectified by
    14120 renumbering. 
    14121 
    14122 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14123 run, but this will probably cause problems later if not rectified by
    14124 renumbering. 
    14125 
    14126 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14127 run, but this will probably cause problems later if not rectified by
    14128 renumbering. 
    14129 
    14130 > select clear
    14131 
    14132 > select /AN:10-40@CA
    14133 
    14134 31 atoms, 31 residues, 1 model selected 
    14135 
    14136 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14137 run, but this will probably cause problems later if not rectified by
    14138 renumbering. 
    14139 
    14140 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14141 run, but this will probably cause problems later if not rectified by
    14142 renumbering. 
    14143 
    14144 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14145 run, but this will probably cause problems later if not rectified by
    14146 renumbering. 
    14147 
    14148 > select /AP:10-40@CA
    14149 
    14150 31 atoms, 31 residues, 1 model selected 
    14151 
    14152 Chain BO, residue 60 specifies more than one residue! The simulation can still
    14153 run, but this will probably cause problems later if not rectified by
    14154 renumbering. 
    14155 
    14156 Chain BP, residue 60 specifies more than one residue! The simulation can still
    14157 run, but this will probably cause problems later if not rectified by
    14158 renumbering. 
    14159 
    14160 > select /AQ:10-40@CA
    14161 
    14162 31 atoms, 31 residues, 1 model selected 
    14163 
    14164 > select up
    14165 
    14166 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14167 
    14168 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    14169 run, but this will probably cause problems later if not rectified by
    14170 renumbering. 
    14171 
    14172 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    14173 run, but this will probably cause problems later if not rectified by
    14174 renumbering. 
    14175 
    14176 > select clear
    14177 
    14178 > select /AS:10-40@CA
    14179 
    14180 31 atoms, 31 residues, 1 model selected 
    14181 
    14182 > select up
    14183 
    14184 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14185 
    14186 Chain BS, residue 60 specifies more than one residue! The simulation can still
    14187 run, but this will probably cause problems later if not rectified by
    14188 renumbering. 
    14189 
    14190 > select clear
    14191 
    14192 > select /AT:10-40@CA
    14193 
    14194 31 atoms, 31 residues, 1 model selected 
    14195 
    14196 > select up
    14197 
    14198 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14199 
    14200 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14201 run, but this will probably cause problems later if not rectified by
    14202 renumbering. 
    14203 
    14204 Chain BS, residue 60 specifies more than one residue! The simulation can still
    14205 run, but this will probably cause problems later if not rectified by
    14206 renumbering. 
    14207 
    14208 Chain BT, residue 60 specifies more than one residue! The simulation can still
    14209 run, but this will probably cause problems later if not rectified by
    14210 renumbering. 
    14211 
    14212 > select clear
    14213 
    14214 > select /AV:10-40@CA
    14215 
    14216 31 atoms, 31 residues, 1 model selected 
    14217 
    14218 > hide #!6 models
    14219 
    14220 Chain BU, residue 60 specifies more than one residue! The simulation can still
    14221 run, but this will probably cause problems later if not rectified by
    14222 renumbering. 
    14223 
    14224 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14225 run, but this will probably cause problems later if not rectified by
    14226 renumbering. 
    14227 
    14228 > select clear
    14229 
    14230 > show #!6 models
    14231 
    14232 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14233 run, but this will probably cause problems later if not rectified by
    14234 renumbering. 
    14235 
    14236 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14237 run, but this will probably cause problems later if not rectified by
    14238 renumbering. 
    14239 
    14240 > select /AW:10-40@CA
    14241 
    14242 31 atoms, 31 residues, 1 model selected 
    14243 
    14244 > select ~protein
    14245 
    14246 31499 atoms, 32362 bonds, 14 pseudobonds, 291 residues, 39 models selected 
    14247 
    14248 > select clear
    14249 
    14250 > select up
    14251 
    14252 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14253 
    14254 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14255 run, but this will probably cause problems later if not rectified by
    14256 renumbering. 
    14257 
    14258 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14259 run, but this will probably cause problems later if not rectified by
    14260 renumbering. 
    14261 
    14262 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14263 run, but this will probably cause problems later if not rectified by
    14264 renumbering. 
    14265 
    14266 > select clear
    14267 
    14268 > select /AA:10-40@CA
    14269 
    14270 31 atoms, 31 residues, 1 model selected 
    14271 
    14272 Chain BA, residue 60 specifies more than one residue! The simulation can still
    14273 run, but this will probably cause problems later if not rectified by
    14274 renumbering. 
    14275 
    14276 Chain BB, residue 60 specifies more than one residue! The simulation can still
    14277 run, but this will probably cause problems later if not rectified by
    14278 renumbering. 
    14279 
    14280 Chain BX, residue 60 specifies more than one residue! The simulation can still
    14281 run, but this will probably cause problems later if not rectified by
    14282 renumbering. 
    14283 
    14284 > select /AD:10-40@CA
    14285 
    14286 31 atoms, 31 residues, 1 model selected 
    14287 
    14288 Chain BC, residue 60 specifies more than one residue! The simulation can still
    14289 run, but this will probably cause problems later if not rectified by
    14290 renumbering. 
    14291 
    14292 Chain BD, residue 60 specifies more than one residue! The simulation can still
    14293 run, but this will probably cause problems later if not rectified by
    14294 renumbering. 
    14295 
    14296 > select /AE:10-40@CA
    14297 
    14298 31 atoms, 31 residues, 1 model selected 
    14299 
    14300 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14301 run, but this will probably cause problems later if not rectified by
    14302 renumbering. 
    14303 
    14304 Chain BE, residue 60 specifies more than one residue! The simulation can still
    14305 run, but this will probably cause problems later if not rectified by
    14306 renumbering. 
    14307 
    14308 > isolde add ligand LMT
    14309 
    14310 > ui mousemode right "translate selected atoms"
    14311 
    14312 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14313 run, but this will probably cause problems later if not rectified by
    14314 renumbering. 
    14315 
    14316 > isolde ignore ~se;
    14317 
    14318 Expected a residues specifier or a keyword 
    14319 
    14320 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14321 run, but this will probably cause problems later if not rectified by
    14322 renumbering. 
    14323 
    14324 > isolde ignore ~sel
    14325 
    14326 ISOLDE: currently ignoring 5370 residues in model 8.2 
    14327 ISOLDE: currently ignoring 1 residues in model 2 
    14328 ISOLDE: currently ignoring 1 residues in model 1.2 
    14329 
    14330 > isolde ~ignore
    14331 
    14332 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14333 run, but this will probably cause problems later if not rectified by
    14334 renumbering. 
    14335 
    14336 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14337 run, but this will probably cause problems later if not rectified by
    14338 renumbering. 
    14339 
    14340 Chain BG, residue 60 specifies more than one residue! The simulation can still
    14341 run, but this will probably cause problems later if not rectified by
    14342 renumbering. 
    14343 
    14344 > select clear
    14345 
    14346 > select clear
    14347 
    14348 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14349 run, but this will probably cause problems later if not rectified by
    14350 renumbering. 
    14351 
    14352 Chain BG, residue 60 specifies more than one residue! The simulation can still
    14353 run, but this will probably cause problems later if not rectified by
    14354 renumbering. 
    14355 
    14356 > save working.cxs
    14357 
    14358 Taking snapshot of stepper: working_2.pdb 
    14359 
    14360 > select ~protein
    14361 
    14362 32000 atoms, 32888 bonds, 14 pseudobonds, 295 residues, 39 models selected 
    14363 
    14364 > select clear
    14365 
    14366 > hide #!6 models
    14367 
    14368 > hide #!8.1 models
    14369 
    14370 > hide protein
    14371 
    14372 > ~cartoon
    14373 
    14374 > show ~HC
    14375 
    14376 > show #!8.1 models
    14377 
    14378 > cartoon
    14379 
    14380 > select clear
    14381 
    14382 > close #6
    14383 
    14384 > select #8
    14385 
    14386 111861 atoms, 114181 bonds, 14 pseudobonds, 5371 residues, 22 models selected 
    14387 
    14388 > select clear
    14389 
    14390 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14391 
    14392 > volume subtract #8.1.1.1 #5 inPlace false
    14393 
    14394 > close #5
    14395 
    14396 > select clear
    14397 
    14398 > select clear
    14399 
    14400 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14401 run, but this will probably cause problems later if not rectified by
    14402 renumbering. 
    14403 
    14404 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14405 run, but this will probably cause problems later if not rectified by
    14406 renumbering. 
    14407 
    14408 > isolde add ligand LMT
    14409 
    14410 > ui mousemode right "translate selected atoms"
    14411 
    14412 > isolde ignore ~sel
    14413 
    14414 ISOLDE: currently ignoring 5371 residues in model 8.2 
    14415 ISOLDE: currently ignoring 1 residues in model 2 
    14416 ISOLDE: currently ignoring 1 residues in model 1.2 
    14417 Traceback (most recent call last): 
    14418 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14419 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    14420 self.start_sim() 
    14421 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14422 packages/chimerax/isolde/isolde.py", line 2727, in start_sim 
    14423 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    14424 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14425 packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__ 
    14426 self._prepare_mdff_managers() 
    14427 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14428 packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    14429 _prepare_mdff_managers 
    14430 focus = False) 
    14431 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14432 packages/chimerax/clipper/symmetry.py", line 982, in
    14433 isolate_and_cover_selection 
    14434 extra_padding=extra_padding) 
    14435 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14436 packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms 
    14437 zm.set_symmetry_map(atoms, transforms, transform_indices) 
    14438 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14439 packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map 
    14440 self.structure = self._unique_structure(atoms) 
    14441 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14442 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    14443 _unique_structure 
    14444 raise TypeError('All atoms for zone mask must be from a single model!') 
    14445 TypeError: All atoms for zone mask must be from a single model! 
    14446  
    14447 TypeError: All atoms for zone mask must be from a single model! 
    14448  
    14449 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14450 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    14451 _unique_structure 
    14452 raise TypeError('All atoms for zone mask must be from a single model!') 
    14453  
    14454 See log for complete Python traceback. 
    14455  
    14456 
    14457 > isolde ~ignore
    14458 
    14459 > show ~HC
    14460 
    14461 > color bychain
    14462 
    14463 > color byhetero
    14464 
    14465 > cartoon
    14466 
    14467 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14468 run, but this will probably cause problems later if not rectified by
    14469 renumbering. 
    14470 
    14471 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14472 run, but this will probably cause problems later if not rectified by
    14473 renumbering. 
    14474 
    14475 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14476 run, but this will probably cause problems later if not rectified by
    14477 renumbering. 
    14478 
    14479 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14480 bonded heavy atom. 
    14481 
    14482 > isolde add ligand LMT
    14483 
    14484 > ui mousemode right "translate selected atoms"
    14485 
    14486 > isolde ignore ~sel
    14487 
    14488 ISOLDE: currently ignoring 5372 residues in model 8.2 
    14489 ISOLDE: currently ignoring 1 residues in model 2 
    14490 ISOLDE: currently ignoring 1 residues in model 1.2 
    14491 
    14492 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14493 bonded heavy atom. 
    14494 
    14495 > isolde ~ignore
    14496 
    14497 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14498 run, but this will probably cause problems later if not rectified by
    14499 renumbering. 
    14500 
    14501 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14502 run, but this will probably cause problems later if not rectified by
    14503 renumbering. 
    14504 
    14505 > isolde ignore sel
    14506 
    14507 ISOLDE: currently ignoring 1 residues in model 8.2 
    14508 
    14509 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14510 run, but this will probably cause problems later if not rectified by
    14511 renumbering. 
    14512 
    14513 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14514 run, but this will probably cause problems later if not rectified by
    14515 renumbering. 
    14516 
    14517 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14518 run, but this will probably cause problems later if not rectified by
    14519 renumbering. 
    14520 
    14521 > isolde ~ignore
    14522 
    14523 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14524 run, but this will probably cause problems later if not rectified by
    14525 renumbering. 
    14526 
    14527 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14528 run, but this will probably cause problems later if not rectified by
    14529 renumbering. 
    14530 
    14531 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14532 run, but this will probably cause problems later if not rectified by
    14533 renumbering. 
    14534 
    14535 > select :LMT
    14536 
    14537 9072 atoms, 9184 bonds, 112 residues, 1 model selected 
    14538 
    14539 > isolde add ligand LMT
    14540 
    14541 > ui mousemode right "translate selected atoms"
    14542 
    14543 > isolde ignore ~sel
    14544 
    14545 ISOLDE: currently ignoring 5373 residues in model 8.2 
    14546 ISOLDE: currently ignoring 1 residues in model 2 
    14547 ISOLDE: currently ignoring 1 residues in model 1.2 
    14548 
    14549 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14550 bonded heavy atom. 
    14551 
    14552 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14553 bonded heavy atom. 
    14554 
    14555 > isolde ~ignore
    14556 
    14557 > isolde ignore sel
    14558 
    14559 ISOLDE: currently ignoring 1 residues in model 8.2 
    14560 
    14561 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14562 run, but this will probably cause problems later if not rectified by
    14563 renumbering. 
    14564 
    14565 Chain BT, residue 60 specifies more than one residue! The simulation can still
    14566 run, but this will probably cause problems later if not rectified by
    14567 renumbering. 
    14568 
    14569 > isolde ~ignore
    14570 
    14571 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14572 run, but this will probably cause problems later if not rectified by
    14573 renumbering. 
    14574 
    14575 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14576 bonded heavy atom. 
    14577 
    14578 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14579 bonded heavy atom. 
    14580 
    14581 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14582 bonded heavy atom. 
    14583 
    14584 > isolde add ligand LMT
    14585 
    14586 > ui mousemode right "translate selected atoms"
    14587 
    14588 > isolde ~ignore
    14589 
    14590 > isolde ignore ~sel
    14591 
    14592 ISOLDE: currently ignoring 5374 residues in model 8.2 
    14593 ISOLDE: currently ignoring 1 residues in model 2 
    14594 ISOLDE: currently ignoring 1 residues in model 1.2 
    14595 
    14596 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14597 bonded heavy atom. 
    14598 
    14599 > isolde ~ignore
    14600 
    14601 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14602 run, but this will probably cause problems later if not rectified by
    14603 renumbering. 
    14604 
    14605 > select ~protein
    14606 
    14607 32324 atoms, 33216 bonds, 14 pseudobonds, 299 residues, 39 models selected 
    14608 
    14609 > select clear
    14610 
    14611 > isolde add ligand LMT
    14612 
    14613 > ui mousemode right "translate selected atoms"
    14614 
    14615 > isolde ignore ~sel
    14616 
    14617 ISOLDE: currently ignoring 5375 residues in model 8.2 
    14618 ISOLDE: currently ignoring 1 residues in model 2 
    14619 ISOLDE: currently ignoring 1 residues in model 1.2 
    14620 
    14621 > isolde ~ignore
    14622 
    14623 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    14624 run, but this will probably cause problems later if not rectified by
    14625 renumbering. 
    14626 
    14627 > select clear
    14628 
    14629 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14630 run, but this will probably cause problems later if not rectified by
    14631 renumbering. 
    14632 
    14633 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14634 run, but this will probably cause problems later if not rectified by
    14635 renumbering. 
    14636 
    14637 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14638 run, but this will probably cause problems later if not rectified by
    14639 renumbering. 
    14640 
    14641 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14642 bonded heavy atom. 
    14643 
    14644 > isolde add ligand LMT
    14645 
    14646 > ui mousemode right "translate selected atoms"
    14647 
    14648 > isolde ignore ~sel
    14649 
    14650 ISOLDE: currently ignoring 5376 residues in model 8.2 
    14651 ISOLDE: currently ignoring 1 residues in model 2 
    14652 ISOLDE: currently ignoring 1 residues in model 1.2 
    14653 
    14654 > isolde ~ignore
    14655 
    14656 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14657 run, but this will probably cause problems later if not rectified by
    14658 renumbering. 
    14659 
    14660 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14661 run, but this will probably cause problems later if not rectified by
    14662 renumbering. 
    14663 
    14664 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14665 run, but this will probably cause problems later if not rectified by
    14666 renumbering. 
    14667 
    14668 Chain BL, residue 60 specifies more than one residue! The simulation can still
    14669 run, but this will probably cause problems later if not rectified by
    14670 renumbering. 
    14671 
    14672 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14673 run, but this will probably cause problems later if not rectified by
    14674 renumbering. 
    14675 
    14676 > isolde add ligand LMT
    14677 
    14678 > ui mousemode right "translate selected atoms"
    14679 
    14680 > isolde ignore ~sel
    14681 
    14682 ISOLDE: currently ignoring 5377 residues in model 8.2 
    14683 ISOLDE: currently ignoring 1 residues in model 2 
    14684 ISOLDE: currently ignoring 1 residues in model 1.2 
    14685 
    14686 > isolde ~ignore
    14687 
    14688 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14689 run, but this will probably cause problems later if not rectified by
    14690 renumbering. 
    14691 
    14692 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14693 run, but this will probably cause problems later if not rectified by
    14694 renumbering. 
    14695 
    14696 > isolde add ligand LMT
    14697 
    14698 > ui mousemode right "translate selected atoms"
    14699 
    14700 > isolde ignore ~sel
    14701 
    14702 ISOLDE: currently ignoring 5378 residues in model 8.2 
    14703 ISOLDE: currently ignoring 1 residues in model 2 
    14704 ISOLDE: currently ignoring 1 residues in model 1.2 
    14705 
    14706 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14707 bonded heavy atom. 
    14708 
    14709 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14710 bonded heavy atom. 
    14711 
    14712 > isolde ~ignore
    14713 
    14714 > select up
    14715 
    14716 81 atoms, 82 bonds, 1 residue, 1 model selected 
    14717 
    14718 > isolde ignore sel
    14719 
    14720 ISOLDE: currently ignoring 1 residues in model 8.2 
    14721 
    14722 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14723 run, but this will probably cause problems later if not rectified by
    14724 renumbering. 
    14725 
    14726 > isolde ~ignore
    14727 
    14728 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14729 run, but this will probably cause problems later if not rectified by
    14730 renumbering. 
    14731 
    14732 Chain BK, residue 60 specifies more than one residue! The simulation can still
    14733 run, but this will probably cause problems later if not rectified by
    14734 renumbering. 
    14735 
    14736 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14737 bonded heavy atom. 
    14738 
    14739 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14740 bonded heavy atom. 
    14741 
    14742 > isolde ~ignore
    14743 
    14744 > select up
    14745 
    14746 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14747 
    14748 > isolde ignore ~sel
    14749 
    14750 ISOLDE: currently ignoring 5378 residues in model 8.2 
    14751 ISOLDE: currently ignoring 1 residues in model 2 
    14752 ISOLDE: currently ignoring 1 residues in model 1.2 
    14753 
    14754 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14755 bonded heavy atom. 
    14756 
    14757 > isolde ~ignore
    14758 
    14759 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14760 run, but this will probably cause problems later if not rectified by
    14761 renumbering. 
    14762 
    14763 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14764 run, but this will probably cause problems later if not rectified by
    14765 renumbering. 
    14766 
    14767 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14768 run, but this will probably cause problems later if not rectified by
    14769 renumbering. 
    14770 
    14771 > select clear
    14772 
    14773 > isolde add ligand LMT
    14774 
    14775 > ui mousemode right "translate selected atoms"
    14776 
    14777 > isolde ignore ~sel
    14778 
    14779 ISOLDE: currently ignoring 5379 residues in model 8.2 
    14780 ISOLDE: currently ignoring 1 residues in model 2 
    14781 ISOLDE: currently ignoring 1 residues in model 1.2 
    14782 
    14783 > isolde ~ignore
    14784 
    14785 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14786 run, but this will probably cause problems later if not rectified by
    14787 renumbering. 
    14788 
    14789 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14790 run, but this will probably cause problems later if not rectified by
    14791 renumbering. 
    14792 
    14793 > save working.cxs
    14794 
    14795 Taking snapshot of stepper: working_2.pdb 
    14796 
    14797 > isolde add ligand LMT
    14798 
    14799 > ui mousemode right "translate selected atoms"
    14800 
    14801 > isolde ignore ~sel
    14802 
    14803 ISOLDE: currently ignoring 5380 residues in model 8.2 
    14804 ISOLDE: currently ignoring 1 residues in model 2 
    14805 ISOLDE: currently ignoring 1 residues in model 1.2 
    14806 
    14807 > isolde ~ignore
    14808 
    14809 > isolde ignore sel
    14810 
    14811 ISOLDE: currently ignoring 1 residues in model 8.2 
    14812 
    14813 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14814 run, but this will probably cause problems later if not rectified by
    14815 renumbering. 
    14816 
    14817 Chain BH, residue 60 specifies more than one residue! The simulation can still
    14818 run, but this will probably cause problems later if not rectified by
    14819 renumbering. 
    14820 
    14821 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14822 run, but this will probably cause problems later if not rectified by
    14823 renumbering. 
    14824 
    14825 > isolde ~ignore
    14826 
    14827 Chain BH, residue 60 specifies more than one residue! The simulation can still
    14828 run, but this will probably cause problems later if not rectified by
    14829 renumbering. 
    14830 
    14831 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14832 run, but this will probably cause problems later if not rectified by
    14833 renumbering. 
    14834 
    14835 > isolde add ligand LMT
    14836 
    14837 > ui mousemode right "translate selected atoms"
    14838 
    14839 > isolde ignore ~sel
    14840 
    14841 ISOLDE: currently ignoring 5381 residues in model 8.2 
    14842 ISOLDE: currently ignoring 1 residues in model 2 
    14843 ISOLDE: currently ignoring 1 residues in model 1.2 
    14844 
    14845 > isolde ~ignore
    14846 
    14847 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14848 run, but this will probably cause problems later if not rectified by
    14849 renumbering. 
    14850 
    14851 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14852 run, but this will probably cause problems later if not rectified by
    14853 renumbering. 
    14854 
    14855 > isolde add ligand LMT
    14856 
    14857 > ui mousemode right "rotate selected models"
    14858 
    14859 > ui mousemode right "translate selected atoms"
    14860 
    14861 > isolde ignore ~sel
    14862 
    14863 ISOLDE: currently ignoring 5382 residues in model 8.2 
    14864 ISOLDE: currently ignoring 1 residues in model 2 
    14865 ISOLDE: currently ignoring 1 residues in model 1.2 
    14866 
    14867 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14868 bonded heavy atom. 
    14869 
    14870 > isolde ~ignore
    14871 
    14872 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14873 run, but this will probably cause problems later if not rectified by
    14874 renumbering. 
    14875 
    14876 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14877 bonded heavy atom. 
    14878 
    14879 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14880 bonded heavy atom. 
    14881 
    14882 > select up
    14883 
    14884 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14885 
    14886 > isolde ignore ~sel
    14887 
    14888 ISOLDE: currently ignoring 5382 residues in model 8.2 
    14889 ISOLDE: currently ignoring 1 residues in model 2 
    14890 ISOLDE: currently ignoring 1 residues in model 1.2 
    14891 
    14892 > isolde ignore ~sel
    14893 
    14894 ISOLDE: currently ignoring 5382 residues in model 8.2 
    14895 ISOLDE: currently ignoring 1 residues in model 2 
    14896 ISOLDE: currently ignoring 1 residues in model 1.2 
    14897 
    14898 > isolde add ligand LMT
    14899 
    14900 > ui mousemode right "translate selected atoms"
    14901 
    14902 > isolde ignore ~sel
    14903 
    14904 ISOLDE: currently ignoring 5383 residues in model 8.2 
    14905 ISOLDE: currently ignoring 1 residues in model 2 
    14906 ISOLDE: currently ignoring 1 residues in model 1.2 
    14907 
    14908 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14909 bonded heavy atom. 
    14910 
    14911 > isolde ~ignore
    14912 
    14913 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14914 run, but this will probably cause problems later if not rectified by
    14915 renumbering. 
    14916 
    14917 Chain BC, residue 60 specifies more than one residue! The simulation can still
    14918 run, but this will probably cause problems later if not rectified by
    14919 renumbering. 
    14920 
    14921 Chain BD, residue 60 specifies more than one residue! The simulation can still
    14922 run, but this will probably cause problems later if not rectified by
    14923 renumbering. 
    14924 
    14925 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14926 run, but this will probably cause problems later if not rectified by
    14927 renumbering. 
    14928 
    14929 Chain BC, residue 60 specifies more than one residue! The simulation can still
    14930 run, but this will probably cause problems later if not rectified by
    14931 renumbering. 
    14932 
    14933 Chain BD, residue 60 specifies more than one residue! The simulation can still
    14934 run, but this will probably cause problems later if not rectified by
    14935 renumbering. 
    14936 
    14937 > setattr #8 bonds radius 0.05
    14938 
    14939 Assigning radius attribute to 115247 items 
    14940 
    14941 > setattr #8 bonds radius 0.2
    14942 
    14943 Assigning radius attribute to 115247 items 
    14944 
    14945 > save working.cxs
    14946 
    14947 Taking snapshot of stepper: working_2.pdb 
    14948 
    14949 > close #6
    14950 
    14951 > select #8
    14952 
    14953 112914 atoms, 115247 bonds, 14 pseudobonds, 5384 residues, 22 models selected 
    14954 
    14955 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14956 
    14957 > volume subtract #8.1.1.1 #5
    14958 
    14959 > close #5
    14960 
    14961 > select clear
    14962 
    14963 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    14964 run, but this will probably cause problems later if not rectified by
    14965 renumbering. 
    14966 
    14967 > isolde add ligand LMT
    14968 
    14969 > ui mousemode right "translate selected atoms"
    14970 
    14971 > isolde ignore ~sel
    14972 
    14973 ISOLDE: currently ignoring 5384 residues in model 8.2 
    14974 ISOLDE: currently ignoring 1 residues in model 2 
    14975 ISOLDE: currently ignoring 1 residues in model 1.2 
    14976 
    14977 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14978 bonded heavy atom. 
    14979 
    14980 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14981 bonded heavy atom. 
    14982 
    14983 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14984 bonded heavy atom. 
    14985 
    14986 > isolde ~ignore
    14987 
    14988 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    14989 run, but this will probably cause problems later if not rectified by
    14990 renumbering. 
    14991 
    14992 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14993 bonded heavy atom. 
    14994 
    14995 > select up
    14996 
    14997 81 atoms, 82 bonds, 1 residue, 1 model selected 
    14998 
    14999 > delete sel
    15000 
    15001 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    15002 run, but this will probably cause problems later if not rectified by
    15003 renumbering. 
    15004 
    15005 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    15006 run, but this will probably cause problems later if not rectified by
    15007 renumbering. 
    15008 
    15009 > isolde add ligand PEE
    15010 
    15011 Deleted the following atoms from residue PEE AQ63: H83 
    15012 
    15013 > ui mousemode right "translate selected atoms"
    15014 
    15015 > isolde ignore ~sel
    15016 
    15017 ISOLDE: currently ignoring 5384 residues in model 8.2 
    15018 ISOLDE: currently ignoring 1 residues in model 2 
    15019 ISOLDE: currently ignoring 1 residues in model 1.2 
    15020 
    15021 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15022 bonded heavy atom. 
    15023 
    15024 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15025 bonded heavy atom. 
    15026 
    15027 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15028 bonded heavy atom. 
    15029 
    15030 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15031 bonded heavy atom. 
    15032 
    15033 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15034 bonded heavy atom. 
    15035 
    15036 > isolde ~ignore
    15037 
    15038 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    15039 run, but this will probably cause problems later if not rectified by
    15040 renumbering. 
    15041 
    15042 > save working.cxs
    15043 
    15044 Taking snapshot of stepper: working_2.pdb 
    15045 
    15046 > isolde add ligand LMT
    15047 
    15048 > ui mousemode right "translate selected atoms"
    15049 
    15050 > select ~protein
    15051 
    15052 33267 atoms, 34168 bonds, 14 pseudobonds, 310 residues, 39 models selected 
    15053 
    15054 > select clear
    15055 
    15056 > isolde add ligand P5S
    15057 
    15058 Deleted the following atoms from residue P5S M705: HXT, HO15 
    15059 
    15060 > ui mousemode right "translate selected atoms"
    15061 
    15062 > isolde ignore ~sel
    15063 
    15064 ISOLDE: currently ignoring 5386 residues in model 8.2 
    15065 ISOLDE: currently ignoring 1 residues in model 2 
    15066 ISOLDE: currently ignoring 1 residues in model 1.2 
    15067 
    15068 > hide #!6 models
    15069 
    15070 > select up
    15071 
    15072 135 atoms, 134 bonds, 1 residue, 1 model selected 
    15073 
    15074 > delete sel
    15075 
    15076 > isolde add ligand PSF
    15077 
    15078 Fetching CCD PSF from http://ligand-expo.rcsb.org/reports/P/PSF/PSF.cif 
    15079 Deleted the following atoms from residue PSF M705: HO3, HXT 
    15080 
    15081 > ui mousemode right "translate selected atoms"
    15082 
    15083 > isolde ignore ~sel
    15084 
    15085 ISOLDE: currently ignoring 5386 residues in model 8.2 
    15086 ISOLDE: currently ignoring 1 residues in model 2 
    15087 ISOLDE: currently ignoring 1 residues in model 1.2 
    15088 
    15089 > isolde add ligand PSF
    15090 
    15091 Deleted the following atoms from residue PSF ai68: HO3, HXT 
    15092 
    15093 > isolde ignore ~sel
    15094 
    15095 ISOLDE: currently ignoring 5387 residues in model 8.2 
    15096 ISOLDE: currently ignoring 1 residues in model 2 
    15097 ISOLDE: currently ignoring 1 residues in model 1.2 
    15098 
    15099 > ui mousemode right "translate selected atoms"
    15100 
    15101 > isolde ~ignore
    15102 
    15103 Chain AN, residue 62 specifies more than one residue! The simulation can still
    15104 run, but this will probably cause problems later if not rectified by
    15105 renumbering. 
    15106 
    15107 > select up
    15108 
    15109 62 atoms, 61 bonds, 1 residue, 1 model selected 
    15110 
    15111 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15112 bonded heavy atom. 
    15113 
    15114 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15115 bonded heavy atom. 
    15116 
    15117 > show #!6 models
    15118 
    15119 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15120 run, but this will probably cause problems later if not rectified by
    15121 renumbering. 
    15122 
    15123 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15124 run, but this will probably cause problems later if not rectified by
    15125 renumbering. 
    15126 
    15127 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    15128 run, but this will probably cause problems later if not rectified by
    15129 renumbering. 
    15130 
    15131 > select up
    15132 
    15133 140 atoms, 148 bonds, 1 residue, 1 model selected 
    15134 
    15135 > isolde ignore ~sel
    15136 
    15137 ISOLDE: currently ignoring 5387 residues in model 8.2 
    15138 ISOLDE: currently ignoring 1 residues in model 2 
    15139 ISOLDE: currently ignoring 1 residues in model 1.2 
    15140 
    15141 > isolde ~ignore
    15142 
    15143 > isolde ignore se
    15144 
    15145 Expected a residues specifier or a keyword 
    15146 
    15147 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15148 run, but this will probably cause problems later if not rectified by
    15149 renumbering. 
    15150 
    15151 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15152 run, but this will probably cause problems later if not rectified by
    15153 renumbering. 
    15154 
    15155 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    15156 run, but this will probably cause problems later if not rectified by
    15157 renumbering. 
    15158 
    15159 > select up
    15160 
    15161 140 atoms, 148 bonds, 1 residue, 1 model selected 
    15162 
    15163 > isolde ignore sel
    15164 
    15165 ISOLDE: currently ignoring 1 residues in model 8.2 
    15166 
    15167 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15168 run, but this will probably cause problems later if not rectified by
    15169 renumbering. 
    15170 
    15171 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15172 run, but this will probably cause problems later if not rectified by
    15173 renumbering. 
    15174 
    15175 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    15176 run, but this will probably cause problems later if not rectified by
    15177 renumbering. 
    15178 
    15179 > isolde ~ignore
    15180 
    15181 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15182 run, but this will probably cause problems later if not rectified by
    15183 renumbering. 
    15184 
    15185 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15186 run, but this will probably cause problems later if not rectified by
    15187 renumbering. 
    15188 
    15189 > isolde add ligand LMT
    15190 
    15191 > ui mousemode right "translate selected atoms"
    15192 
    15193 > isolde ignore ~sel
    15194 
    15195 ISOLDE: currently ignoring 5388 residues in model 8.2 
    15196 ISOLDE: currently ignoring 1 residues in model 2 
    15197 ISOLDE: currently ignoring 1 residues in model 1.2 
    15198 
    15199 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15200 bonded heavy atom. 
    15201 
    15202 > isolde ~ignore
    15203 
    15204 > save working.cxs
    15205 
    15206 Taking snapshot of stepper: working_2.pdb 
    15207 
    15208 > select ~protein
    15209 
    15210 33472 atoms, 34372 bonds, 14 pseudobonds, 313 residues, 39 models selected 
    15211 
    15212 > select clear
    15213 
    15214 Chain AN, residue 62 specifies more than one residue! The simulation can still
    15215 run, but this will probably cause problems later if not rectified by
    15216 renumbering. 
    15217 
    15218 Chain AN, residue 62 specifies more than one residue! The simulation can still
    15219 run, but this will probably cause problems later if not rectified by
    15220 renumbering. 
    15221 
    15222 > select clear
    15223 
    15224 Chain AW, residue 62 specifies more than one residue! The simulation can still
    15225 run, but this will probably cause problems later if not rectified by
    15226 renumbering. 
    15227 
    15228 Chain BA, residue 60 specifies more than one residue! The simulation can still
    15229 run, but this will probably cause problems later if not rectified by
    15230 renumbering. 
    15231 
    15232 Chain BX, residue 60 specifies more than one residue! The simulation can still
    15233 run, but this will probably cause problems later if not rectified by
    15234 renumbering. 
    15235 
    15236 > select clear
    15237 
    15238 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15239 run, but this will probably cause problems later if not rectified by
    15240 renumbering. 
    15241 
    15242 > save working.cxs
    15243 
    15244 Taking snapshot of stepper: working_2.pdb 
    15245 
    15246 > save working.cif #8
    15247 
    15248 Not saving entity_poly_seq for non-authoritative sequences 
    15249 
    15250 > select #1
    15251 
    15252 256 atoms, 255 bonds, 1 residue, 8 models selected 
    15253 
    15254 > select #8
    15255 
    15256 113333 atoms, 115665 bonds, 14 pseudobonds, 5389 residues, 22 models selected 
    15257 
    15258 > select clear
    15259 
    15260 > view sel
    15261 
    15262 > select /ak:67&~protein
    15263 
    15264 140 atoms, 148 bonds, 1 residue, 1 model selected 
    15265 
    15266 > view sel
    15267 
    15268 > select clear
    15269 
    15270 > view sel
    15271 
    15272 > select clear
    15273 
    15274 > view sel
    15275 
    15276 > select clear
    15277 
    15278 > view sel
    15279 
    15280 > select clear
    15281 
    15282 > view sel
    15283 
    15284 > select clear
    15285 
    15286 > view sel
    15287 
    15288 > select clear
    15289 
    15290 > view sel
    15291 
    15292 > select clear
    15293 
    15294 > view sel
    15295 
    15296 > select clear
    15297 
    15298 > view sel
    15299 
    15300 > select clear
    15301 
    15302 > view sel
    15303 
    15304 > select clear
    15305 
    15306 > view sel
    15307 
    15308 > view sel
    15309 
    15310 > select clear
    15311 
    15312 > select clear
    15313 
    15314 > select clear
    15315 
    15316 > select clear
    15317 
    15318 > select clear
    15319 
    15320 > select clear
    15321 
    15322 > select clear
    15323 
    15324 > select clear
    15325 
    15326 > select clear
    15327 
    15328 > select clear
    15329 
    15330 > select clear
    15331 
    15332 > select clear
    15333 
    15334 > select clear
    15335 
    15336 > select clear
    15337 
    15338 > select clear
    15339 
    15340 > select clear
    15341 
    15342 > select clear
    15343 
    15344 > select clear
    15345 
    15346 > select clear
    15347 
    15348 > select clear
    15349 
    15350 > select clear
    15351 
    15352 > select clear
    15353 
    15354 > select clear
    15355 
    15356 > save working.cif #8
    15357 
    15358 Not saving entity_poly_seq for non-authoritative sequences 
    15359 
    15360 > select ~H
    15361 
    15362 55527 atoms, 116032 bonds, 14 pseudobonds, 5391 residues, 39 models selected 
    15363 
    15364 > save working_noh.cif #8 selectedOnly true
    15365 
    15366 Not saving entity_poly_seq for non-authoritative sequences 
    15367 
    15368 > select clear
    15369 
    15370 > save working.pdb #8
    15371 
    15372 > view /CG:1
    15373 
    15374 > select /C
    15375 
    15376 4865 atoms, 4968 bonds, 4 pseudobonds, 303 residues, 2 models selected 
    15377 
    15378 > select up
    15379 
    15380 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15381 
    15382 > view /MG:MAN
    15383 
    15384 > select up
    15385 
    15386 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15387 
    15388 > save working.cif #8
    15389 
    15390 Not saving entity_poly_seq for non-authoritative sequences 
    15391 
    15392 > select clear
    15393 
    15394 > hide #!6 models
    15395 
    15396 > select up
    15397 
    15398 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15399 
    15400 > save working.cif #8
    15401 
    15402 Not saving entity_poly_seq for non-authoritative sequences 
    15403 
    15404 > ui mousemode right "translate selected atoms"
    15405 
    15406 > select /C:1010-1020
    15407 
    15408 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15409 
    15410 > delete sel
    15411 
    15412 > select /C:1010-1020
    15413 
    15414 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15415 
    15416 > delete sel
    15417 
    15418 > select /M:20-50
    15419 
    15420 435 atoms, 440 bonds, 31 residues, 1 model selected 
    15421 
    15422 > select /D:20-50
    15423 
    15424 Nothing selected 
    15425 
    15426 > open
    15427 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    15428 
    15429 Summary of feedback from opening
    15430 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif 
    15431 --- 
    15432 warnings | Unknown polymer entity '1' near line 475 
    15433 Unknown polymer entity '2' near line 2593 
    15434 Unknown polymer entity '3' near line 5781 
    15435 Unknown polymer entity '4' near line 26370 
    15436 Unknown polymer entity '5' near line 27136 
    15437 10 messages similar to the above omitted 
    15438 Atom H is not in the residue template for MET /AA:1 
    15439 Atom C1 is not in the residue template for GPC /AA:60 
    15440 Atom H is not in the residue template for MET /AB:1 
    15441 Atom C1 is not in the residue template for GPC /AB:60 
    15442 Atom H is not in the residue template for MET /AC:1 
    15443 Atom C1 is not in the residue template for GPC /AC:60 
    15444 Atom H is not in the residue template for MET /AD:1 
    15445 Atom C1 is not in the residue template for GPC /AD:60 
    15446 Atom H is not in the residue template for MET /AE:1 
    15447 Atom C1 is not in the residue template for GPC /AE:60 
    15448 Atom H is not in the residue template for MET /AF:1 
    15449 Atom C1 is not in the residue template for GPC /AF:60 
    15450 Atom H is not in the residue template for MET /AG:1 
    15451 Atom C1 is not in the residue template for GPC /AG:60 
    15452 Atom H is not in the residue template for MET /AH:1 
    15453 Atom C1 is not in the residue template for GPC /AH:60 
    15454 Atom H is not in the residue template for MET /AI:1 
    15455 Atom C1 is not in the residue template for GPC /AI:60 
    15456 Atom H is not in the residue template for MET /AJ:1 
    15457 Atom C1 is not in the residue template for GPC /AJ:60 
    15458 Atom H is not in the residue template for MET /AK:1 
    15459 Atom C1 is not in the residue template for GPC /AK:60 
    15460 Atom C26 is not in the residue template for PEX /AK:62 
    15461 Atom H is not in the residue template for MET /AL:1 
    15462 Atom C1 is not in the residue template for GPC /AL:60 
    15463 Atom H is not in the residue template for MET /AM:1 
    15464 Atom C1 is not in the residue template for GPC /AM:60 
    15465 Atom H is not in the residue template for MET /AN:1 
    15466 Atom C1 is not in the residue template for GPC /AN:60 
    15467 Atom H is not in the residue template for MET /AO:1 
    15468 Atom C1 is not in the residue template for GPC /AO:60 
    15469 Atom H is not in the residue template for MET /AP:1 
    15470 Atom C1 is not in the residue template for GPC /AP:60 
    15471 Atom H is not in the residue template for MET /AQ:1 
    15472 Atom C1 is not in the residue template for GPC /AQ:60 
    15473 Atom H is not in the residue template for MET /AR:1 
    15474 Atom C1 is not in the residue template for GPC /AR:60 
    15475 Atom H is not in the residue template for MET /AS:1 
    15476 Atom C1 is not in the residue template for GPC /AS:60 
    15477 Atom H is not in the residue template for MET /AT:1 
    15478 Atom C1 is not in the residue template for GPC /AT:60 
    15479 Atom H is not in the residue template for MET /AU:1 
    15480 Atom C1 is not in the residue template for GPC /AU:60 
    15481 Atom H is not in the residue template for MET /AV:1 
    15482 Atom C1 is not in the residue template for GPC /AV:60 
    15483 Atom H is not in the residue template for MET /AW:1 
    15484 Atom C1 is not in the residue template for GPC /AW:60 
    15485 Atom H is not in the residue template for MET /AX:1 
    15486 Atom C1 is not in the residue template for GPC /AX:60 
    15487 Atom H is not in the residue template for GLY /BQ:5 
    15488 Atom H is not in the residue template for GLY /BR:5 
    15489 Atom H is not in the residue template for GLY /BS:5 
    15490 Atom H is not in the residue template for GLY /BT:5 
    15491 Atom H11 is not in the residue template for BPH /L:606 
    15492 Atom H11 is not in the residue template for BPH /M:605 
    15493 Atom C1 is not in the residue template for RCC /M:701 
    15494 Atom HN2 is not in the residue template for ARG /ak:71 
    15495 Atom H is not in the residue template for GLY /C1:32 
    15496 Atom C1 is not in the residue template for GPC /Ba:60 
    15497 Atom C1 is not in the residue template for GPC /Bb:60 
    15498 Atom C1 is not in the residue template for GPC /Bc:60 
    15499 Atom C1 is not in the residue template for GPC /Bd:60 
    15500 Atom C1 is not in the residue template for GPC /Be:60 
    15501 11 messages similar to the above omitted 
    15502 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    15503  
    15504 Chain information for model1a.cif #5 
    15505 --- 
    15506 Chain | Description 
    15507 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ? 
    15508 AC AD | ? 
    15509 BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
    15510 bm bo bp | ? 
    15511 BB BD BE BI BQ BR BS BT BV BW bn | ? 
    15512 C | ? 
    15513 C1 | ? 
    15514 H1 | ? 
    15515 H2 | ? 
    15516 L | ? 
    15517 M | ? 
    15518 aa | ? 
    15519 ab ad ae af ag ah ai aj al am an ao ap | ? 
    15520 ac | ? 
    15521 ak | ? 
    15522  
    15523 
    15524 > cartoon #5
    15525 
    15526 > hide #5
    15527 
    15528 > select /M:20-50
    15529 
    15530 736 atoms, 744 bonds, 2 pseudobonds, 52 residues, 3 models selected 
    15531 
    15532 > view /C:1010
    15533 
    15534 No objects specified. 
    15535 
    15536 > view /C:1001
    15537 
    15538 > dssp
    15539 
    15540 > select :BCL
    15541 
    15542 25620 atoms, 26748 bonds, 336 pseudobonds, 183 residues, 3 models selected 
    15543 
    15544 > close #5
    15545 
    15546 > clipper spotlight radius 13.00
    15547 
    15548 > clipper spotlight radius 14.00
    15549 
    15550 > clipper spotlight radius 15.00
    15551 
    15552 > clipper spotlight radius 16.00
    15553 
    15554 > clipper spotlight radius 17.00
    15555 
    15556 > select /ak
    15557 
    15558 1347 atoms, 1369 bonds, 73 residues, 2 models selected 
    15559 
    15560 > view /C:117
    15561 
    15562 > select #8&~protein
    15563 
    15564 33103 atoms, 34005 bonds, 14 pseudobonds, 311 residues, 22 models selected 
    15565 
    15566 > select LMG
    15567 
    15568 Expected an objects specifier or a keyword 
    15569 
    15570 > select :LMG
    15571 
    15572 141 atoms, 141 bonds, 1 residue, 1 model selected 
    15573 
    15574 > view :LMG
    15575 
    15576 > select :LMX
    15577 
    15578 129 atoms, 129 bonds, 1 residue, 1 model selected 
    15579 
    15580 > view sel
    15581 
    15582 > select clear
    15583 
    15584 > save working.cxs
    15585 
    15586 Taking snapshot of stepper: working_2.pdb 
    15587 opened ChimeraX session 
    15588 
    15589 > show #!6 models
    15590 
    15591 > volume #6 level 0.03545
    15592 
    15593 > ui tool show Shell
    15594 
    15595 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    15596 UserWarning: IPython History requires SQLite, your history will not be saved 
    15597 warn("IPython History requires SQLite, your history will not be saved") 
    15598 
    15599 > isolde start
    15600 
    15601 > set selectionWidth 4
    15602 
    15603 Done loading forcefield 
    15604 
    15605 > select #6
    15606 
    15607 4 models selected 
    15608 
    15609 > select :HOH
    15610 
    15611 15 atoms, 10 bonds, 5 residues, 1 model selected 
    15612 
    15613 > hide #!6 models
    15614 
    15615 > select :HOH
    15616 
    15617 3309 atoms, 2206 bonds, 1103 residues, 2 models selected 
    15618 
    15619 > delete sel
    15620 
    15621 > select :HOH
    15622 
    15623 2505 atoms, 1670 bonds, 835 residues, 1 model selected 
    15624 
    15625 > show #!6 models
    15626 
    15627 > hide #!6 models
    15628 
    15629 > delete :HOH
    15630 
    15631 > select :HOH
    15632 
    15633 498 atoms, 332 bonds, 166 residues, 1 model selected 
    15634 
    15635 > show #!6 models
    15636 
    15637 > hide #!6 models
    15638 
    15639 > select :HOH
    15640 
    15641 498 atoms, 332 bonds, 166 residues, 1 model selected 
    15642 
    15643 > show #!6 models
    15644 
    15645 > delete :HOH
    15646 
    15647 > select :HOH
    15648 
    15649 1497 atoms, 998 bonds, 499 residues, 1 model selected 
    15650 
    15651 > hide #!6 models
    15652 
    15653 > show #!6 models
    15654 
    15655 > hide #!6 models
    15656 
    15657 > show #!6 models
    15658 
    15659 > select :HOH
    15660 
    15661 1926 atoms, 1284 bonds, 642 residues, 1 model selected 
    15662 
    15663 > hide #!6 models
    15664 
    15665 Loading residue template for LMG from internal database 
    15666 Loading residue template for PEE from internal database 
    15667 Loading residue template for PEX from internal database 
    15668 Loading residue template for PSF from internal database 
    15669 
    15670 > select :HOH
    15671 
    15672 1926 atoms, 1284 bonds, 642 residues, 1 model selected 
    15673 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15674 more memory-efficient implementation. 
    15675 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15676 more memory-efficient implementation. 
    15677 
    15678 > select clear
    15679 
    15680 > select clear
    15681 
    15682 > select clear
    15683 
    15684 > select :HOH
    15685 
    15686 1926 atoms, 1284 bonds, 642 residues, 1 model selected 
    15687 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15688 more memory-efficient implementation. 
    15689 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15690 more memory-efficient implementation. 
    15691 
    15692 > select clear
    15693 
    15694 > select #8.1.1.1
    15695 
    15696 3 models selected 
    15697 
    15698 > select clear
    15699 
    15700 > select :HOH
    15701 
    15702 2085 atoms, 1390 bonds, 695 residues, 1 model selected 
    15703 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15704 more memory-efficient implementation. 
    15705 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15706 more memory-efficient implementation. 
    15707 
    15708 > select clear
    15709 
    15710 > close #6
    15711 
    15712 > select #1
    15713 
    15714 256 atoms, 255 bonds, 1 residue, 8 models selected 
    15715 Traceback (most recent call last): 
    15716 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15717 packages/chimerax/isolde/isolde.py", line 2580, in _xtal_mask_to_selection 
    15718 self._xtal_mask_to_atoms(sel, focus) 
    15719 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15720 packages/chimerax/isolde/isolde.py", line 2589, in _xtal_mask_to_atoms 
    15721 atoms, 0, context, cutoff, focus=focus) 
    15722 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15723 packages/chimerax/clipper/symmetry.py", line 982, in
    15724 isolate_and_cover_selection 
    15725 extra_padding=extra_padding) 
    15726 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15727 packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms 
    15728 zm.set_symmetry_map(atoms, transforms, transform_indices) 
    15729 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15730 packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map 
    15731 self.structure = self._unique_structure(atoms) 
    15732 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15733 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    15734 _unique_structure 
    15735 raise TypeError('All atoms for zone mask must be from a single model!') 
    15736 TypeError: All atoms for zone mask must be from a single model! 
    15737  
    15738 TypeError: All atoms for zone mask must be from a single model! 
    15739  
    15740 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15741 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    15742 _unique_structure 
    15743 raise TypeError('All atoms for zone mask must be from a single model!') 
    15744  
    15745 See log for complete Python traceback. 
    15746  
    15747 
    15748 > select #8
    15749 
    15750 115418 atoms, 117055 bonds, 14 pseudobonds, 6084 residues, 22 models selected 
    15751 
    15752 > select clear
    15753 
    15754 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    15755 
    15756 > volume subtract #8.1.1.1 #5
    15757 
    15758 > close #5
    15759 
    15760 > select clear
    15761 
    15762 > select clear
    15763 
    15764 > select :HOH
    15765 
    15766 2085 atoms, 1390 bonds, 695 residues, 1 model selected 
    15767 
    15768 > select clear
    15769 
    15770 > hide #!6 models
    15771 
    15772 > show #!6 models
    15773 
    15774 > select clear
    15775 
    15776 > select #6
    15777 
    15778 4 models selected 
    15779 
    15780 > select :HOH
    15781 
    15782 1494 atoms, 996 bonds, 498 residues, 1 model selected 
    15783 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15784 more memory-efficient implementation. 
    15785 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15786 more memory-efficient implementation. 
    15787 
    15788 > hide #!6 models
    15789 
    15790 > select clear
    15791 
    15792 > select :HOH
    15793 
    15794 1494 atoms, 996 bonds, 498 residues, 1 model selected 
    15795 
    15796 > isolde add water
    15797 
    15798 > isolde sim start sel
    15799 
    15800 > select :HOH
    15801 
    15802 1095 atoms, 730 bonds, 365 residues, 1 model selected 
    15803 
    15804 > select clear
    15805 
    15806 > save working.cxs
    15807 
    15808 Taking snapshot of stepper: working_2.pdb 
    15809 
    15810 > delete sel
    15811 
    15812 > delete sel
    15813 
    15814 > isolde add water
    15815 
    15816 > isolde sim start sel
    15817 
    15818 > isolde add water
    15819 
    15820 > isolde sim start sel
    15821 
    15822 > isolde add water
    15823 
    15824 > isolde sim start sel
    15825 
    15826 > isolde add water
    15827 
    15828 > isolde sim start sel
    15829 
    15830 > delete sel
    15831 
    15832 > setattr sel atoms name H
    15833 
    15834 Assigning name attribute to 1 item 
    15835 
    15836 > isolde add water
    15837 
    15838 > isolde sim start sel
    15839 
    15840 > select up
    15841 
    15842 3 atoms, 2 bonds, 1 residue, 1 model selected 
    15843 
    15844 > delete sel
    15845 
    15846 > isolde add water
    15847 
    15848 > isolde sim start sel
    15849 
    15850 > isolde add water
    15851 
    15852 > isolde sim start sel
    15853 
    15854 > isolde add water
    15855 
    15856 > isolde sim start sel
    15857 
    15858 > isolde add water simSettle false
    15859 
    15860 > isolde add water simSettle false
    15861 
    15862 > show #!6 models
    15863 
    15864 > hide #!6 models
    15865 
    15866 > show #!6 models
    15867 
    15868 > isolde add water
    15869 
    15870 > isolde sim start sel
    15871 
    15872 > hide #!6 models
    15873 
    15874 > isolde add water
    15875 
    15876 > isolde sim start sel
    15877 
    15878 > isolde add water simSettle false
    15879 
    15880 > isolde add water simSettle false
    15881 
    15882 > isolde add water simSettle false
    15883 
    15884 > isolde add water
    15885 
    15886 > isolde sim start sel
    15887 
    15888 > isolde add water
    15889 
    15890 > isolde sim start sel
    15891 
    15892 > isolde add water simSettle false
    15893 
    15894 > isolde add water simSettle false
    15895 
    15896 > isolde add water simSettle false
    15897 
    15898 > isolde add water
    15899 
    15900 > isolde sim start sel
    15901 
    15902 > isolde add water
    15903 
    15904 > isolde sim start sel
    15905 
    15906 > show #!6 models
    15907 
    15908 > hide #!6 models
    15909 
    15910 > show #!6 models
    15911 
    15912 > hide #!6 models
    15913 
    15914 > isolde add water simSettle false
    15915 
    15916 > isolde add water simSettle false
    15917 
    15918 > isolde add water
    15919 
    15920 > isolde sim start sel
    15921 
    15922 > show #!6 models
    15923 
    15924 > volume #6 level 0.02957
    15925 
    15926 > volume #6 level 0.02196
    15927 
    15928 > volume #6 level 0.02872
    15929 
    15930 > hide #!6 models
    15931 
    15932 > isolde add water
    15933 
    15934 > isolde sim start sel
    15935 
    15936 > isolde add water
    15937 
    15938 > isolde sim start sel
    15939 
    15940 > isolde add water simSettle false
    15941 
    15942 > isolde add water simSettle false
    15943 
    15944 > select /ak
    15945 
    15946 1380 atoms, 1391 bonds, 84 residues, 2 models selected 
    15947 
    15948 > isolde add water simSettle false
    15949 
    15950 > select /ak
    15951 
    15952 1380 atoms, 1391 bonds, 84 residues, 2 models selected 
    15953 
    15954 > select up
    15955 
    15956 114625 atoms, 116562 bonds, 5784 residues, 2 models selected 
    15957 
    15958 > select clear
    15959 
    15960 > isolde add water simSettle false
    15961 
    15962 > select /ak
    15963 
    15964 1383 atoms, 1393 bonds, 85 residues, 2 models selected 
    15965 
    15966 > select /ak
    15967 
    15968 1383 atoms, 1393 bonds, 85 residues, 2 models selected 
    15969 
    15970 > isolde add water simSettle false
    15971 
    15972 > isolde add water simSettle false
    15973 
    15974 > isolde add water simSettle false
    15975 
    15976 > isolde add water simSettle false
    15977 
    15978 > select clear
    15979 
    15980 > isolde add water simSettle false
    15981 
    15982 > select clear
    15983 
    15984 > view /aa:45
    15985 
    15986 > view /ab:45
    15987 
    15988 > isolde add water simSettle false
    15989 
    15990 > isolde add water simSettle false
    15991 
    15992 > view /ac:45
    15993 
    15994 > select clear
    15995 
    15996 > view /ad:45
    15997 
    15998 > view /ae:45
    15999 
    16000 > view /af:45
    16001 
    16002 > view /ag:45
    16003 
    16004 > view /ah:45
    16005 
    16006 > isolde add water simSettle false
    16007 
    16008 > select clear
    16009 
    16010 > view /ai:45
    16011 
    16012 > view /aj:45
    16013 
    16014 > view /ak:45
    16015 
    16016 > view /al:45
    16017 
    16018 > isolde add water simSettle false
    16019 
    16020 > isolde add water simSettle false
    16021 
    16022 > select clear
    16023 
    16024 > view /am:45
    16025 
    16026 > isolde add water simSettle false
    16027 
    16028 > select clear
    16029 
    16030 > view /an:45
    16031 
    16032 > isolde add water simSettle false
    16033 
    16034 > select clear
    16035 
    16036 > view /ao:45
    16037 
    16038 > view /ap:45
    16039 
    16040 > isolde add water simSettle false
    16041 
    16042 > select clear
    16043 
    16044 > view /aa:5
    16045 
    16046 > view /AA:45
    16047 
    16048 > view /AB:4
    16049 
    16050 > view /AB:43
    16051 
    16052 > view /AC:43
    16053 
    16054 > view /AD:43
    16055 
    16056 > view /AE:43
    16057 
    16058 > select clear
    16059 
    16060 > view /AF:43
    16061 
    16062 > view /AG:43
    16063 
    16064 > view /AH:43
    16065 
    16066 > view /AI:43
    16067 
    16068 > save working.cxs
    16069 
    16070 Taking snapshot of stepper: working_2.pdb 
    16071 
    16072 > close #8.1
    16073 
    16074 > clipper associate #3 toModel #8
    16075 
    16076 > volume gaussian #8 bfactor 50
    16077 
    16078 > clipper associate #3 toModel #1
    16079 
    16080 > close #1.1
    16081 
    16082 > volume gaussian #8 bfactor 50
    16083 
    16084 > clipper associate #3 toModel #8
    16085 
    16086 > clipper set contourSensitivity 0.25
    16087 
    16088 > select /D1
    16089 
    16090 Nothing selected 
    16091 
    16092 > delete /C2
    16093 
    16094 > select /H1
    16095 
    16096 1580 atoms, 1586 bonds, 75 residues, 1 model selected 
    16097 
    16098 > select /M
    16099 
    16100 6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected 
    16101 
    16102 > select clear
    16103 
    16104 > isolde restrain distances #8
    16105 
    16106 > select :HOH
    16107 
    16108 1218 atoms, 812 bonds, 406 residues, 1 model selected 
    16109 
    16110 > select /M
    16111 
    16112 6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected 
    16113 
    16114 > select clear
    16115 
    16116 > select /M:20-50
    16117 
    16118 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16119 
    16120 > isolde release distances sel
    16121 
    16122 > select clear
    16123 
    16124 > select #8
    16125 
    16126 112951 atoms, 114855 bonds, 14 pseudobonds, 5695 residues, 22 models selected 
    16127 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16128 more memory-efficient implementation. 
    16129 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16130 more memory-efficient implementation. 
    16131 
    16132 > select clear
    16133 
    16134 > close #8.2.10
    16135 
    16136 > select clear
    16137 
    16138 > select /M:20-50
    16139 
    16140 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16141 
    16142 > open
    16143 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    16144 
    16145 Summary of feedback from opening
    16146 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif 
    16147 --- 
    16148 warnings | Unknown polymer entity '1' near line 475 
    16149 Unknown polymer entity '2' near line 2593 
    16150 Unknown polymer entity '3' near line 5781 
    16151 Unknown polymer entity '4' near line 26370 
    16152 Unknown polymer entity '5' near line 27136 
    16153 10 messages similar to the above omitted 
    16154 Atom H is not in the residue template for MET /AA:1 
    16155 Atom C1 is not in the residue template for GPC /AA:60 
    16156 Atom H is not in the residue template for MET /AB:1 
    16157 Atom C1 is not in the residue template for GPC /AB:60 
    16158 Atom H is not in the residue template for MET /AC:1 
    16159 Atom C1 is not in the residue template for GPC /AC:60 
    16160 Atom H is not in the residue template for MET /AD:1 
    16161 Atom C1 is not in the residue template for GPC /AD:60 
    16162 Atom H is not in the residue template for MET /AE:1 
    16163 Atom C1 is not in the residue template for GPC /AE:60 
    16164 Atom H is not in the residue template for MET /AF:1 
    16165 Atom C1 is not in the residue template for GPC /AF:60 
    16166 Atom H is not in the residue template for MET /AG:1 
    16167 Atom C1 is not in the residue template for GPC /AG:60 
    16168 Atom H is not in the residue template for MET /AH:1 
    16169 Atom C1 is not in the residue template for GPC /AH:60 
    16170 Atom H is not in the residue template for MET /AI:1 
    16171 Atom C1 is not in the residue template for GPC /AI:60 
    16172 Atom H is not in the residue template for MET /AJ:1 
    16173 Atom C1 is not in the residue template for GPC /AJ:60 
    16174 Atom H is not in the residue template for MET /AK:1 
    16175 Atom C1 is not in the residue template for GPC /AK:60 
    16176 Atom C26 is not in the residue template for PEX /AK:62 
    16177 Atom H is not in the residue template for MET /AL:1 
    16178 Atom C1 is not in the residue template for GPC /AL:60 
    16179 Atom H is not in the residue template for MET /AM:1 
    16180 Atom C1 is not in the residue template for GPC /AM:60 
    16181 Atom H is not in the residue template for MET /AN:1 
    16182 Atom C1 is not in the residue template for GPC /AN:60 
    16183 Atom H is not in the residue template for MET /AO:1 
    16184 Atom C1 is not in the residue template for GPC /AO:60 
    16185 Atom H is not in the residue template for MET /AP:1 
    16186 Atom C1 is not in the residue template for GPC /AP:60 
    16187 Atom H is not in the residue template for MET /AQ:1 
    16188 Atom C1 is not in the residue template for GPC /AQ:60 
    16189 Atom H is not in the residue template for MET /AR:1 
    16190 Atom C1 is not in the residue template for GPC /AR:60 
    16191 Atom H is not in the residue template for MET /AS:1 
    16192 Atom C1 is not in the residue template for GPC /AS:60 
    16193 Atom H is not in the residue template for MET /AT:1 
    16194 Atom C1 is not in the residue template for GPC /AT:60 
    16195 Atom H is not in the residue template for MET /AU:1 
    16196 Atom C1 is not in the residue template for GPC /AU:60 
    16197 Atom H is not in the residue template for MET /AV:1 
    16198 Atom C1 is not in the residue template for GPC /AV:60 
    16199 Atom H is not in the residue template for MET /AW:1 
    16200 Atom C1 is not in the residue template for GPC /AW:60 
    16201 Atom H is not in the residue template for MET /AX:1 
    16202 Atom C1 is not in the residue template for GPC /AX:60 
    16203 Atom H is not in the residue template for GLY /BQ:5 
    16204 Atom H is not in the residue template for GLY /BR:5 
    16205 Atom H is not in the residue template for GLY /BS:5 
    16206 Atom H is not in the residue template for GLY /BT:5 
    16207 Atom H11 is not in the residue template for BPH /L:606 
    16208 Atom H11 is not in the residue template for BPH /M:605 
    16209 Atom C1 is not in the residue template for RCC /M:701 
    16210 Atom HN2 is not in the residue template for ARG /ak:71 
    16211 Atom H is not in the residue template for GLY /C1:32 
    16212 Atom C1 is not in the residue template for GPC /Ba:60 
    16213 Atom C1 is not in the residue template for GPC /Bb:60 
    16214 Atom C1 is not in the residue template for GPC /Bc:60 
    16215 Atom C1 is not in the residue template for GPC /Bd:60 
    16216 Atom C1 is not in the residue template for GPC /Be:60 
    16217 11 messages similar to the above omitted 
    16218 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    16219  
    16220 Chain information for model1a.cif #3 
    16221 --- 
    16222 Chain | Description 
    16223 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ? 
    16224 AC AD | ? 
    16225 BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
    16226 bm bo bp | ? 
    16227 BB BD BE BI BQ BR BS BT BV BW bn | ? 
    16228 C | ? 
    16229 C1 | ? 
    16230 H1 | ? 
    16231 H2 | ? 
    16232 L | ? 
    16233 M | ? 
    16234 aa | ? 
    16235 ab ad ae af ag ah ai aj al am an ao ap | ? 
    16236 ac | ? 
    16237 ak | ? 
    16238  
    16239 
    16240 > delete #3&~/M
    16241 
    16242 > select #3/M
    16243 
    16244 5881 atoms, 5992 bonds, 16 pseudobonds, 333 residues, 3 models selected 
    16245 
    16246 > style sel stick
    16247 
    16248 Changed 5881 atom styles 
    16249 
    16250 > hide HC
    16251 
    16252 > color sel green
    16253 
    16254 > color sel byhetero
    16255 
    16256 > select clear
    16257 
    16258 > select #8/M:20-50
    16259 
    16260 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16261 
    16262 > select clear
    16263 
    16264 > hide #!3 models
    16265 
    16266 > select #8/M:20-50
    16267 
    16268 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16269 
    16270 > delete #8/M:22-35
    16271 
    16272 > select #8/M:20-50
    16273 
    16274 242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected 
    16275 
    16276 > select #8/M:20-50
    16277 
    16278 242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected 
    16279 
    16280 > isolde add water simSettle false
    16281 
    16282 > select clear
    16283 
    16284 > save working.cxs
    16285 
    16286 Taking snapshot of stepper: working_2.pdb 
    16287 
    16288 > close #6
    16289 
    16290 > close #4
    16291 
    16292 > close #3
    16293 
    16294 > close #2
    16295 
    16296 > close #1
    16297 
    16298 > save working.cxs
    16299 
    16300 Taking snapshot of stepper: working_2.pdb 
    16301 
    16302 > select #8
    16303 
    16304 112761 atoms, 114661 bonds, 15 pseudobonds, 5682 residues, 23 models selected 
    16305 
    16306 > select clear
    16307 
    16308 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    16309 
    16310 > volume subtract #8.1.1.1 #1
    16311 
    16312 > close #1
    16313 
    16314 > select /M:4-12
    16315 
    16316 162 atoms, 163 bonds, 9 residues, 1 model selected 
    16317 
    16318 > select clear
    16319 
    16320 > select up
    16321 
    16322 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16323 
    16324 > select up
    16325 
    16326 215 atoms, 216 bonds, 12 residues, 1 model selected 
    16327 
    16328 > select clear
    16329 
    16330 > select clear
    16331 
    16332 > select /AA/AX:BCL
    16333 
    16334 1311 atoms, 1345 bonds, 57 residues, 1 model selected 
    16335 
    16336 > select /AA-AX:BCL
    16337 
    16338 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16339 
    16340 > select /AA-AX:BCL
    16341 
    16342 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16343 
    16344 > isolde add water sel f
    16345 
    16346 Expected a keyword 
    16347 
    16348 > isolde add water simSettle false
    16349 
    16350 > select /AA-AX:BCL
    16351 
    16352 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16353 
    16354 > select /AA-AX:BCL
    16355 
    16356 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16357 
    16358 > select /AA-AX:BCL
    16359 
    16360 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16361 
    16362 > select up
    16363 
    16364 140 atoms, 148 bonds, 1 residue, 1 model selected 
    16365 
    16366 > select /AD:10-40@CA
    16367 
    16368 31 atoms, 31 residues, 1 model selected 
    16369 
    16370 > select /AB:10-40@CA
    16371 
    16372 31 atoms, 31 residues, 1 model selected 
    16373 
    16374 > select /AB
    16375 
    16376 1212 atoms, 1234 bonds, 53 residues, 1 model selected 
    16377 
    16378 > select /AA-AX:BCL
    16379 
    16380 5600 atoms, 5920 bonds, 40 residues, 1 model selected 
    16381 
    16382 > select clear
    16383 
    16384 > select /AB
    16385 
    16386 1352 atoms, 1382 bonds, 54 residues, 1 model selected 
    16387 
    16388 > select /AA-AX:BCL
    16389 
    16390 5600 atoms, 5920 bonds, 40 residues, 1 model selected 
    16391 
    16392 > select /AX:10-40@CA
    16393 
    16394 31 atoms, 31 residues, 1 model selected 
    16395 
    16396 > select /AX
    16397 
    16398 1302 atoms, 1322 bonds, 57 residues, 1 model selected 
    16399 
    16400 > delete /AX:73
    16401 
    16402 > select /AX:10-40@CA
    16403 
    16404 31 atoms, 31 residues, 1 model selected 
    16405 
    16406 > select /AA-AX:BCL
    16407 
    16408 5740 atoms, 6068 bonds, 41 residues, 1 model selected 
    16409 
    16410 > select up
    16411 
    16412 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16413 
    16414 > delete sel
    16415 
    16416 > select /AA-AX:BCL
    16417 
    16418 5740 atoms, 6068 bonds, 41 residues, 1 model selected 
    16419 
    16420 > select /AU:10-40@CA
    16421 
    16422 31 atoms, 31 residues, 1 model selected 
    16423 
    16424 > select /AU
    16425 
    16426 1218 atoms, 1238 bonds, 55 residues, 1 model selected 
    16427 
    16428 > select /AA-AX:BCL
    16429 
    16430 5880 atoms, 6216 bonds, 42 residues, 1 model selected 
    16431 
    16432 > select /AA-AX:BCL
    16433 
    16434 5880 atoms, 6216 bonds, 42 residues, 1 model selected 
    16435 
    16436 > select up
    16437 
    16438 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16439 
    16440 > delete sel
    16441 
    16442 > select /AA-AX:BCL
    16443 
    16444 5880 atoms, 6216 bonds, 42 residues, 1 model selected 
    16445 
    16446 > select /AR:10-40@CA
    16447 
    16448 31 atoms, 31 residues, 1 model selected 
    16449 
    16450 > select /AR
    16451 
    16452 1215 atoms, 1236 bonds, 54 residues, 1 model selected 
    16453 
    16454 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16455 bonded heavy atom. 
    16456 
    16457 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16458 bonded heavy atom. 
    16459 
    16460 > select /AA-AX:BCL
    16461 
    16462 6020 atoms, 6364 bonds, 43 residues, 1 model selected 
    16463 
    16464 > select /AA-AX:BCL
    16465 
    16466 6020 atoms, 6364 bonds, 43 residues, 1 model selected 
    16467 
    16468 > select /AA-AX:BCL
    16469 
    16470 6020 atoms, 6364 bonds, 43 residues, 1 model selected 
    16471 
    16472 > select /Ao:10-40@CA
    16473 
    16474 Nothing selected 
    16475 
    16476 > select /AO:10-40@CA
    16477 
    16478 31 atoms, 31 residues, 1 model selected 
    16479 
    16480 > select /AO
    16481 
    16482 1134 atoms, 1154 bonds, 53 residues, 1 model selected 
    16483 
    16484 > select up
    16485 
    16486 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16487 
    16488 > delete sel
    16489 
    16490 > select /AO
    16491 
    16492 1274 atoms, 1302 bonds, 54 residues, 1 model selected 
    16493 
    16494 > select /AA-AX:BCL
    16495 
    16496 6160 atoms, 6512 bonds, 44 residues, 1 model selected 
    16497 
    16498 > select /AL:10-40@CA
    16499 
    16500 31 atoms, 31 residues, 1 model selected 
    16501 
    16502 > select /AL
    16503 
    16504 1305 atoms, 1324 bonds, 58 residues, 1 model selected 
    16505 
    16506 > select /AL:10-40@CA
    16507 
    16508 31 atoms, 31 residues, 1 model selected 
    16509 
    16510 > select /AA-AX:BCL
    16511 
    16512 6300 atoms, 6660 bonds, 45 residues, 1 model selected 
    16513 
    16514 > select clear
    16515 
    16516 > select up
    16517 
    16518 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16519 
    16520 > delete sel
    16521 
    16522 > select /AA-AX:BCL
    16523 
    16524 6300 atoms, 6660 bonds, 45 residues, 1 model selected 
    16525 
    16526 > select /AA-AX:BCL
    16527 
    16528 6300 atoms, 6660 bonds, 45 residues, 1 model selected 
    16529 
    16530 > select clear
    16531 
    16532 > select up
    16533 
    16534 81 atoms, 82 bonds, 1 residue, 1 model selected 
    16535 
    16536 > delete sel
    16537 
    16538 > select /AF:10-40@CA
    16539 
    16540 31 atoms, 31 residues, 1 model selected 
    16541 
    16542 > select /AF
    16543 
    16544 1389 atoms, 1408 bonds, 60 residues, 1 model selected 
    16545 
    16546 > select clear
    16547 
    16548 > select /AA-AX:BCL
    16549 
    16550 6440 atoms, 6808 bonds, 46 residues, 1 model selected 
    16551 
    16552 > select /AA-AX:BCL
    16553 
    16554 6440 atoms, 6808 bonds, 46 residues, 1 model selected 
    16555 
    16556 > select /AI:10-40@CA
    16557 
    16558 31 atoms, 31 residues, 1 model selected 
    16559 
    16560 > select /AI
    16561 
    16562 1464 atoms, 1486 bonds, 59 residues, 1 model selected 
    16563 
    16564 > select up
    16565 
    16566 81 atoms, 82 bonds, 1 residue, 1 model selected 
    16567 
    16568 > delete sel
    16569 
    16570 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16571 bonded heavy atom. 
    16572 
    16573 > select /AA-AX:BCL
    16574 
    16575 6580 atoms, 6956 bonds, 47 residues, 1 model selected 
    16576 
    16577 > select /AC:10-40@CA
    16578 
    16579 31 atoms, 31 residues, 1 model selected 
    16580 
    16581 > select /AC
    16582 
    16583 1207 atoms, 1225 bonds, 55 residues, 1 model selected 
    16584 
    16585 > select up
    16586 
    16587 140 atoms, 148 bonds, 1 residue, 1 model selected 
    16588 
    16589 > isolde ignore sel
    16590 
    16591 ISOLDE: currently ignoring 1 residues in model 8.2 
    16592 
    16593 > isolde ~ignore
    16594 
    16595 > select /AA-AX:BCL
    16596 
    16597 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    16598 
    16599 > select /AA-AX:BCL
    16600 
    16601 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    16602 
    16603 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16604 bonded heavy atom. 
    16605 
    16606 > select /AA-AX:BCL
    16607 
    16608 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    16609 
    16610 > select clear
    16611 
    16612 > save working.cxs
    16613 
    16614 Taking snapshot of stepper: working_2.pdb 
    16615 
    16616 > select /ba-bp:BCL
    16617 
    16618 2240 atoms, 2368 bonds, 16 residues, 1 model selected 
    16619 
    16620 > select /ba-bp,aa-ap:BCL
    16621 
    16622 4480 atoms, 4736 bonds, 32 residues, 1 model selected 
    16623 
    16624 > select clear
    16625 
    16626 > select clear
    16627 
    16628 > isolde add water simSettle false
    16629 
    16630 > view /aa:26
    16631 
    16632 > view /ab:26
    16633 
    16634 > select clear
    16635 
    16636 > view /ac:26
    16637 
    16638 > view /ad:26
    16639 
    16640 > view /ae:26
    16641 
    16642 > view /af:26
    16643 
    16644 > view /ag:26
    16645 
    16646 > view /ah:26
    16647 
    16648 > view /ai:26
    16649 
    16650 > view /ap:26
    16651 
    16652 > view /aj:26
    16653 
    16654 > select clear
    16655 
    16656 > select clear
    16657 
    16658 > save working.cxs
    16659 
    16660 Taking snapshot of stepper: working_2.pdb 
    16661 
    16662 > isolde add water simSettle false
    16663 
    16664 > select :HOH
    16665 
    16666 1218 atoms, 812 bonds, 406 residues, 1 model selected 
    16667 
    16668 > select #8.1.1.1
    16669 
    16670 3 models selected 
    16671 
    16672 > select clear
    16673 
    16674 > close #2
    16675 
    16676 > select #8
    16677 
    16678 113595 atoms, 115653 bonds, 15 pseudobonds, 5601 residues, 23 models selected 
    16679 
    16680 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    16681 
    16682 > volume subtract #8.1.1.1 #1
    16683 
    16684 > close #1
    16685 
    16686 > select clear
    16687 
    16688 > select #2
    16689 
    16690 4 models selected 
    16691 
    16692 > select clear
    16693 
    16694 > select :HOH
    16695 
    16696 2655 atoms, 1770 bonds, 885 residues, 1 model selected 
    16697 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16698 more memory-efficient implementation. 
    16699 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16700 more memory-efficient implementation. 
    16701 
    16702 > select clear
    16703 
    16704 > select clear
    16705 
    16706 > select :HOH
    16707 
    16708 2655 atoms, 1770 bonds, 885 residues, 1 model selected 
    16709 
    16710 > select clear
    16711 
    16712 > select :HOH
    16713 
    16714 2799 atoms, 1866 bonds, 933 residues, 1 model selected 
    16715 
    16716 > select clear
    16717 
    16718 > style sel sphere
    16719 
    16720 Changed 672 atom styles 
    16721 
    16722 > select :HOH
    16723 
    16724 2799 atoms, 1866 bonds, 933 residues, 1 model selected 
    16725 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16726 more memory-efficient implementation. 
    16727 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16728 more memory-efficient implementation. 
    16729 
    16730 > select clear
    16731 
    16732 > select :HOH
    16733 
    16734 2799 atoms, 1866 bonds, 933 residues, 1 model selected 
    16735 
    16736 > style sel stick
    16737 
    16738 Changed 2799 atom styles 
    16739 
    16740 > select :HOH
    16741 
    16742 2334 atoms, 1556 bonds, 778 residues, 1 model selected 
    16743 
    16744 > select clear
    16745 
    16746 > hide #!2 models
    16747 
    16748 > select ~:HOH&~H
    16749 
    16750 55004 atoms, 115015 bonds, 15 pseudobonds, 5282 residues, 27 models selected 
    16751 
    16752 > select up
    16753 
    16754 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16755 
    16756 > delete sel
    16757 
    16758 > select up
    16759 
    16760 9 atoms, 6 bonds, 3 residues, 1 model selected 
    16761 
    16762 > delete sel
    16763 
    16764 > delete sel
    16765 
    16766 > select up
    16767 
    16768 9 atoms, 6 bonds, 3 residues, 1 model selected 
    16769 
    16770 > delete sel
    16771 
    16772 > select #8
    16773 
    16774 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16775 
    16776 > select clear
    16777 
    16778 > select #8
    16779 
    16780 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16781 
    16782 > select clear
    16783 
    16784 > select #8
    16785 
    16786 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16787 
    16788 > select clear
    16789 
    16790 > select clear
    16791 
    16792 > select #8
    16793 
    16794 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16795 
    16796 > select clear
    16797 
    16798 > select up
    16799 
    16800 405 atoms, 410 bonds, 5 residues, 1 model selected 
    16801 
    16802 > style sel sphere
    16803 
    16804 Changed 405 atom styles 
    16805 
    16806 > style sel ball
    16807 
    16808 Changed 405 atom styles 
    16809 
    16810 > style sel stick
    16811 
    16812 Changed 405 atom styles 
    16813 
    16814 > color sel lightgreen
    16815 
    16816 > color sel byhetero
    16817 
    16818 > color ~sel lightgrey
    16819 
    16820 > color ~sel byhetero
    16821 
    16822 > color sel green
    16823 
    16824 > color sel byhetero
    16825 
    16826 > select clear
    16827 
    16828 > hide :HOH
    16829 
    16830 > select clear
    16831 
    16832 > save sideways_detergents.jpg
    16833 
    16834 > save sideways_detergents.jpg
    16835 
    16836 > color bychain
    16837 
    16838 > color byhetero
    16839 
    16840 > save working.cxs
    16841 
    16842 Taking snapshot of stepper: working_2.pdb 
    16843 Restoring stepper: working_2.pdb 
    16844 opened ChimeraX session 
    16845 
    16846 > close #8.1
    16847 
    16848 > close #2
    16849 
    16850 > open
    16851 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class2a_26A.mrc
    16852 
    16853 Opened class2a_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    16854 0.0249, step 2, values float32 
    16855 
    16856 > volume gaussian #1 bfactor 50
    16857 
    16858 > clipper associate #1,2 toModel #8
    16859 
    16860 Traceback (most recent call last): 
    16861 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16862 packages/chimerax/isolde/isolde.py", line 2615, in
    16863 _set_map_to_transparent_surface 
    16864 volumecommand.volume(self.session, [v], **map_style_settings[style]) 
    16865 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    16866 packages/chimerax/map/volumecommand.py", line 410, in volume 
    16867 apply_volume_options(v, dsettings, rsettings, session) 
    16868 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    16869 packages/chimerax/map/volumecommand.py", line 444, in apply_volume_options 
    16870 v.set_display_style(doptions['style']) 
    16871 File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
    16872 line 660, in set_display_style 
    16873 self._drawings_need_update() 
    16874 File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
    16875 line 742, in _drawings_need_update 
    16876 s._volume_update_manager = vm = VolumeUpdateManager(s) 
    16877 File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
    16878 line 3950, in __init__ 
    16879 t = session.triggers 
    16880 AttributeError: 'NoneType' object has no attribute 'triggers' 
    16881  
    16882 AttributeError: 'NoneType' object has no attribute 'triggers' 
    16883  
    16884 File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
    16885 line 3950, in __init__ 
    16886 t = session.triggers 
    16887  
    16888 See log for complete Python traceback. 
    16889  
    16890 
    16891 > clipper set contourSensitivity 0.25
    16892 
    16893 > select #8
    16894 
    16895 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 22 models selected 
    16896 
    16897 > isolde restrain distances #8
    16898 
    16899 > select clear
    16900 
    16901 > open
    16902 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/working.cif
    16903 
    16904 Summary of feedback from opening
    16905 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/working.cif 
    16906 --- 
    16907 warnings | Unknown polymer entity '1' near line 609 
    16908 Unknown polymer entity '2' near line 3150 
    16909 Unknown polymer entity '3' near line 7200 
    16910 Unknown polymer entity '4' near line 33507 
    16911 Unknown polymer entity '5' near line 34519 
    16912 5 messages similar to the above omitted 
    16913 Unable to fetch template for 'LMX': might have incorrect bonds 
    16914 Unknown polymer entity '11' near line 75429 
    16915 Unknown polymer entity '12' near line 81996 
    16916 Unknown polymer entity '13' near line 83073 
    16917 Unknown polymer entity '14' near line 93894 
    16918 Unknown polymer entity '15' near line 113722 
    16919 Atom H is not in the residue template for MET /AA:1 
    16920 Atom C1 is not in the residue template for GPC /AA:60 
    16921 Atom H is not in the residue template for MET /AB:1 
    16922 Atom C1 is not in the residue template for GPC /AB:60 
    16923 Atom C26 is not in the residue template for PEX /AB:62 
    16924 Atom H is not in the residue template for MET /AC:1 
    16925 Atom C1 is not in the residue template for GPC /AC:60 
    16926 Atom C26 is not in the residue template for PEX /AC:62 
    16927 Atom H is not in the residue template for MET /AD:1 
    16928 Atom C1 is not in the residue template for GPC /AD:60 
    16929 Atom H is not in the residue template for MET /AE:1 
    16930 Atom C1 is not in the residue template for GPC /AE:60 
    16931 Atom C26 is not in the residue template for PEX /AE:62 
    16932 Atom H is not in the residue template for MET /AF:1 
    16933 Atom C1 is not in the residue template for GPC /AF:60 
    16934 Atom C26 is not in the residue template for PEX /AF:62 
    16935 Atom H is not in the residue template for MET /AG:1 
    16936 Atom C1 is not in the residue template for GPC /AG:60 
    16937 Atom H is not in the residue template for MET /AH:1 
    16938 Atom C1 is not in the residue template for GPC /AH:60 
    16939 Atom C26 is not in the residue template for PEX /AH:62 
    16940 Atom H is not in the residue template for MET /AI:1 
    16941 Atom C1 is not in the residue template for GPC /AI:60 
    16942 Atom C26 is not in the residue template for PEX /AI:62 
    16943 Atom H is not in the residue template for MET /AJ:1 
    16944 Atom C1 is not in the residue template for GPC /AJ:60 
    16945 Atom H is not in the residue template for MET /AK:1 
    16946 Atom C1 is not in the residue template for GPC /AK:60 
    16947 Atom C26 is not in the residue template for PEX /AK:62 
    16948 Atom H is not in the residue template for MET /AL:1 
    16949 Atom C1 is not in the residue template for GPC /AL:60 
    16950 Atom C26 is not in the residue template for PEX /AL:62 
    16951 Atom H is not in the residue template for MET /AM:1 
    16952 Atom C1 is not in the residue template for GPC /AM:60 
    16953 Atom H is not in the residue template for MET /AN:1 
    16954 Atom C1 is not in the residue template for GPC /AN:60 
    16955 Atom C26 is not in the residue template for PEX /AN:62 
    16956 Atom H is not in the residue template for MET /AO:1 
    16957 Atom C1 is not in the residue template for GPC /AO:60 
    16958 Atom C26 is not in the residue template for PEX /AO:62 
    16959 Atom H is not in the residue template for MET /AP:1 
    16960 Atom C1 is not in the residue template for GPC /AP:60 
    16961 Atom H is not in the residue template for MET /AQ:1 
    16962 Atom C1 is not in the residue template for GPC /AQ:60 
    16963 Atom C26 is not in the residue template for PEX /AQ:62 
    16964 Atom H is not in the residue template for MET /AR:1 
    16965 Atom C1 is not in the residue template for GPC /AR:60 
    16966 Atom C26 is not in the residue template for PEX /AR:62 
    16967 Atom H is not in the residue template for MET /AS:1 
    16968 Atom C1 is not in the residue template for GPC /AS:60 
    16969 Atom H is not in the residue template for MET /AT:1 
    16970 Atom C1 is not in the residue template for GPC /AT:60 
    16971 Atom C26 is not in the residue template for PEX /AT:62 
    16972 Atom H is not in the residue template for MET /AU:1 
    16973 Atom C1 is not in the residue template for GPC /AU:60 
    16974 Atom C26 is not in the residue template for PEX /AU:62 
    16975 Atom H is not in the residue template for MET /AV:1 
    16976 Atom C1 is not in the residue template for GPC /AV:60 
    16977 Atom H is not in the residue template for MET /AW:1 
    16978 Atom C1 is not in the residue template for GPC /AW:60 
    16979 Atom C26 is not in the residue template for PEX /AW:62 
    16980 Atom H is not in the residue template for MET /AX:1 
    16981 Atom C1 is not in the residue template for GPC /AX:60 
    16982 Atom C26 is not in the residue template for PEX /AX:62 
    16983 Atom H is not in the residue template for GLY /BQ:5 
    16984 Atom H is not in the residue template for GLY /BR:5 
    16985 Atom H is not in the residue template for GLY /BS:5 
    16986 Atom H is not in the residue template for GLY /BT:5 
    16987 Atom H is not in the residue template for ALA /C:15 
    16988 Atom H6 is not in the residue template for P5S /H1:1001 
    16989 Atom H11 is not in the residue template for BPH /L:606 
    16990 Atom H11 is not in the residue template for BPH /M:605 
    16991 Atom C1 is not in the residue template for RCC /M:701 
    16992 Atom HN2 is not in the residue template for ARG /ak:71 
    16993 Atom H is not in the residue template for GLY /C1:32 
    16994 Atom C1 is not in the residue template for GPC /Ba:60 
    16995 Atom C1 is not in the residue template for GPC /Bb:60 
    16996 Atom C1 is not in the residue template for GPC /Bc:60 
    16997 Atom C1 is not in the residue template for GPC /Bd:60 
    16998 Atom C1 is not in the residue template for GPC /Be:60 
    16999 11 messages similar to the above omitted 
    17000 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    17001  
    17002 Chain information for working.cif #1 
    17003 --- 
    17004 Chain | Description 
    17005 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ? 
    17006 AC AD | ? 
    17007 BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
    17008 bm bo bp | ? 
    17009 BB BD BE BI BQ BR BS BT BV BW bn | ? 
    17010 C | ? 
    17011 C1 | ? 
    17012 H1 | ? 
    17013 H2 | ? 
    17014 L | ? 
    17015 M | ? 
    17016 aa | ? 
    17017 ab ad ae af ag ah ai aj al am an ao ap | ? 
    17018 ac | ? 
    17019 ak | ? 
    17020  
    17021 
    17022 > select #1
    17023 
    17024 114906 atoms, 116079 bonds, 464 pseudobonds, 6038 residues, 3 models selected 
    17025 
    17026 > show sel cartoons
    17027 
    17028 > hide sel atoms
    17029 
    17030 > select clear
    17031 
    17032 > select #8/C,H2,L,M,C1
    17033 
    17034 22623 atoms, 22703 bonds, 15 pseudobonds, 1551 residues, 3 models selected 
    17035 
    17036 > select #8/C,H2,L,M,C1&protein
    17037 
    17038 18620 atoms, 18935 bonds, 1 pseudobond, 1192 residues, 2 models selected 
    17039 
    17040 > select #8/C,H2,L,M,C1&protein&@CA
    17041 
    17042 1192 atoms, 1192 residues, 1 model selected 
    17043 
    17044 > delete #1&~/C,H2,L,M,C1
    17045 
    17046 > fitmap #1 inMap #8.1.1.1
    17047 
    17048 Fit molecule working.cif (#1) to map class2a_26A.mrc (#8.1.1.1) using 22623
    17049 atoms 
    17050 average map value = 0.05124, steps = 144 
    17051 shifted from previous position = 0.474 
    17052 rotated from previous position = 22.5 degrees 
    17053 atoms outside contour = 17046, contour level = 0.070771 
    17054  
    17055 Position of working.cif (#1) relative to class2a_26A.mrc (#8.1.1.1)
    17056 coordinates: 
    17057 Matrix rotation and translation 
    17058 0.92374096 0.38273145 -0.01480832 -58.21505213 
    17059 -0.38287530 0.92376145 -0.00844378 93.76317888 
    17060 0.01044766 0.01346961 0.99985470 -4.82454281 
    17061 Axis 0.02859500 -0.03295677 -0.99904763 
    17062 Axis point 206.42003168 193.23813197 0.00000000 
    17063 Rotation angle (degrees) 22.53007222 
    17064 Shift along axis 0.06515675 
    17065  
    17066 
    17067 > hide #!8.2 models
    17068 
    17069 > open
    17070 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cif
    17071 
    17072 Summary of feedback from opening
    17073 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cif 
    17074 --- 
    17075 warnings | Unknown polymer entity '1' near line 564 
    17076 Unknown polymer entity '2' near line 2935 
    17077 Unknown polymer entity '3' near line 6791 
    17078 Unknown polymer entity '4' near line 31845 
    17079 Unknown polymer entity '5' near line 32854 
    17080 6 messages similar to the above omitted 
    17081 Unable to fetch template for 'LMX': might have incorrect bonds 
    17082 Unknown polymer entity '12' near line 74416 
    17083 Unknown polymer entity '13' near line 80927 
    17084 Unknown polymer entity '14' near line 81989 
    17085 Unknown polymer entity '15' near line 92567 
    17086 Unknown polymer entity '16' near line 112107 
    17087 Atom H is not in the residue template for MET /AA:1 
    17088 Atom C1 is not in the residue template for GPC /AA:60 
    17089 Atom H is not in the residue template for MET /AB:1 
    17090 Atom C1 is not in the residue template for GPC /AB:60 
    17091 Atom C26 is not in the residue template for PEX /AB:62 
    17092 Atom H is not in the residue template for MET /AC:1 
    17093 Atom C1 is not in the residue template for GPC /AC:60 
    17094 Atom C26 is not in the residue template for PEX /AC:62 
    17095 Atom H is not in the residue template for MET /AD:1 
    17096 Atom C1 is not in the residue template for GPC /AD:60 
    17097 Atom H is not in the residue template for MET /AE:1 
    17098 Atom C1 is not in the residue template for GPC /AE:60 
    17099 Atom C26 is not in the residue template for PEX /AE:62 
    17100 Atom H is not in the residue template for MET /AF:1 
    17101 Atom C1 is not in the residue template for GPC /AF:60 
    17102 Atom C26 is not in the residue template for PEX /AF:62 
    17103 Atom H is not in the residue template for MET /AG:1 
    17104 Atom C1 is not in the residue template for GPC /AG:60 
    17105 Atom H is not in the residue template for MET /AH:1 
    17106 Atom C1 is not in the residue template for GPC /AH:60 
    17107 Atom C26 is not in the residue template for PEX /AH:62 
    17108 Atom H is not in the residue template for MET /AI:1 
    17109 Atom C1 is not in the residue template for GPC /AI:60 
    17110 Atom C26 is not in the residue template for PEX /AI:62 
    17111 Atom H is not in the residue template for MET /AJ:1 
    17112 Atom C1 is not in the residue template for GPC /AJ:60 
    17113 Atom H is not in the residue template for MET /AK:1 
    17114 Atom C1 is not in the residue template for GPC /AK:60 
    17115 Atom C26 is not in the residue template for PEX /AK:62 
    17116 Atom H is not in the residue template for MET /AL:1 
    17117 Atom C1 is not in the residue template for GPC /AL:60 
    17118 Atom C26 is not in the residue template for PEX /AL:62 
    17119 Atom H is not in the residue template for MET /AM:1 
    17120 Atom C1 is not in the residue template for GPC /AM:60 
    17121 Atom H is not in the residue template for MET /AN:1 
    17122 Atom C1 is not in the residue template for GPC /AN:60 
    17123 Atom C26 is not in the residue template for PEX /AN:62 
    17124 Atom H is not in the residue template for MET /AO:1 
    17125 Atom C1 is not in the residue template for GPC /AO:60 
    17126 Atom C26 is not in the residue template for PEX /AO:62 
    17127 Atom H is not in the residue template for MET /AP:1 
    17128 Atom C1 is not in the residue template for GPC /AP:60 
    17129 Atom H is not in the residue template for MET /AQ:1 
    17130 Atom C1 is not in the residue template for GPC /AQ:60 
    17131 Atom C26 is not in the residue template for PEX /AQ:62 
    17132 Atom H is not in the residue template for MET /AR:1 
    17133 Atom C1 is not in the residue template for GPC /AR:60 
    17134 Atom C26 is not in the residue template for PEX /AR:62 
    17135 Atom H is not in the residue template for MET /AS:1 
    17136 Atom C1 is not in the residue template for GPC /AS:60 
    17137 Atom H is not in the residue template for MET /AT:1 
    17138 Atom C1 is not in the residue template for GPC /AT:60 
    17139 Atom C26 is not in the residue template for PEX /AT:62 
    17140 Atom H is not in the residue template for MET /AU:1 
    17141 Atom C1 is not in the residue template for GPC /AU:60 
    17142 Atom C26 is not in the residue template for PEX /AU:62 
    17143 Atom H is not in the residue template for MET /AV:1 
    17144 Atom C1 is not in the residue template for GPC /AV:60 
    17145 Atom H is not in the residue template for MET /AW:1 
    17146 Atom C1 is not in the residue template for GPC /AW:60 
    17147 Atom C26 is not in the residue template for PEX /AW:62 
    17148 Atom H is not in the residue template for MET /AX:1 
    17149 Atom C1 is not in the residue template for GPC /AX:60 
    17150 Atom C26 is not in the residue template for PEX /AX:62 
    17151 Atom H is not in the residue template for GLY /BQ:5 
    17152 Atom H is not in the residue template for GLY /BR:5 
    17153 Atom H is not in the residue template for GLY /BS:5 
    17154 Atom H is not in the residue template for GLY /BT:5 
    17155 Atom H6 is not in the residue template for P5S /H1:1001 
    17156 Atom H11 is not in the residue template for BPH /L:606 
    17157 Atom H11 is not in the residue template for BPH /M:605 
    17158 Atom C1 is not in the residue template for RCC /M:701 
    17159 Atom HN2 is not in the residue template for ARG /ak:71 
    17160 Atom H is not in the residue template for GLY /C1:32 
    17161 Atom C1 is not in the residue template for GPC /Ba:60 
    17162 Atom C1 is not in the residue template for GPC /Bb:60 
    17163 Atom C1 is not in the residue template for GPC /Bc:60 
    17164 Atom C1 is not in the residue template for GPC /Bd:60 
    17165 Atom C1 is not in the residue template for GPC /Be:60 
    17166 11 messages similar to the above omitted 
    17167 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    17168  
    17169 Chain information for working.cif #2 
    17170 --- 
    17171 Chain | Description 
    17172 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ? 
    17173 AC AD | ? 
    17174 BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
    17175 bm bo bp | ? 
    17176 BB BD BE BI BQ BR BS BT BV BW bn | ? 
    17177 C | ? 
    17178 C1 | ? 
    17179 C2 | ? 
    17180 H1 | ? 
    17181 H2 | ? 
    17182 L | ? 
    17183 M | ? 
    17184 aa | ? 
    17185 ab ad ae af ag ah ai aj al am an ao ap | ? 
    17186 ac | ? 
    17187 ak | ? 
    17188  
    17189 
    17190 > cartoon #2
    17191 
    17192 > hide #2
    17193 
    17194 > matchmaker #2 to #1
    17195 
    17196 Parameters 
    17197 --- 
    17198 Chain pairing | bb 
    17199 Alignment algorithm | Needleman-Wunsch 
    17200 Similarity matrix | BLOSUM-62 
    17201 SS fraction | 0.3 
    17202 Gap open (HH/SS/other) | 18/18/6 
    17203 Gap extend | 1 
    17204 SS matrix |  |  | H | S | O 
    17205 ---|---|---|--- 
    17206 H | 6 | -9 | -6 
    17207 S |  | 6 | -6 
    17208 O |  |  | 4 
    17209 Iteration cutoff | 2 
    17210  
    17211 Matchmaker working.cif, chain M (#1) with working.cif, chain M (#2), sequence
    17212 alignment score = 1682.6 
    17213 RMSD between 291 pruned atom pairs is 0.195 angstroms; (across all 323 pairs:
    17214 4.491) 
    17215  
    17216 
    17217 > color #1 red
    17218 
    17219 > color #2 green
    17220 
    17221 > delete #2&~/C,H2,L,M,C1,H1
    17222 
    17223 > hide #!1 models
    17224 
    17225 > show #!8.2 models
    17226 
    17227 > select clear
    17228 
    17229 > delete #2/M:22-36
    17230 
    17231 > delete #2/M:22-52
    17232 
    17233 > select #2
    17234 
    17235 22948 atoms, 23331 bonds, 47 pseudobonds, 1275 residues, 3 models selected 
    17236 
    17237 > select #2&protein
    17238 
    17239 19393 atoms, 19722 bonds, 1 pseudobond, 1237 residues, 2 models selected 
    17240 
    17241 > hide #!2 models
    17242 
    17243 > select #8
    17244 
    17245 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 22 models selected 
    17246 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    17247 more memory-efficient implementation. 
    17248 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    17249 more memory-efficient implementation. 
    17250 
    17251 > select clear
    17252 
    17253 > select #8:C,H2,L,M,C1,H1
    17254 
    17255 Nothing selected 
    17256 
    17257 > select #8/C,H2,L,M,C1,H1
    17258 
    17259 24224 atoms, 24303 bonds, 15 pseudobonds, 1633 residues, 3 models selected 
    17260 
    17261 > isolde release distances sel externalOnly true
    17262 
    17263 > select clear
    17264 
    17265 > select #8/C,H2,L,M,C1,H1
    17266 
    17267 24224 atoms, 24303 bonds, 15 pseudobonds, 1633 residues, 3 models selected 
    17268 
    17269 > isolde adjust distances sel kappa 40
    17270 
    17271 > select clear
    17272 
    17273 > select clear
    17274 
    17275 > select /ak
    17276 
    17277 1282 atoms, 1289 bonds, 88 residues, 1 model selected 
    17278 
    17279 > close #8.2.10
    17280 
    17281 > delete :HOH
    17282 
    17283 > select up
    17284 
    17285 19 atoms, 18 bonds, 1 residue, 1 model selected 
    17286 
    17287 > select up
    17288 
    17289 267 atoms, 271 bonds, 21 residues, 1 model selected 
    17290 
    17291 > select up
    17292 
    17293 14 atoms, 14 bonds, 1 residue, 1 model selected 
    17294 
    17295 > select up
    17296 
    17297 267 atoms, 271 bonds, 21 residues, 1 model selected 
    17298 
    17299 > select clear
    17300 
    17301 > select up
    17302 
    17303 14 atoms, 14 bonds, 1 residue, 1 model selected 
    17304 
    17305 > delete sel
    17306 
    17307 > select clear
    17308 
    17309 > select clear
    17310 
    17311 > select up
    17312 
    17313 20 atoms, 19 bonds, 2 residues, 1 model selected 
    17314 
    17315 > delete sel
    17316 
    17317 > select up
    17318 
    17319 10 atoms, 9 bonds, 1 residue, 1 model selected 
    17320 
    17321 > select up
    17322 
    17323 253 atoms, 255 bonds, 20 residues, 1 model selected 
    17324 
    17325 > isolde ignore sel
    17326 
    17327 ISOLDE: currently ignoring 20 residues in model 8.2 
    17328 
    17329 > select /ak:59-71
    17330 
    17331 175 atoms, 177 bonds, 13 residues, 1 model selected 
    17332 
    17333 > setattr sel residues chain_id al
    17334 
    17335 Assigning chain_id attribute to 13 items 
    17336 Cannot set attribute 'chain_id' to 'al' 
    17337 
    17338 > save working.cxs
    17339 
    17340 Taking snapshot of stepper: working_2.pdb 
    17341 opened ChimeraX session 
    17342 
    17343 > ui tool show Shell
    17344 
    17345 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    17346 UserWarning: IPython History requires SQLite, your history will not be saved 
    17347 warn("IPython History requires SQLite, your history will not be saved") 
    17348 
    17349 > close #1-2
    17350 
    17351 > isolde start
    17352 
    17353 > set selectionWidth 4
    17354 
    17355 Done loading forcefield 
    17356 Loading residue template for LMG from internal database 
    17357 Loading residue template for PSF from internal database 
    17358 
    17359 > select up
    17360 
    17361 10 atoms, 9 bonds, 1 residue, 1 model selected 
    17362 
    17363 > ui mousemode right "translate selected atoms"
    17364 
    17365 > select /al:5-65
    17366 
    17367 923 atoms, 934 bonds, 61 residues, 1 model selected 
    17368 
    17369 Chain al, residue 67 specifies more than one residue! The simulation can still
    17370 run, but this will probably cause problems later if not rectified by
    17371 renumbering. 
    17372 
    17373 > cartoon
    17374 
    17375 > select clear
    17376 
    17377 > ~cartoon
    17378 
    17379 > cartoon
    17380 
    17381 > select up
    17382 
    17383 14 atoms, 14 bonds, 1 residue, 1 model selected 
    17384 
    17385 > select up
    17386 
    17387 92 atoms, 93 bonds, 8 residues, 1 model selected 
    17388 
    17389 > select up
    17390 
    17391 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
     20[deleted bulk of large, and largely irrelevant, log]
    1739221
    1739322> ~cartoon