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Opened 5 years ago

Last modified 5 years ago

#3892 closed defect

ChimeraX bug report submission — at Initial Version

Reported by:	Tristan Croll	Owned by:
Priority:	normal	Milestone:
Component:	Structure Editing	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
If I merge a fragment of peptide onto the end of an existing chain (in the middle of the model), the cartoon is broken at the join. If I reorder the residues in the model:

m.reorder_residues(Residues(sorted(m.residues, key=lambda r:(r.chain_id, r.number))))

... then the cartoon draws correctly.

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Thu Oct 29 17:29:15 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Thu Oct 29 16:35:33 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Wed Oct 28 21:12:33 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Tue Oct 27 22:03:57 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Fri Oct 23 21:33:44 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Fri Oct 23 12:38:35 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Thu Oct 22 21:38:47 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working_3.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Thu Oct 22 17:00:13 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/reopened.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Thu Oct 22 16:23:14 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open working_2.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Thu Oct 22 16:02:14 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Thu Oct 22 13:56:05 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open ../old_model_in_map_1b.cxs

Log from Thu Oct 22 06:57:21 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open model1b_working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Wed Oct 21 20:17:18 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open model1b_working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Wed Oct 21 20:13:59 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/model1b_working.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Wed Oct 21 19:55:36 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/rc-
> dlh1-model1b_rearranged.pdb format pdb

Chain information for rc-dlh1-model1b_rearranged.pdb #1  
---  
Chain | Description  
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
description available  
Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available  
Ag | No description available  
B | No description available  
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
Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available  
C | No description available  
C1 | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
  

> open
> /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/class1b_26A.mrc

Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
0.0224, step 2, values float32  

> clipper associate #2 toModel #1

Chain information for rc-dlh1-model1b_rearranged.pdb  
---  
Chain | Description  
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
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
1.2/AW 1.2/AX | No description available  
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
1.2/Am 1.2/An 1.2/Ao 1.2/Ap | No description available  
1.2/Ag | No description available  
1.2/B | No description available  
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
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
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
1.2/Bj 1.2/Bk 1.2/Bl 1.2/Bm 1.2/Bn 1.2/Bo 1.2/Bp | No description available  
1.2/C | No description available  
1.2/C1 | No description available  
1.2/H1 | No description available  
1.2/H2 | No description available  
1.2/L | No description available  
1.2/M | No description available  
  

> delete :GPC@HO45

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select ~protein

10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 8 models selected  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> select ~protein

10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 13 models selected  

> addh

Summary of feedback from adding hydrogens to rc-dlh1-model1b_rearranged.pdb
#1.2  
---  
warning | Skipped 8 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2)
chain AA; guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AB;
guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AC;
guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AD;
guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AE;
guessing termini instead  
82 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2, /AC
HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2, /AJ
HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2, /AQ
HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2, /AX
HIS 2, /Aa MET 1, /Ab MET 1, /Ac MET 1, /Ad MET 1, /Ae MET 1, /Af MET 1, /Ag
MET 1, /Ah MET 1, /Ai MET 1, /Aj MET 1, /Ak MET 1, /Al MET 1, /Am MET 1, /An
MET 1, /Ao MET 1, /Ap MET 1, /B PRO 25, /BA MET 1, /BB MET 1, /BC MET 1, /BD
MET 1, /BE MET 1, /BF MET 1, /BG MET 1, /BH MET 1, /BI MET 1, /BJ MET 1, /BK
MET 1, /BL MET 1, /BM MET 1, /BN MET 1, /BO MET 1, /BP MET 1, /BQ MET 1, /BR
MET 1, /BS MET 1, /BT MET 1, /BU MET 1, /BV MET 1, /BW MET 1, /BX MET 1, /Ba
MET 1, /Bb MET 1, /Bc MET 1, /Bd MET 1, /Be MET 1, /Bf MET 1, /Bg MET 1, /Bh
MET 1, /Bi MET 1, /Bj MET 1, /Bk MET 1, /Bl MET 1, /Bm MET 1, /Bn MET 1, /Bo
MET 1, /Bp MET 1, /C ALA 15, /H1 MET 1, /H2 SER 1, /L ALA 1, /M MET 1  
Chain-initial residues that are not actual N termini: /C1 GLN 1, /H2 ARG 38  
Chain-final residues that are actual C termini: /BA PHE 38, /BB PHE 38, /BC
PHE 38, /BD PHE 38, /BE PHE 38, /BF PHE 38, /BG PHE 38, /BH PHE 38, /BI PHE
38, /BJ PHE 38, /BK PHE 38, /BL PHE 38, /BM PHE 38, /BN PHE 38, /BO PHE 38,
/BP PHE 38, /BQ PHE 38, /BR PHE 38, /BS PHE 38, /BT PHE 38, /BU PHE 38, /BV
PHE 38, /BW PHE 38, /BX PHE 38, /Ba PHE 38, /Bb PHE 38, /Bc PHE 38, /Bd PHE
38, /Be PHE 38, /Bf PHE 38, /Bg PHE 38, /Bh PHE 38, /Bi PHE 38, /Bj PHE 38,
/Bk PHE 38, /Bl PHE 38, /Bm PHE 38, /Bn PHE 38, /Bo PHE 38, /Bp PHE 38  
Chain-final residues that are not actual C termini: /AA PRO 48, /AB PRO 48,
/AC PRO 48, /AD PRO 48, /AE PRO 48, /AF PRO 48, /AG PRO 48, /AH PRO 48, /AI
PRO 48, /AJ PRO 48, /AK PRO 48, /AL PRO 48, /AM PRO 48, /AN PRO 48, /AO PRO
48, /AP PRO 48, /AQ PRO 48, /AR PRO 48, /AS PRO 48, /AT PRO 48, /AU PRO 48,
/AV PRO 48, /AW PRO 48, /AX PRO 48, /Aa ALA 60, /Ab ALA 60, /Ac ALA 60, /Ad
ALA 60, /Ae ALA 60, /Af ALA 60, /Ag LEU 67, /Ah ALA 60, /Ai ALA 60, /Aj ALA
60, /Ak ALA 60, /Al ALA 60, /Am ALA 60, /An ALA 60, /Ao ALA 60, /Ap ALA 60, /B
ILE 123, /C ILE 313, /C1 LEU 92, /H1 HIS 67, /H2 ILE 181, /H2 ARG 36, /L TRP
272, /M TYR 324  
Skipping possible acceptor with bad geometry: /C ARG 302 O  
Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O  
  
Skipping possible acceptor with bad geometry: /C ARG 302 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT  
  
Skipping possible acceptor with bad geometry: /C ARG 302 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT  
  
Skipping possible acceptor with bad geometry: /C ARG 302 O  
Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O  
  
Skipping possible acceptor with bad geometry: /C ARG 302 O  
Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O  
  
3 messages similar to the above omitted  
4746 hydrogen bonds  
Adding 'H' to /H2 ARG 38  
/AA PRO 48 is not terminus, removing H atom from 'C'  
/AB PRO 48 is not terminus, removing H atom from 'C'  
/AC PRO 48 is not terminus, removing H atom from 'C'  
/AD PRO 48 is not terminus, removing H atom from 'C'  
/AE PRO 48 is not terminus, removing H atom from 'C'  
42 messages similar to the above omitted  
44090 hydrogens added  
  

> save model1b_working.cxs

opened ChimeraX session  

> select up

101 atoms, 100 bonds, 1 residue, 1 model selected  

> show sel

> select clear

> style sel ball

Changed 100 atom styles  

> select :GPC

4013 atoms, 3973 bonds, 40 residues, 1 model selected  

> show sel

> select :GPC@HC19

40 atoms, 40 residues, 1 model selected  

> select :GPC

4013 atoms, 3973 bonds, 40 residues, 1 model selected  

> delete sel

MD template USER_BCL for residue BCL L604 contains extra atoms that are not in
a coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

> select sel&@CBD

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> select up

139 atoms, 147 bonds, 1 residue, 1 model selected  
Deleted the following atoms from residue BCL L604: HHC1, HHD1  
Deleted the following atoms from residue BCL L602: HHD2, HHC2, HHD1, HHC1  
Deleted the following atoms from residue BPH L606: H12, H92, HHD1, H41, H93,
H91, H52, H11, HHD2, H43, H61, H51, H62, H42, H71, H72  

> save model1b_working.cxs

opened ChimeraX session  
Deleted the following atoms from residue MQ8 M405: H272, H9, H502, H122, C49,
C46, H172, H503, C50, H461, H471, H222, H11, H422, H492, H6, H472, C48, H462,
H7, H501, C47, H8, H491, H372, H322  
Deleted the following atoms from residue BCL M601: HHD2, HHD1  
Deleted the following atoms from residue BCL M603: HHD1, HHD2, HHC1, HHC2  
Deleted the following atoms from residue BPH M605: H11, H62, H72, H42, H12,
H91, H52, H71, HHD2, H93, H51, H92, HHD1, H61, H43, H41  
Residue RCC M701 has only 0 connected atoms in common with template GPC. At
least 3 matching atoms are needed.  

> save model1b_working.cxs

> delete sel

> save model1b_working.cxs

opened ChimeraX session  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb  
---  
warnings | Ignored bad PDB record found on line 317  
LINK NE2 HIS AA 29 MG BCL AA 57  
  
Ignored bad PDB record found on line 318  
LINK NE2 HIS AB 29 MG BCL AB 57  
  
Ignored bad PDB record found on line 319  
LINK NE2 HIS AC 29 MG BCL AC 57  
  
Ignored bad PDB record found on line 320  
LINK NE2 HIS AD 29 MG BCL AD 57  
  
Ignored bad PDB record found on line 321  
LINK NE2 HIS AE 29 MG BCL AE 57  
  
75 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 PROAA 10 PHEAA 36 1
26  
Start residue of secondary structure not found: HELIX 2 2 ALAAA 40 LYSAA 45 1
5  
Start residue of secondary structure not found: HELIX 3 3 ARGAB 3 TRPAB 5 1 2  
Start residue of secondary structure not found: HELIX 4 4 PROAB 10 GLNAB 35 1
25  
Start residue of secondary structure not found: HELIX 5 5 ALAAB 40 LEUAB 42 1
2  
207 messages similar to the above omitted  
  
Chain information for working_noh_real_space_refined.pdb #2  
---  
Chain | Description  
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
description available  
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
bi bj bk bl bm bo bp | No description available  
BB BD BE BI BV BW bn | No description available  
C | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
UA | No description available  
UB | No description available  
UC | No description available  
aa | No description available  
ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker rc-dlh1-model1b_rearranged.pdb, chain M (#1.2) with
working_noh_real_space_refined.pdb, chain M (#2), sequence alignment score =
1582  
RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 324 pairs:
1.723)  
  

> delete #2/UA,UB,UC

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc

Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
0.0224, step 2, values float32  

> clipper associate #3 toModel #2

Chain information for working_noh_real_space_refined.pdb  
---  
Chain | Description  
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
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
2.2/AW 2.2/AX | No description available  
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
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
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 |
No description available  
2.2/BB 2.2/BD 2.2/BE 2.2/BI 2.2/BV 2.2/BW 2.2/bn | No description available  
2.2/C | No description available  
2.2/H1 | No description available  
2.2/H2 | No description available  
2.2/L | No description available  
2.2/M | No description available  
2.2/aa | No description available  
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
2.2/am 2.2/an 2.2/ao 2.2/ap | No description available  
  

> select #2:GPC

1800 atoms, 1760 bonds, 40 residues, 1 model selected  

> select #2:RCC

Nothing selected  

> select #1:RCC

100 atoms, 99 bonds, 1 residue, 1 model selected  

> select #2:GPC

1800 atoms, 1760 bonds, 40 residues, 1 model selected  

> select #1:GPC

4000 atoms, 3960 bonds, 40 residues, 1 model selected  

> select #2:GPC

1800 atoms, 1760 bonds, 40 residues, 1 model selected  

> delete sel

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> delete #2:GP1

> select #1:RCC

100 atoms, 99 bonds, 1 residue, 1 model selected  

> select #1:RCC,GCC

100 atoms, 99 bonds, 1 residue, 1 model selected  

> select #1:RCC,GPC

4100 atoms, 4059 bonds, 41 residues, 1 model selected  

> close #1

> addh

Summary of feedback from adding hydrogens to
working_noh_real_space_refined.pdb #2.2  
---  
notes | No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2)
chain AA; guessing termini instead  
No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
AB; guessing termini instead  
No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
AC; guessing termini instead  
No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
AD; guessing termini instead  
No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
AE; guessing termini instead  
80 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2, /AC
HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2, /AJ
HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2, /AQ
HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2, /AX
HIS 2, /BA GLY 6, /BB GLY 5, /BC GLY 6, /BD GLY 5, /BE GLY 5, /BF GLY 6, /BG
GLY 6, /BH GLY 6, /BI GLY 5, /BJ GLY 6, /BK GLY 6, /BL GLY 6, /BM GLY 6, /BN
GLY 6, /BO GLY 6, /BP GLY 6, /BQ GLY 6, /BR GLY 6, /BS GLY 6, /BT GLY 6, /BU
GLY 6, /BV GLY 5, /BW GLY 5, /BX GLY 6, /C ALA 15, /H1 MET 1, /H2 SER 1, /L
ALA 1, /M MET 1, /aa HIS 2, /ab MET 1, /ac MET 1, /ad MET 1, /ae MET 1, /af
MET 1, /ag MET 1, /ah MET 1, /ai MET 1, /aj MET 1, /ak MET 1, /al MET 1, /am
MET 1, /an MET 1, /ao MET 1, /ap MET 1, /ba GLY 6, /bb GLY 6, /bc GLY 6, /bd
GLY 6, /be GLY 6, /bf GLY 6, /bg GLY 6, /bh GLY 6, /bi GLY 6, /bj GLY 6, /bk
GLY 6, /bl GLY 6, /bm GLY 6, /bn GLY 5, /bo GLY 6, /bp GLY 6  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /BA PHE 44, /BB PHE 44, /BC
PHE 44, /BD PHE 44, /BE PHE 44, /BF PHE 44, /BG PHE 44, /BH PHE 44, /BI PHE
44, /BJ PHE 44, /BK PHE 44, /BL PHE 44, /BM PHE 44, /BN PHE 44, /BO PHE 44,
/BP PHE 44, /BQ PHE 44, /BR PHE 44, /BS PHE 44, /BT PHE 44, /BU PHE 44, /BV
PHE 44, /BW PHE 44, /BX PHE 44, /C ARG 302, /H2 ILE 181, /L LYS 273, /ba PHE
44, /bb PHE 44, /bc PHE 44, /bd PHE 44, /be PHE 44, /bf PHE 44, /bg PHE 44,
/bh PHE 44, /bi PHE 44, /bj PHE 44, /bk PHE 44, /bl PHE 44, /bm PHE 44, /bn
PHE 44, /bo PHE 44, /bp PHE 44  
Chain-final residues that are not actual C termini: /AA TYR 46, /AB TYR 46,
/AC TYR 46, /AD TYR 46, /AE TYR 46, /AF TYR 46, /AG TYR 46, /AH TYR 46, /AI
TYR 46, /AJ TYR 46, /AK TYR 46, /AL TYR 46, /AM TYR 46, /AN TYR 46, /AO TYR
46, /AP TYR 46, /AQ TYR 46, /AR TYR 46, /AS TYR 46, /AT TYR 46, /AU TYR 46,
/AV TYR 46, /AW TYR 46, /AX TYR 46, /H1 LYS 53, /M TYR 324, /aa ALA 60, /ab
ALA 60, /ac ALA 60, /ad ALA 60, /ae ALA 60, /af ALA 60, /ag ALA 60, /ah ALA
60, /ai ALA 60, /aj ALA 60, /ak ALA 60, /al ALA 60, /am ALA 60, /an ALA 60,
/ao ALA 60, /ap ALA 60  
4864 hydrogen bonds  
/AA TYR 46 is not terminus, removing H atom from 'C'  
/AB TYR 46 is not terminus, removing H atom from 'C'  
/AC TYR 46 is not terminus, removing H atom from 'C'  
/AD TYR 46 is not terminus, removing H atom from 'C'  
/AE TYR 46 is not terminus, removing H atom from 'C'  
37 messages similar to the above omitted  
43714 hydrogens added  
  

> hide HC

> select ~protein

16594 atoms, 16919 bonds, 365 pseudobonds, 133 residues, 8 models selected  

> select clear

> save old_model_in_map_1b.cxs

opened ChimeraX session  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select :GPC

4013 atoms, 3973 bonds, 40 residues, 1 model selected  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select clear

> delete sel

> delete sel

> delete sel

> delete sel

> save ready.cxs

> select gpc

Expected an objects specifier or a keyword  

> select :GPC

4000 atoms, 3960 bonds, 40 residues, 1 model selected  

> select :GPC

4000 atoms, 3960 bonds, 40 residues, 1 model selected  

> show sel

> select clear

> show sel

> save ready.cxs

> volume gaussian #1 bfactor 50

> volume gaussian #2 bfactor 50

> clipper associate #1 toModel #2

> hide HC

> select #1

Nothing selected  

> select #2

91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected  

> clipper set contourSensitivity 0.25

> select clear

> set bgColor white

> select #1

Nothing selected  

> select #2

91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected  

> select clear

> select #2

91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected  

> select #1

Nothing selected  

> select #2

91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE B 5
TYR B 9 1 5  
Start residue of secondary structure not found: HELIX 2 2 ARG B 22 ARG B 52 1
31  
Start residue of secondary structure not found: HELIX 3 3 VAL B 55 ARG B 86 1
32  
  
Chain information for assigned_sequence.pdb #1  
---  
Chain | Description  
Ba | No description available  
  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR C 19
GLY C 21 1 3  
Start residue of secondary structure not found: HELIX 2 2 VAL C 28 VAL C 31 1
4  
Start residue of secondary structure not found: HELIX 3 3 VAL C 32 HIS C 34 1
3  
Start residue of secondary structure not found: HELIX 4 4 GLY C 61 ILE C 64 1
4  
Start residue of secondary structure not found: HELIX 5 5 MET C 71 LYS C 74 1
4  
3 messages similar to the above omitted  
  
Chain information for sequence_assigned.pdb #3  
---  
Chain | Description  
C1 | No description available  
  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/rc-
> dlh1-model1b_rearranged.pdb

Chain information for rc-dlh1-model1b_rearranged.pdb #4  
---  
Chain | Description  
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
description available  
Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available  
Ag | No description available  
B | No description available  
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
Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available  
C | No description available  
C1 | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
  

> hide #!4 models

> select #3

1472 atoms, 1487 bonds, 92 residues, 1 model selected  

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> hide #3 models

> select #1

1516 atoms, 1537 bonds, 99 residues, 1 model selected  

> select #2/Ba

100 atoms, 99 bonds, 1 residue, 1 model selected  

> view sel

> select #1

1516 atoms, 1537 bonds, 99 residues, 1 model selected  

> select clear

> select /AA

1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected  

> select /BA

1151 atoms, 1189 bonds, 4 pseudobonds, 79 residues, 3 models selected  

> isolde stepto /AA

Multiple residues selected! Going to the first...  

> select /AA

1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected  

> select clear

> select clear

> select /AA

1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected  

> select clear

> sequence chain /AA

Chains must have same sequence  

> sequence chain #1/AA

Chains must have same sequence  

> sequence chain #2/AA

Alignment identifier is 2.2/AA  

> select /AA

1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected  

> select clear

> select clear

> select /AA

1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected  

> select clear

> select clear

> show #!4 models

> select #4/AS

540 atoms, 558 bonds, 4 pseudobonds, 49 residues, 2 models selected  

> select clear

> select #4

51294 atoms, 53027 bonds, 354 pseudobonds, 5083 residues, 3 models selected  

> style sel stick

Changed 51294 atom styles  

> select clear

> hide #!4 models

> select clear

> isolde stepto /C

Multiple residues selected! Going to the first...  

> select /C:15-200

4296 atoms, 4372 bonds, 372 residues, 2 models selected  

> select clear

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> isolde stepto

> isolde stepto

> isolde stepto

> show #!4 models

> hide #!4 models

reverting to start  

> select /C1

4416 atoms, 4461 bonds, 276 residues, 3 models selected  

> isolde ignore /C1:30-300

ISOLDE: currently ignoring 63 residues in model 2.2  
ISOLDE: currently ignoring 63 residues in model 3  
ISOLDE: currently ignoring 63 residues in model 4  

> select /C:15-200

4296 atoms, 4372 bonds, 372 residues, 2 models selected  

> select /M:311-400

359 atoms, 361 bonds, 28 residues, 2 models selected  

> select clear

> isolde ~ignore

> show #!4 models

> hide #!4 models

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> select /C:15-200

4296 atoms, 4372 bonds, 372 residues, 2 models selected  

> select clear

> isolde stepto

> hide #1 models

> isolde ignore /C2

ISOLDE: currently ignoring 99 residues in model 2.2  

> select /H2:120-129

241 atoms, 251 bonds, 20 residues, 2 models selected  

> select clear

> select clear

> isolde ~ignore

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 2.2  

> isolde ~ignore

> select clear

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 2.2  

> isolde ~ignore

> select up

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

105 atoms, 108 bonds, 7 residues, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 8 residues in model 2.2  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

939 atoms, 951 bonds, 60 residues, 1 model selected  

> select clear

> show #!4 models

> select clear

> hide #!4 models

> select clear

> select clear

> select clear

> select clear

> select clear

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> select /C:15-200

4296 atoms, 4372 bonds, 372 residues, 2 models selected  

> select clear

> isolde stepto /C

Multiple residues selected! Going to the first...  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> show #!4 models

> hide #!4 models

> isolde stepto

> isolde stepto

> isolde stepto

> show #!4 models

> hide #!4 models

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> select clear

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

450 atoms, 459 bonds, 30 residues, 1 model selected  

> select clear

> select clear

> select /C:64-200

3217 atoms, 3269 bonds, 274 residues, 2 models selected  

> select clear

> select clear

> select clear

> isolde stepto /C:64

Multiple residues selected! Going to the first...  

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> delete sel

> select /C:99-200

2415 atoms, 2455 bonds, 204 residues, 2 models selected  

> select clear

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> show #!4 models

> hide #!4 models

> select /C:179-189

241 atoms, 241 bonds, 22 residues, 2 models selected  

> select #2/C:179-189

162 atoms, 162 bonds, 11 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> select /C:200-400

2486 atoms, 2541 bonds, 217 residues, 2 models selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> show #!4 models

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> select #4/C:303-313

83 atoms, 87 bonds, 11 residues, 1 model selected  

> select clear

> hide #!4 models

> select #2/C:303-400

83 atoms, 87 bonds, 11 residues, 1 model selected  

> show sel

> delete sell

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> addh #4

Summary of feedback from adding hydrogens to rc-dlh1-model1b_rearranged.pdb #4  
---  
warning | Skipped 8 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain
AA; guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AB;
guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AC;
guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AD;
guessing termini instead  
No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AE;
guessing termini instead  
82 messages similar to the above omitted  
Chain-initial residues that are actual N termini: rc-
dlh1-model1b_rearranged.pdb #4/AA HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AB
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AC HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/AD HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AE
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AF HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/AG HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AH
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AI HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/AJ HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AK
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AL HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/AM HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AN
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AO HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/AP HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AQ
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AR HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/AS HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AT
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AU HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/AV HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AW
HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AX HIS 2, rc-
dlh1-model1b_rearranged.pdb #4/Aa MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ab
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ac MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Ad MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ae
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Af MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Ag MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ah
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ai MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Aj MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ak
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Al MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Am MET 1, rc-dlh1-model1b_rearranged.pdb #4/An
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ao MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Ap MET 1, rc-dlh1-model1b_rearranged.pdb #4/B
PRO 25, rc-dlh1-model1b_rearranged.pdb #4/BA MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BB MET 1, rc-dlh1-model1b_rearranged.pdb #4/BC
MET 1, rc-dlh1-model1b_rearranged.pdb #4/BD MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BE MET 1, rc-dlh1-model1b_rearranged.pdb #4/BF
MET 1, rc-dlh1-model1b_rearranged.pdb #4/BG MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BH MET 1, rc-dlh1-model1b_rearranged.pdb #4/BI
MET 1, rc-dlh1-model1b_rearranged.pdb #4/BJ MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BK MET 1, rc-dlh1-model1b_rearranged.pdb #4/BL
MET 1, rc-dlh1-model1b_rearranged.pdb #4/BM MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BN MET 1, rc-dlh1-model1b_rearranged.pdb #4/BO
MET 1, rc-dlh1-model1b_rearranged.pdb #4/BP MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BQ MET 1, rc-dlh1-model1b_rearranged.pdb #4/BR
MET 1, rc-dlh1-model1b_rearranged.pdb #4/BS MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BT MET 1, rc-dlh1-model1b_rearranged.pdb #4/BU
MET 1, rc-dlh1-model1b_rearranged.pdb #4/BV MET 1, rc-
dlh1-model1b_rearranged.pdb #4/BW MET 1, rc-dlh1-model1b_rearranged.pdb #4/BX
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ba MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Bb MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bc
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bd MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Be MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bf
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bg MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Bh MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bi
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bj MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Bk MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bl
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bm MET 1, rc-
dlh1-model1b_rearranged.pdb #4/Bn MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bo
MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bp MET 1, rc-
dlh1-model1b_rearranged.pdb #4/C ALA 15, rc-dlh1-model1b_rearranged.pdb #4/H1
MET 1, rc-dlh1-model1b_rearranged.pdb #4/H2 SER 1, rc-
dlh1-model1b_rearranged.pdb #4/L ALA 1, rc-dlh1-model1b_rearranged.pdb #4/M
MET 1  
Chain-initial residues that are not actual N termini: rc-
dlh1-model1b_rearranged.pdb #4/C1 GLN 1, rc-dlh1-model1b_rearranged.pdb #4/H2
ARG 38  
Chain-final residues that are actual C termini: rc-dlh1-model1b_rearranged.pdb
#4/BA PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BB PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BC PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BD
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BE PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BF PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BG
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BH PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BI PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BJ
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BK PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BL PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BM
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BN PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BO PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BP
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BQ PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BR PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BS
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BT PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BU PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BV
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BW PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/BX PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Ba
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bb PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/Bc PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bd
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Be PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/Bf PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bg
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bh PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/Bi PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bj
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bk PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/Bl PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bm
PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bn PHE 38, rc-
dlh1-model1b_rearranged.pdb #4/Bo PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bp
PHE 38  
Chain-final residues that are not actual C termini: rc-
dlh1-model1b_rearranged.pdb #4/AA PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AB
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/AD PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AE
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AF PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/AG PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AH
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AI PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/AJ PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AK
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AL PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/AM PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AN
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AO PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/AP PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AQ
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AR PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/AS PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AT
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AU PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/AV PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AW
PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AX PRO 48, rc-
dlh1-model1b_rearranged.pdb #4/Aa ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ab
ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ac ALA 60, rc-
dlh1-model1b_rearranged.pdb #4/Ad ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ae
ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Af ALA 60, rc-
dlh1-model1b_rearranged.pdb #4/Ag LEU 67, rc-dlh1-model1b_rearranged.pdb #4/Ah
ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ai ALA 60, rc-
dlh1-model1b_rearranged.pdb #4/Aj ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ak
ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Al ALA 60, rc-
dlh1-model1b_rearranged.pdb #4/Am ALA 60, rc-dlh1-model1b_rearranged.pdb #4/An
ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ao ALA 60, rc-
dlh1-model1b_rearranged.pdb #4/Ap ALA 60, rc-dlh1-model1b_rearranged.pdb #4/B
ILE 123, rc-dlh1-model1b_rearranged.pdb #4/C ILE 313, rc-
dlh1-model1b_rearranged.pdb #4/C1 LEU 92, rc-dlh1-model1b_rearranged.pdb #4/H1
HIS 67, rc-dlh1-model1b_rearranged.pdb #4/H2 ILE 181, rc-
dlh1-model1b_rearranged.pdb #4/H2 ARG 36, rc-dlh1-model1b_rearranged.pdb #4/L
TRP 272, rc-dlh1-model1b_rearranged.pdb #4/M TYR 324  
Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
#4/C ARG 302 O  
Wrong number of grandchild atoms for phi/psi acceptor rc-
dlh1-model1b_rearranged.pdb #4/C ARG 302 O  
  
Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
#4/C ARG 302 OXT  
Wrong number of grandchild atoms for phi/psi acceptor rc-
dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT  
  
Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
#4/C ARG 302 OXT  
Wrong number of grandchild atoms for phi/psi acceptor rc-
dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT  
  
Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
#4/C ARG 302 O  
Wrong number of grandchild atoms for phi/psi acceptor rc-
dlh1-model1b_rearranged.pdb #4/C ARG 302 O  
  
Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
#4/C ARG 302 O  
Wrong number of grandchild atoms for phi/psi acceptor rc-
dlh1-model1b_rearranged.pdb #4/C ARG 302 O  
  
3 messages similar to the above omitted  
4768 hydrogen bonds  
Adding 'H' to rc-dlh1-model1b_rearranged.pdb #4/H2 ARG 38  
rc-dlh1-model1b_rearranged.pdb #4/AA PRO 48 is not terminus, removing H atom
from 'C'  
rc-dlh1-model1b_rearranged.pdb #4/AB PRO 48 is not terminus, removing H atom
from 'C'  
rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48 is not terminus, removing H atom
from 'C'  
rc-dlh1-model1b_rearranged.pdb #4/AD PRO 48 is not terminus, removing H atom
from 'C'  
rc-dlh1-model1b_rearranged.pdb #4/AE PRO 48 is not terminus, removing H atom
from 'C'  
42 messages similar to the above omitted  
44090 hydrogens added  
  

> select #2/C:303-400

157 atoms, 161 bonds, 11 residues, 1 model selected  

> select clear

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> show #!4 models

> hide #!4 models

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

874 atoms, 890 bonds, 53 residues, 1 model selected  

> select #2/H1:3-100

838 atoms, 854 bonds, 51 residues, 1 model selected  

> show #!4 models

> hide #!4 models

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> show #!4 models

> hide #!4 models

> select up

38 atoms, 40 bonds, 2 residues, 1 model selected  

> select clear

> select clear

> select #1

1516 atoms, 1537 bonds, 99 residues, 1 model selected  

> select #2

94789 atoms, 96857 bonds, 14 pseudobonds, 5061 residues, 22 models selected  

> style sel sphere

Changed 94789 atom styles  

> select clear

> style #!2.2 stick

Changed 94789 atom styles  

> delete sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> delete sel

> delete sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> delete sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select #2/H2

2777 atoms, 2816 bonds, 180 residues, 1 model selected  

> select clear

> isolde jumpto

> select #2/H2:3-100

1476 atoms, 1499 bonds, 97 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

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> select #2/H2:3-100

1476 atoms, 1499 bonds, 97 residues, 1 model selected  

> select clear

> isolde stepto

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> select #2/H1:95-205

Nothing selected  

> select #2/H1:95-205

Nothing selected  

> select #2/H2:95-205

1376 atoms, 1394 bonds, 87 residues, 1 model selected  

> select clear

> isolde stepto

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> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> isolde stepto

> select #2/L:1-100

1563 atoms, 1592 bonds, 100 residues, 1 model selected  

> select clear

> isolde stepto

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> select clear

> isolde stepto

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> select clear

> isolde stepto

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> select #2/L:100-300

2756 atoms, 2816 bonds, 174 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

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> select clear

> isolde stepto

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> select clear

> isolde stepto

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> select clear

> isolde stepto

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> select clear

> isolde stepto

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> swapaa mousemode sel ILE

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> color sel bychain

> color sel byhetero

> select #2/L:227-400

777 atoms, 798 bonds, 47 residues, 1 model selected  

> hide HC

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

> color bychain

> color byhetero

> hide HC

> select #2/L:227-400

777 atoms, 798 bonds, 47 residues, 1 model selected  

> select clear

> isolde stepto

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> select clear

> show H&~HC

> select clear

> show H&~HC

> show ~H

> select #2/L:227-400

777 atoms, 798 bonds, 47 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

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> isolde stepto

> select #2/M

5833 atoms, 5950 bonds, 6 pseudobonds, 330 residues, 2 models selected  

> select #2/M:1-50

763 atoms, 772 bonds, 50 residues, 1 model selected  

> select clear

> isolde stepto

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> select clear

> select clear

> isolde stepto

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> select #2/M:58-158

1664 atoms, 1698 bonds, 101 residues, 1 model selected  

> select clear

> select #2/M:58-158

1664 atoms, 1698 bonds, 101 residues, 1 model selected  

> select clear

> isolde stepto

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> select clear

> isolde stepto

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> isolde stepto

> sequence chain #2/M

Alignment identifier is 2.2/M  

> select #2/M:58-158

1665 atoms, 1699 bonds, 101 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

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> select clear

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> select clear

> isolde stepto

> isolde stepto

> isolde stepto

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> select clear

> isolde stepto

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> select clear

> isolde stepto

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> isolde stepto

> isolde stepto

> delete sel

> select #2/M:178-400

2337 atoms, 2378 bonds, 147 residues, 1 model selected  

> select clear

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

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> select clear

> isolde stepto

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> isolde stepto

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> select clear

> isolde stepto

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> select clear

> isolde stepto

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> isolde stepto

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> isolde stepto

> isolde stepto

> select clear

> isolde stepto

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> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> show #!4 models

> hide #!4 models

> swapaa mousemode sel GLY

> select up

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

255 atoms, 259 bonds, 18 residues, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 26 residues in model 2.2  

> select clear

> isolde ~ignore

> select up

23 atoms, 21 bonds, 2 residues, 1 model selected  

> select clear

> delete sel

> delete sel

> select clear

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> ui tool show "Build Structure"

> build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> rotLib Dunbrack

Chain information for custom built #5  
---  
Chain | Description  
A | No description available  
  

> build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> rotLib Dunbrack

Chain information for custom built #6  
---  
Chain | Description  
A | No description available  
  

> close #5

> select #6

258 atoms, 263 bonds, 36 residues, 1 model selected  

> show sel&:1

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> hide #6 models

> delete #2/M:332-367

> addh #6

Summary of feedback from adding hydrogens to custom built #6  
---  
notes | No usable SEQRES records for custom built (#6) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: custom built #6/A PHE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: custom built #6/A GLN 36  
Chain-final residues that are not actual C termini:  
37 hydrogen bonds  
250 hydrogens added  
  

> isolde ignore #2/C

ISOLDE: currently ignoring 303 residues in model 2.2  

> select #2/M:332-367

506 atoms, 511 bonds, 36 residues, 1 model selected  

> hide HC

> delete #2/M:339-367

> isolde ~ignore

> select clear

> select clear

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

92 atoms, 94 bonds, 6 residues, 1 model selected  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> delete sel

> save ser_M331_O_glycan.jpg

> open 3e80

3e80 title:  
Structure of Heparinase II complexed with heparan sulfate degradation
disaccharide product [more info...]  
  
Chain information for 3e80 #5  
---  
Chain | Description  
A B C | Heparinase II protein  
  
Non-standard residues in 3e80 #5  
---  
GCD — 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid  
GCU — alpha-D-glucopyranuronic acid  
MAN — alpha-D-mannopyranose  
NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose  
PO4 — phosphate ion  
RAM — alpha-L-rhamnopyranose  
XYS — alpha-D-xylopyranose  
ZN — zinc ion  
  
3e80 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  

> addh #5

Summary of feedback from adding hydrogens to 3e80 #5  
---  
warning | Not adding hydrogens to 3e80 #5/C LEU 732 CB because it is missing
heavy-atom bond partners  
notes | Termini for 3e80 (#5) chain A determined from SEQRES records  
Termini for 3e80 (#5) chain B determined from SEQRES records  
Termini for 3e80 (#5) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 3e80 #5/A PCA 26, 3e80
#5/B PCA 26, 3e80 #5/C PCA 26  
Chain-final residues that are actual C termini: 3e80 #5/A ARG 772, 3e80 #5/B
ARG 772, 3e80 #5/C ARG 772  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 3e80 #5/A ARG 772  
Missing OXT added to C-terminal residue 3e80 #5/B ARG 772  
Missing OXT added to C-terminal residue 3e80 #5/C ARG 772  
3540 hydrogen bonds  
Adding 'H' to 3e80 #5/A PCA 26  
Adding 'H' to 3e80 #5/B PCA 26  
Adding 'H' to 3e80 #5/C PCA 26  
18911 hydrogens added  
  

> select #5

37630 atoms, 37586 bonds, 17 pseudobonds, 2807 residues, 2 models selected  

> hide #!2 models

> select clear

> select clear

> select #5/B:134|(#5/E:1-4)

90 atoms, 93 bonds, 5 residues, 1 model selected  

> hide #5&~sel

> ~cartoon #5

> show #!2 models

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select (#5/E:1-4)

77 atoms, 80 bonds, 4 residues, 1 model selected  

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  
Restoring stepper: working_noh_real_space_refined.pdb  
opened ChimeraX session  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 55 55 THR C 19
GLY C 21 1 3  
Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C 34
1 7  
Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C 55
1 3  
Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C 69
1 6  
Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C 81
1 7  
Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C 91
1 3  
5 messages similar to the above omitted  
Cannot find LINK/SSBOND residue GCU (2 )  
Cannot find LINK/SSBOND residue XYS (3 )  
Cannot find LINK/SSBOND residue RAM (4 )  
Cannot find LINK/SSBOND residue MAN (1 )  
Cannot find LINK/SSBOND residue GCU (2 )  
3 messages similar to the above omitted  
  
Chain information for working.pdb #7  
---  
Chain | Description  
AA | No description available  
AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
description available  
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
bi bj bk bl bm bo bp | No description available  
BB BD BE BI BV BW bn | No description available  
C | No description available  
C1 | No description available  
C2 | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
aa | No description available  
ab ac ad ae af ag ah ai aj am an ao ap | No description available  
ak | No description available  
  

> select clear

> hide #7&protein

> hide #!5 models

> select #7/CG

78 atoms, 81 bonds, 4 residues, 1 model selected  

> hide #!7 models

> delete sel

> select clear

> select clear

> view #2/M:330

> show #!7 models

> select #7/MG

78 atoms, 81 bonds, 4 residues, 1 model selected  

> hide #!7 models

> delete sel

> select clear

> select clear

> save M331_glycan.jpg

> save working.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  

> select #2/ak

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> ui tool show "Build Structure"

> build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack

Chain information for custom built #8  
---  
Chain | Description  
A | No description available  
  

> addh #8

Summary of feedback from adding hydrogens to custom built #8  
---  
notes | No usable SEQRES records for custom built (#8) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: custom built #8/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: custom built #8/A ARG 11  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
80 hydrogens added  
  

> select #8

158 atoms, 160 bonds, 11 residues, 1 model selected  

> show sel

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> save working_2.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  
Restoring stepper: working_noh_real_space_refined.pdb  
opened ChimeraX session  

> save
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
> models #2

> close #2

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 55 55 THR C 19
GLY C 21 1 3  
Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C 34
1 7  
Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C 55
1 3  
Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C 69
1 6  
Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C 81
1 7  
Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C 91
1 3  
5 messages similar to the above omitted  
Cannot find LINK/SSBOND residue GCU (2 )  
Cannot find LINK/SSBOND residue XYS (3 )  
Cannot find LINK/SSBOND residue RAM (4 )  
Cannot find LINK/SSBOND residue MAN (1 )  
Cannot find LINK/SSBOND residue GCU (2 )  
3 messages similar to the above omitted  
  
Chain information for working_2.pdb #8  
---  
Chain | Description  
AA | No description available  
AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
description available  
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
bi bj bk bl bm bo bp | No description available  
BB BD BE BI BV BW bn | No description available  
C | No description available  
C1 | No description available  
C2 | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
aa | No description available  
ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available  
  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc

Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
0.0224, step 2, values float32  

> clipper associate #9 toModel #8

Chain information for working_2.pdb  
---  
Chain | Description  
8.2/AA | No description available  
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
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
8.2/AX | No description available  
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
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
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 |
No description available  
8.2/BB 8.2/BD 8.2/BE 8.2/BI 8.2/BV 8.2/BW 8.2/bn | No description available  
8.2/C | No description available  
8.2/C1 | No description available  
8.2/C2 | No description available  
8.2/H1 | No description available  
8.2/H2 | No description available  
8.2/L | No description available  
8.2/M | No description available  
8.2/aa | No description available  
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
8.2/am 8.2/an 8.2/ao 8.2/ap | No description available  
  

> close #1

> close #2

> select #3

508 atoms, 513 bonds, 36 residues, 8 models selected  

> hide #!4 models

> select #8/ak

1079 atoms, 1095 bonds, 4 pseudobonds, 61 residues, 2 models selected  

> hide #!3 models

> show #!3 models

> close #4

> view #3

> show #3

> hide #!3 models

> show #!3 models

> view #3

> close #3

> close #5

> close #6

> close #7

> volume gaussian #8 bfactor 50

> clipper associate #1 toModel #8

> select clear

> save reopened.cxs

Taking snapshot of stepper: working_noh_real_space_refined.pdb  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 633, in take_snapshot  
data = {'structure': self.structure,  
File "cymol.pyx", line 1437, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
saving session data for 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
saving session data for 'isolde residue stepper 1' -> ->  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 633, in take_snapshot  
data = {'structure': self.structure,  
File "cymol.pyx", line 1437, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
saving session data for 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
saving session data for 'isolde residue stepper 1' -> ->  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> isolde stepto sel

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> save reopened.cxs

Taking snapshot of stepper: working_2.pdb  
Taking snapshot of stepper: working_noh_real_space_refined.pdb  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 633, in take_snapshot  
data = {'structure': self.structure,  
File "cymol.pyx", line 1437, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
saving session data for 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
saving session data for 'isolde residue stepper 1' -> ->  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 633, in take_snapshot  
data = {'structure': self.structure,  
File "cymol.pyx", line 1437, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
saving session data for 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
<chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
saving session data for 'isolde residue stepper 1' -> ->  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save reopened.cxs

Taking snapshot of stepper: working_2.pdb  

> ui tool show "Build Structure"

> build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack

Chain information for custom built #1  
---  
Chain | Description  
A | No description available  
  

> addh #1

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: custom built #1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: custom built #1/A ARG 11  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
80 hydrogens added  
  

> select #1

158 atoms, 160 bonds, 11 residues, 1 model selected  

> show sel

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> save reopened.cxs

Taking snapshot of stepper: working_2.pdb  
Restoring stepper: working_2.pdb  
opened ChimeraX session  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select clear

> select clear

> select ~protein

16729 atoms, 17062 bonds, 366 pseudobonds, 140 residues, 23 models selected  

> select /ak

1238 atoms, 1261 bonds, 72 residues, 1 model selected  

> hide #!1 models

> select up

45 atoms, 44 bonds, 2 residues, 1 model selected  

> select up

71 atoms, 71 bonds, 4 residues, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 4 residues in model 8.2  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

939 atoms, 951 bonds, 60 residues, 1 model selected  

> select up

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select up

1179 atoms, 1198 bonds, 62 residues, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 66 residues in model 8.2  

> select up

20 atoms, 19 bonds, 1 residue, 1 model selected  

> select up

159 atoms, 161 bonds, 11 residues, 1 model selected  

Chain CG, residue 1 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain CG, residue 2 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain CG, residue 3 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain CG, residue 1 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain CG, residue 2 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain CG, residue 3 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> delete sel

> delete sel

> delete sel

> delete sel

> select up

99 atoms, 102 bonds, 4 residues, 1 model selected  

> select clear

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /ak

1234 atoms, 1257 bonds, 72 residues, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

155 atoms, 157 bonds, 11 residues, 1 model selected  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /MG

99 atoms, 102 bonds, 4 residues, 1 model selected  

> select up

42 atoms, 42 bonds, 1 residue, 1 model selected  

> select clear

> select sel&:MG

Nothing selected  

> select sel&/MG

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

42 atoms, 42 bonds, 1 residue, 1 model selected  

> select clear

> select up

99 atoms, 102 bonds, 4 residues, 1 model selected  

> select clear

> select up

42 atoms, 42 bonds, 1 residue, 1 model selected  

> delete sel

> isolde add ligand RAM

Deleted the following atoms from residue RAM CG4: O1, HO1  

> ui mousemode right "translate selected atoms"

> clipper set contourSensitivity 0.25

> select clear

> isolde add ligand RAM

Deleted the following atoms from residue RAM MG4: HO1, O1  

> delete sel

> isolde add ligand RAM

Deleted the following atoms from residue RAM MG4: HO1, O1  

> ui mousemode right "translate selected atoms"

> select clear

> select /ak

1234 atoms, 1257 bonds, 72 residues, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

155 atoms, 157 bonds, 11 residues, 1 model selected  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

155 atoms, 157 bonds, 11 residues, 1 model selected  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> isolde ~ignore

> save working_3.cxs

Taking snapshot of stepper: working_2.pdb  
Restoring stepper: working_2.pdb  
opened ChimeraX session  

> select /ak

1234 atoms, 1257 bonds, 72 residues, 1 model selected  

> select clear

> dssp

> select /AA

981 atoms, 1002 bonds, 48 residues, 1 model selected  

> isolde stepto /AB

Multiple residues selected! Going to the first...  

> clipper set contourSensitivity 0.25

> select /AB

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AC

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto prev

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> select /AD

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> select /AE

980 atoms, 1001 bonds, 48 residues, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AF

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> swapaa mousemode sel PRO

Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2724, in start_sim  
main_sel = self._last_main_sel = self._get_main_sim_selection()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
  
See log for complete Python traceback.  
  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AG

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AG

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select /AG, ak

2214 atoms, 2258 bonds, 120 residues, 1 model selected  

> select /AG

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AH

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AI

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> save working_4.cxs

Taking snapshot of stepper: working_2.pdb  

> select /AJ

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AK

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> select /AK

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AL

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AM

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> select /AM

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AN

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde ignore sel

ISOLDE: currently ignoring 2 residues in model 8.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde ~ignore

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AO

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AP

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AQ

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AR

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AS

980 atoms, 1001 bonds, 48 residues, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AT

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AU

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto prev

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AV

980 atoms, 1001 bonds, 48 residues, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AW

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /AX

980 atoms, 1001 bonds, 48 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> select /AA

981 atoms, 1002 bonds, 48 residues, 1 model selected  

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /BA

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select /BB

773 atoms, 794 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> isolde stepto

> isolde stepto

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde add ligand LMT

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> isolde ~ignore

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> delete sel

> save working.cxs

Taking snapshot of stepper: working_2.pdb  
opened ChimeraX session  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde stepto

> clipper set contourSensitivity 0.25

> select /AA

1019 atoms, 1041 bonds, 51 residues, 1 model selected  

> show #!1 models

> select #1

158 atoms, 160 bonds, 11 residues, 8 models selected  

> select #1

158 atoms, 160 bonds, 11 residues, 8 models selected  

> close #1

> isolde stepto /BA

Multiple residues selected! Going to the first...  

> isolde stepto /BB

Multiple residues selected! Going to the first...  

> select clear

> select /BB

773 atoms, 794 bonds, 41 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> select up

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 4 residues, 1 model selected  

> select up

773 atoms, 794 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 4 residues, 1 model selected  

> select up

773 atoms, 794 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select up

96639 atoms, 98747 bonds, 5194 residues, 1 model selected  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> select clear

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select up

96639 atoms, 98747 bonds, 5194 residues, 1 model selected  

> select down

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 4 residues, 1 model selected  

> select up

773 atoms, 794 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

100 atoms, 99 bonds, 1 residue, 1 model selected  

> show sel

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

503 atoms, 512 bonds, 32 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

38 atoms, 37 bonds, 3 residues, 1 model selected  

> select up

771 atoms, 792 bonds, 41 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

38 atoms, 37 bonds, 3 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

503 atoms, 512 bonds, 32 residues, 1 model selected  

> select up

771 atoms, 792 bonds, 41 residues, 1 model selected  

> select down

503 atoms, 512 bonds, 32 residues, 1 model selected  

> select up

771 atoms, 792 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

38 atoms, 37 bonds, 3 residues, 1 model selected  

> select up

771 atoms, 792 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

38 atoms, 37 bonds, 3 residues, 1 model selected  

> select up

771 atoms, 792 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

63 atoms, 60 bonds, 3 residues, 1 model selected  

> select up

1073 atoms, 1092 bonds, 67 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 4 residues, 1 model selected  

> select up

773 atoms, 794 bonds, 41 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 4 residues, 1 model selected  

> select up

773 atoms, 794 bonds, 41 residues, 1 model selected  

> select clear

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde stepto

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 3 residues, 1 model selected  

> select up

766 atoms, 787 bonds, 40 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> select clear

> isolde stepto /aa

Multiple residues selected! Going to the first...  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

86 atoms, 87 bonds, 4 residues, 1 model selected  

> select up

1062 atoms, 1082 bonds, 60 residues, 1 model selected  

> select clear

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select up

84 atoms, 86 bonds, 4 residues, 1 model selected  

> select up

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select up

96659 atoms, 98767 bonds, 5198 residues, 1 model selected  

> select down

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> view /ab:2

> select clear

> isolde stepto

> view /ab:2

> select clear

> select clear

> isolde stepto

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

84 atoms, 86 bonds, 4 residues, 1 model selected  

> select up

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> delete sel

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select clear

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select up

96615 atoms, 98722 bonds, 5194 residues, 1 model selected  

> select down

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select clear

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde add ligand CDL

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 5194 residues in model 8.2  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> isolde ~ignore

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> isolde ~ignore

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> clipper isolate sel contextDistance 0 maskRadius 3

> select clear

> ~cartoon

> hide HC

> hide #!8.1.1.2 models

> show #!8.1.1.2 models

> select clear

> save resolved_cdl.jpg

> cartoon

> select /ae:CDL

256 atoms, 255 bonds, 1 residue, 1 model selected  

> select /ae:11-30@CA

20 atoms, 20 residues, 1 model selected  

> select /af:11-30@CA

20 atoms, 20 residues, 1 model selected  

> save working_cdl.cxs

Taking snapshot of stepper: working_2.pdb  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 5195 residues in model 8.2  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 5196 residues in model 8.2  
Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2727, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__  
self._prepare_mdff_managers()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
_prepare_mdff_managers  
focus = False)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 982, in
isolate_and_cover_selection  
extra_padding=extra_padding)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> isolde ~ignore

> color bychain

> color byhetero

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> isolde ignore ~sel

ISOLDE: currently ignoring 5195 residues in model 8.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /ag:11-30@CA

20 atoms, 20 residues, 1 model selected  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 5196 residues in model 8.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> select clear

> isolde ~ignore

> select clear

> save working_cdl.cxs

Taking snapshot of stepper: working_2.pdb  

> select /ah:11-30@CA

20 atoms, 20 residues, 1 model selected  

> select /AH

1018 atoms, 1040 bonds, 51 residues, 1 model selected  

> cartoon

> select :CDL

768 atoms, 765 bonds, 3 residues, 1 model selected  

> select /ae, af, ag

4005 atoms, 4062 bonds, 186 residues, 1 model selected  

> select /ae, af, ag,ah

5084 atoms, 5161 bonds, 247 residues, 1 model selected  

> select clear

> select /ah:11-30@CA

20 atoms, 20 residues, 1 model selected  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> delete sel

> select /ad

1079 atoms, 1099 bonds, 61 residues, 1 model selected  

> select /ad,ae

2414 atoms, 2453 bonds, 123 residues, 1 model selected  

> select /ad:11-30@CA

20 atoms, 20 residues, 1 model selected  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> isolde stepto

> select clear

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

84 atoms, 86 bonds, 4 residues, 1 model selected  

> select up

184 atoms, 185 bonds, 5 residues, 1 model selected  

> select up

2037 atoms, 2081 bonds, 102 residues, 1 model selected  

> select down

184 atoms, 185 bonds, 5 residues, 1 model selected  

> select up

2037 atoms, 2081 bonds, 102 residues, 1 model selected  

> select down

184 atoms, 185 bonds, 5 residues, 1 model selected  

> select up

2037 atoms, 2081 bonds, 102 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select up

1018 atoms, 1040 bonds, 51 residues, 1 model selected  

> select clear

> select clear

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

1004 atoms, 1025 bonds, 50 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> select clear

> isolde stepto

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

1004 atoms, 1025 bonds, 50 residues, 1 model selected  

> select clear

> usage isolde jupm

Subcommands are:

  * isolde add ligand
  * isolde add water
  * isolde adjust distances
  * isolde adjust torsions
  * isolde cisflip
  * isolde demo
  * isolde ignore
  * isolde ~ignore
  * isolde jumpto
  * isolde pepflip
  * isolde release distances
  * isolde release torsions
  * isolde remote rest info
  * isolde remote rest start
  * isolde remote rest stop
  * isolde remote xmlrpc
  * isolde replace ligand
  * isolde report
  * isolde reset forcefield
  * isolde restrain distances
  * isolde restrain ligands
  * isolde restrain single distance
  * isolde restrain torsions
  * isolde set
  * isolde sim
  * isolde start
  * isolde stepto
  * isolde tutorial

  

> usage isolde jump

isolde jumpto [direction]  
— Jump the view to the first residue of the next chain or the last residue of
the previous chain.  
direction: one of next or prev  

> isolde jumpto prev

> isolde jumpto prev

> isolde jumpto prev

> isolde jumpto prev

> save working.cxs

Taking snapshot of stepper: working_2.pdb  
Restoring stepper: working_2.pdb  
opened ChimeraX session  

> usage volume mask

volume mask volumes surfaces a surfaces specifier [pad a number] [extend an
integer] [fullMap true or false] [slab slab] [invertMask true or false] [axis
an axis vector] [sandwich true or false] [fillOverlap true or false] [modelId
modelId]  
— Mask a map to a surface  
slab: a number or some numbers  
modelId: a model id  

> usage volume zone

volume zone volumes nearAtoms an atoms specifier [range a number]
[bondPointSpacing a number] [minimalBounds true or false] [newMap true or
false] [invert true or false] [subregion map region] [step map step] [modelId
modelId]  
— Zero map values beyond a distance range from atoms  
modelId: a model id  

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> close #1

> select #1

Nothing selected  

> select #8

97383 atoms, 99487 bonds, 14 pseudobonds, 5197 residues, 21 models selected  

> select clear

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> usage volume subtr

volume subtract volumes [onGrid a density maps specifier] [boundingGrid true
or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3
floats] [valueType numeric value type] [hideMaps true or false] [subregion map
region] [step map step] [modelId modelId] [inPlace true or false]
[scaleFactors scaleFactors] [minRms true or false]  
— Subtract maps pointwise  
modelId: a model id  
scaleFactors: some numbers  

> volume subtract #8.1.1.1 #1 inPlace false

> close #1

> volume #2 level 0.03352

> volume #2 level 0.03748

> select :CDL

768 atoms, 765 bonds, 3 residues, 1 model selected  

> select /C1

1472 atoms, 1487 bonds, 92 residues, 1 model selected  

> select clear

> delete sel

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

125 atoms, 128 bonds, 9 residues, 1 model selected  

> hide #!2 models

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> show #!2 models

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> ui tool show "Build Structure"

> build start peptide "custom built" AAAAAAAAAAAAAA -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 rotLib Dunbrack

Chain information for custom built #1  
---  
Chain | Description  
A | No description available  
  

> select #1

71 atoms, 70 bonds, 14 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> delete /C1:1-14

> addh #1

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: custom built #1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: custom built #1/A ALA 14  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
72 hydrogens added  
  

> hide #1 models

> select /C1:1-14

143 atoms, 142 bonds, 14 residues, 1 model selected  

> select /C1:1-14

143 atoms, 142 bonds, 14 residues, 1 model selected  

> swapaa mousemode sel PRO

> select clear

> swapaa mousemode sel PRO

> swapaa mousemode sel GLN

> swapaa mousemode sel THR

> swapaa mousemode sel GLY

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1a_24A.mrc

Opened class1a_24A.mrc, grid size 400,400,400, pixel 0.999, shown at level
0.0212, step 2, values float32  

> ui tool show "Volume Viewer"

> volume #3 step 1

> volume #3 level 0.04119

> volume #3 level 0.03163

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class2a_26A.mrc

Opened class2a_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
0.0249, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.05455

> fitmap #4 inMap #8.1.1.1

Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points  
correlation = 0.0582, correlation about mean = 0.003368, overlap = 2.152  
steps = 964, shift = 6.3, angle = 5.34 degrees  
  
Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
coordinates:  
Matrix rotation and translation  
0.99577666 -0.02365016 -0.08871027 25.10161578  
0.02499610 0.99958822 0.01409207 -14.07791580  
0.08834046 -0.01624996 0.99595778 -13.06451755  
Axis -0.16303956 -0.95136249 0.26139533  
Axis point 178.35759174 0.00000000 285.28764281  
Rotation angle (degrees) 5.33916146  
Shift along axis 5.88564083  
  

> fitmap #4 inMap #8.1.1.1

Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points  
correlation = 0.1152, correlation about mean = 0.06419, overlap = 9.627  
steps = 672, shift = 6.89, angle = 21.3 degrees  
  
Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
coordinates:  
Matrix rotation and translation  
0.92701975 -0.37501178 0.00074524 89.89128138  
0.37500543 0.92701261 0.00430577 -61.35976247  
-0.00230557 -0.00371206 0.99999045 1.56396515  
Axis -0.01068950 0.00406739 0.99993459  
Axis point 202.60869093 200.28337525 0.00000000  
Rotation angle (degrees) 22.02636092  
Shift along axis 0.35339585  
  

> select /C1:1-14

159 atoms, 160 bonds, 14 residues, 1 model selected  

> select /C1

1784 atoms, 1805 bonds, 117 residues, 1 model selected  

> volume #4 level 0.04206

> swapaa mousemode sel GLN

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

166 atoms, 167 bonds, 14 residues, 1 model selected  

> swapaa mousemode sel ASSP

Missing or invalid "restype" argument: Should be one of 'ALA', 'ARG', 'ASN',
'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE',
'PRO', 'SER', 'THR', 'TRP', 'TYR', or 'VAL'  

> swapaa mousemode sel ASP

> swapaa mousemode sel ARG

> swapaa mousemode sel GLY

> swapaa mousemode sel VAL

> swapaa mousemode sel PRO

> select up

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

190 atoms, 193 bonds, 14 residues, 1 model selected  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Unable to flip peptide bond after 50 rounds. Giving up.  

> select /C1:1-14

190 atoms, 193 bonds, 14 residues, 1 model selected  

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select /C1

1815 atoms, 1838 bonds, 117 residues, 1 model selected  

> select clear

> select /ak

1234 atoms, 1257 bonds, 72 residues, 1 model selected  

> isolde stepto /c

Selection contains no residues!  

> isolde stepto /ac

Multiple residues selected! Going to the first...  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select up

84 atoms, 86 bonds, 4 residues, 1 model selected  

> select up

1035 atoms, 1054 bonds, 57 residues, 1 model selected  

> select clear

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> isolde stepto

> close #1

> show #!2 models

> select :CDL

768 atoms, 765 bonds, 3 residues, 1 model selected  

> hide #!2 models

> clipper set contourSensitivity o.25

Missing or invalid "sensitivity" argument: Expected a number  

> clipper set contourSensitivity 0.25

> show #!2 models

> select :BCL

11760 atoms, 12432 bonds, 84 residues, 1 model selected  

> hide #!2 models

> show #!2 models

> select clear

> hide #!2 models

> select /af

1335 atoms, 1354 bonds, 62 residues, 1 model selected  

> select /ag

1335 atoms, 1354 bonds, 62 residues, 1 model selected  

> select /ae

1335 atoms, 1354 bonds, 62 residues, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde add ligand CDL

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

> show #!2 models

> hide #!2 models

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> hide ~sel

> isolde ignore ~sel

ISOLDE: currently ignoring 5222 residues in model 8.2  

> show #!2 models

> show ~HC

> hide protein&~@CA

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> select up

1282 atoms, 1300 bonds, 63 residues, 1 model selected  

> select down

256 atoms, 255 bonds, 1 residue, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> select clear

> isolde ~ignore

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> show ~HC

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> hide

> hide #!8 models

> volume #2 level 0.03016

> volume #2 level 0.03131

> show #!8 models

> show ~HC

> hide #!8 models

> show #!8 models

> select :CDL

1024 atoms, 1020 bonds, 4 residues, 1 model selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> select clear

> select :CDL

1024 atoms, 1020 bonds, 4 residues, 1 model selected  

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> save cdl_ref.pdb #8 selectedOnly true

> open cdl_ref.pdb

Summary of feedback from opening cdl_ref.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
TRP A 5 1 4  
Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
26  
Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
6  
Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3  
Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
27  
267 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (95 )  
Cannot find LINK/SSBOND residue CYS (98 )  
Cannot find LINK/SSBOND residue THR (108 )  
Cannot find LINK/SSBOND residue CYS (146 )  
Cannot find LINK/SSBOND residue CYS (149 )  
25 messages similar to the above omitted  
  

> select #1

256 atoms, 255 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> hide #1 models

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> isolde ignore ~sel

ISOLDE: currently ignoring 5223 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 1  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> show #!2 models

> close #2

> select #8

98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models selected  

> select clear

> volume zone #8.1.1.1 nearAtoms #8 dist 1.5 newMap true

Expected a keyword  

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #2 inPlace false

> close #2

> volume #5 level 0.03153

> volume #5 color #73d216

> select clear

> hide #!5 models

> show #!5 models

> volume #5 level 0.03261

> select :CDL

1536 atoms, 1530 bonds, 6 residues, 2 models selected  

> volume #3 level 0.03461

> volume #5 level 0.03526

> volume #5 level 0.0345

> hide #!5 models

> select :MAN

40 atoms, 40 bonds, 2 residues, 1 model selected  

> show #!5 models

> select ~CDL

Expected an objects specifier or a keyword  

> select :CDL

1536 atoms, 1530 bonds, 6 residues, 2 models selected  

> hide #!5 models

> select :GPC

4000 atoms, 3960 bonds, 40 residues, 1 model selected  

> select clear

> select ~protein

18265 atoms, 18944 bonds, 14 pseudobonds, 147 residues, 35 models selected  

> select clear

> select clear

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> show sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> select clear

> select clear

> show sel

> show sel

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> show sel

> select clear

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> select clear

> select clear

> select clear

> select clear

> show sel

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> select clear

> select clear

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

Chain L, residue 68 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select clear

> select clear

> select clear

> select clear

> select up

138 atoms, 139 bonds, 1 residue, 1 model selected  

> show sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> isolde ignore ~sel

ISOLDE: currently ignoring 5223 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 1  

> isolde ~ignore

> select clear

> isolde ~ignore

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> view /C:234

> swapaa mousemode sel GLN

Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2724, in start_sim  
main_sel = self._last_main_sel = self._get_main_sim_selection()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
  
See log for complete Python traceback.  
  

> swapaa mousemode sel ALA

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select up

100 atoms, 99 bonds, 1 residue, 1 model selected  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select up

98238 atoms, 100348 bonds, 5224 residues, 1 model selected  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> close #5

> select #8

98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models selected  

> select clear

> volume zone #8.1.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #2 inPlace false

> close #2

> volume #5 level 0.04033

> volume #5 level 0.03573

> isolde add ligand LMT

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5224 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 1  

Chain L, residue 68 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AG:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select /AH:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> delete sel

> show #!5 models

> select /AG,AH,AI,AJ

4153 atoms, 4242 bonds, 205 residues, 1 model selected  

> select /AI:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select clear

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> hide #!5 models

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AG,AI:LMT

162 atoms, 164 bonds, 2 residues, 1 model selected  

> show #!5 models

> select /AG,AJ

2117 atoms, 2162 bonds, 103 residues, 1 model selected  

> select /AJ:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select /AG:LMT

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select /AI:LMT

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select /AJ:10-30@CA

21 atoms, 21 residues, 1 model selected  

> hide #!5 models

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select clear

> view /AL:LMT

> select clear

> select /AM:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select /AM:10-30@CA

21 atoms, 21 residues, 1 model selected  

> view /AM:LMT

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AO:LMT

> select /AP:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AP:LMT

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AR:LMT

> select clear

> select /AS:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AS:LMT

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AU:LMT

> select /AV:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AV:LMT

> view /AV:LMT

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select clear

> view /AX:LMT

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select /AA:10-30@CA

21 atoms, 21 residues, 1 model selected  

> view /AA:LMT

> select clear

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AC:LMT

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select /AD:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AD:LMT

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> view /AF:LMT

> save working.cxs

Taking snapshot of stepper: working_2.pdb  
opened ChimeraX session  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
TRP A 5 1 4  
Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
26  
Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
6  
Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3  
Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
27  
264 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (95 )  
Cannot find LINK/SSBOND residue CYS (98 )  
Cannot find LINK/SSBOND residue THR (108 )  
Cannot find LINK/SSBOND residue CYS (146 )  
Cannot find LINK/SSBOND residue CYS (149 )  
25 messages similar to the above omitted  
  

> view #2

> select #2/AJ:61@C5'

1 atom, 1 residue, 1 model selected  

> select #2:61

162 atoms, 164 bonds, 2 residues, 1 model selected  

> delete sel

> close #2

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
TRP A 5 1 4  
Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
26  
Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
6  
Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3  
Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
27  
264 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (95 )  
Cannot find LINK/SSBOND residue CYS (98 )  
Cannot find LINK/SSBOND residue THR (108 )  
Cannot find LINK/SSBOND residue CYS (146 )  
Cannot find LINK/SSBOND residue CYS (149 )  
25 messages similar to the above omitted  
  

> delete #2/AJ:61

> isolde start

> set selectionWidth 4

Done loading forcefield  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select #2

194 atoms, 194 bonds, 2 residues, 1 model selected  

> hide #2 models

> hide #!1 models

> select clear

> select clear

> select /AK

1406 atoms, 1428 bonds, 55 residues, 2 models selected  

> select /AK:10-30@CA

21 atoms, 21 residues, 1 model selected  

> view /AA:PEX

> select /AA:PEX

113 atoms, 112 bonds, 1 residue, 1 model selected  

> select up

194 atoms, 194 bonds, 2 residues, 1 model selected  

> delete sel

> view /AC:PEX

> select up

113 atoms, 112 bonds, 1 residue, 1 model selected  

> select up

194 atoms, 194 bonds, 2 residues, 1 model selected  

> delete sel

> view /AE:PEX

> select /AA, AC, AE,

Expected an objects specifier or a keyword  

> select /AA, AC, AE

3397 atoms, 3464 bonds, 156 residues, 1 model selected  

> select clear

> view /AG:PEX

> select /AG:PEX

113 atoms, 112 bonds, 1 residue, 1 model selected  

> delete /AA,AC,AE,AG,AI,AM,AO,AQ,AS,AU,AW:61,62

> view /AB:PEX

> view /AE:PEX

> view /AH:PEX

> view /AB:PEX

> select /AB:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AE:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> select clear

> select /AH:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> select clear

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde add ligand BCL

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 2 residues in model 2  
ISOLDE: currently ignoring 5249 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> delete sel

> isolde add ligand BPH

> ui mousemode right "translate selected atoms"

> isolde add ligand BCL

> ui mousemode right "translate selected atoms"

> select up

141 atoms, 146 bonds, 1 residue, 1 model selected  

> delete sel

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> select clear

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> save extra_bcl.pdb #1 selectedOnly true

> select /AN:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> select clear

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 2 residues in model 2  
ISOLDE: currently ignoring 5250 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AQ:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> select clear

> select /AT:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> select clear

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> select /AW:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> select clear

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> close #5

> select #8

100821 atoms, 102950 bonds, 14 pseudobonds, 5252 residues, 22 models selected  

> select clear

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume diff #8.1.1.1 #5 inpl f

Expected a density maps specifier or a keyword  

> volume subtract #8.1.1.1 #5 inPlace false

> close #5

> show #2 models

> select #2

194 atoms, 194 bonds, 2 residues, 1 model selected  

> select clear

> select #2

194 atoms, 194 bonds, 2 residues, 1 model selected  

> hide #!6 models

> show #!6 models

> ui mousemode right "translate selected models"

> select #2:PEX

113 atoms, 112 bonds, 1 residue, 1 model selected  

> select clear

> volume #6 level 0.0417

> hide #2 models

> hide #!6 models

> select up

113 atoms, 112 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 2 residues in model 2  
ISOLDE: currently ignoring 5252 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> select clear

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> select up

194 atoms, 194 bonds, 2 residues, 1 model selected  

> select /AX:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select /AC:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> select /AF:PEX,LMT

275 atoms, 276 bonds, 3 residues, 1 model selected  

> view sel

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AI:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> select /AL:PEX,LMT

275 atoms, 276 bonds, 3 residues, 1 model selected  

> view sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AO:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> delete sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AR:PEX,LMT

275 atoms, 276 bonds, 3 residues, 1 model selected  

> view sel

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> delete sel

> select /AU:PEX,LMT

194 atoms, 194 bonds, 2 residues, 1 model selected  

> view sel

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> close #6

> select #8

102454 atoms, 104584 bonds, 14 pseudobonds, 5269 residues, 22 models selected  

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #5 inPlace false

> close #5

> select clear

> select :LMT

2349 atoms, 2378 bonds, 29 residues, 2 models selected  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> delete sel

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> save working.cxs

Taking snapshot of stepper: working_2.pdb  
opened ChimeraX session  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select up

162 atoms, 164 bonds, 2 residues, 1 model selected  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select /BH:10-30@CA

21 atoms, 21 residues, 1 model selected  

> select /BH:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> select /BG:10-40@CA

31 atoms, 31 residues, 1 model selected  
Loading residue template for PEX from internal database  

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BA, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BB, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BC, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BD, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BE, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BF, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BG, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BK, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BL, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BO, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BP, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BQ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BR, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BS, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BT, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BU, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BX, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain L, residue 68 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BK, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BK, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BL, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select ~protein

28426 atoms, 29196 bonds, 14 pseudobonds, 265 residues, 39 models selected  

> select clear

Chain BL, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BO, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BO, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BP, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Chain BP, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BQ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BQ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BR, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> hide #!6 models

Chain BR, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BS, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BS, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BT, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BT, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BU, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Chain BU, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BX, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BA, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BX, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BA, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BB, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BB, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BC, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BC, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BD, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BD, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BE, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BE, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BF, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BE, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BF, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BF, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BG, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BG, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BK, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BK, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BL, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Chain BL, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> close #6

> select #8

108286 atoms, 110488 bonds, 14 pseudobonds, 5341 residues, 22 models selected  

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #5 inPlace false

> close #5

> select clear

> hide #!6 models

> show #!6 models

> isolde add ligand PC1

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5341 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> volume #6 level 0.04625

> hide #!6 models

> isolde ~ignore

> select up

142 atoms, 141 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> isolde ~ignore

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> select clear

Chain L, residue 68 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

142 atoms, 141 bonds, 1 residue, 1 model selected  

> isolde replace ligand sel P5S

Deleted the following atoms from residue PC1 H11001: H143, H151, H122, C14,
C15, H152, H131, H142, H141, H153, H132, C13, H133  

126 atoms were automatically renamed to match the template: C12->CA, C11->CB,
O13->OG, P->P12, H111->HB, H112->HBA, H121->HA, O11->O16, C1->C3, C3->C1,
O21->O37, C21->C38, C22->C39, C23->C40, C24->C41, C25->C42, C26->C43,
C27->C44, C28->C45, C29->C46, C2A->C48, C2B->C49, C2C->C50, C2D->C51,
C2E->C52, C2F->C53, C2G->C54, C2H->C55, C2I->C56, O31->O19, C31->C17,
C32->C20, C33->C21, C34->C22, C35->C23, C36->C24, C37->C25, C38->C26,
C39->C27, C3A->C28, C3B->C29, C3C->C30, C3D->C31, C3E->C32, C3F->C33,
C3G->C34, C3H->C35, C3I->C36, O22->O47, O32->O18, H11->H3, H12->H3A,
H221->H39, H222->H39A, H231->H40, H232->H40A, H241->H41, H242->H41A,
H251->H42, H252->H42A, H261->H43, H262->H43A, H271->H44, H272->H44A,
H281->H45, H282->H45A, H291->H46, H292->H46A, H2A1->H48, H2A2->H48A,
H2B1->H49, H2B2->H49A, H2C1->H50, H2C2->H50A, H2D1->H51, H2D2->H51A,
H2E1->H52, H2E2->H52A, H2F1->H53, H2F2->H53A, H2G1->H54, H2G2->H54A,
H2H1->H55, H2H2->H55A, H31->H1, H32->H1A, H321->H20, H322->H20A, H331->H21,
H332->H21A, H341->H22, H342->H22A, H351->H23, H352->H23A, H361->H24,
H362->H24A, H371->H25, H372->H25A, H381->H26, H382->H26A, H391->H27,
H392->H27A, H3A1->H28, H3A2->H28A, H3B1->H29, H3B2->H29A, H3C1->H30,
H3C2->H30A, H3D1->H31, H3D2->H31A, H3E1->H32, H3E2->H32A, H3F1->H33,
H3F2->H33A, H3G1->H34, H3G2->H34A, H3H1->H35, H3H2->H35A, O12->O15, O14->O13,
H2I1->H56, H2I2->H56A, H2I3->H56B, H3I1->H36, H3I2->H36A, H3I3->H36B  

Rebuilt ligand P5S has chiral centres at atoms CA,C2 (highlighted). Since the
current algorithm used to match topologies is not chirality aware, you should
check these sites carefully to ensure they are sensible. If in doubt, it is
best to delete with "del #8.2/H1:1001" and replace with "isolde add ligand
P5S".  

> isolde replace ligand sel P5S

Deleted the following atoms from residue P5S H11001: HXT, HO15  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 44, in replace_residue  
chiral_centers = Atoms([a for a in residue.atoms if
residue.ideal_chirality(a.name) != 'N'])  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 44, in <listcomp>  
chiral_centers = Atoms([a for a in residue.atoms if
residue.ideal_chirality(a.name) != 'N'])  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality  
return f(self.name.encode('utf-8'), atom_name.encode('utf-8'))  
KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S'  
  
KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S'  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality  
return f(self.name.encode('utf-8'), atom_name.encode('utf-8'))  
  
See log for complete Python traceback.  
  

Chain L, residue 68 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> isolde add ligand P5S

Deleted the following atoms from residue P5S H11002: HO15, HXT  

> ui mousemode right "translate selected atoms"

> delete sel

Chain L, residue 68 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> show #!6 models

running convert_amber_files  

> isolde add ligand 2Y5

Fetching CCD 2Y5 from http://ligand-expo.rcsb.org/reports/2/2Y5/2Y5.cif  
Deleted the following atoms from residue 2Y5 L607: H81, H18, H78  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5342 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> hide #!6 models

> delete sel

> isolde add ligand LMG

Fetching CCD LMG from http://ligand-expo.rcsb.org/reports/L/LMG/LMG.cif  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5342 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> delete sel

> select up

129 atoms, 129 bonds, 1 residue, 1 model selected  

> save LMX.pdb #8 selectedOnly true

running convert_amber_files  

> isolde ~ignore

> select clear

Failed to add
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/PEE.xml:
Residue template USER_PEE with the same override level 0 already exists.  

> isolde add ligand PEE

Deleted the following atoms from residue PEE L608: H83  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5343 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

> select up

133 atoms, 132 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> select clear

> select up

256 atoms, 255 bonds, 1 residue, 1 model selected  

> isolde ~ignore

> select clear

> select :PEE@H35

1 atom, 1 residue, 1 model selected  

> select up

133 atoms, 132 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> isolde ~ignore

> select clear

> select clear

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde add ligand LMG

> ui mousemode right "translate selected atoms"

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> isolde ~ignore

> isolde ignore ~sel

ISOLDE: currently ignoring 5346 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> select clear

> isolde add ligand PEE

Deleted the following atoms from residue PEE H11002: H83  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5347 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

> select up

133 atoms, 132 bonds, 1 residue, 1 model selected  

> select clear

> show #!6 models

> hide #!6 models

> isolde add ligand PEE

Deleted the following atoms from residue PEE M704: H83  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5348 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain ak, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select #8

109253 atoms, 111453 bonds, 14 pseudobonds, 5349 residues, 22 models selected  

> close #6

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #5 new t

Expected a keyword  

> volume subtract #8.1.1.1 #5 inPlace true

Can't modify volume in place: class1b_26A.mrc  

> volume subtract #8.1.1.1 #5 inPlace false

> close #5

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde add ligand LMT

> hide #!6 models

> ui mousemode right "translate selected atoms"

> isolde add ligand LMT

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected atoms"

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected atoms"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> show #!6 models

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> hide #!6 models

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select clear

> show #!6 models

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> close #6

> select #8

109739 atoms, 111945 bonds, 14 pseudobonds, 5355 residues, 22 models selected  

> select clear

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #5 inPlace false

> close #5

> select ~BCL

Expected an objects specifier or a keyword  

> select :BCL

11900 atoms, 12580 bonds, 85 residues, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> select /AG:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AH:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BG, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> ui mousemode right "translate selected atoms"

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AJ:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /AK:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BK, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /AM:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain BL, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select /AN:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /AP:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain BO, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BP, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /AQ:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

Chain AQ, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BQ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select /AS:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

Chain BS, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select /AT:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

Chain AT, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BS, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BT, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select /AV:10-40@CA

31 atoms, 31 residues, 1 model selected  

> hide #!6 models

Chain BU, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> show #!6 models

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /AW:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select ~protein

31499 atoms, 32362 bonds, 14 pseudobonds, 291 residues, 39 models selected  

> select clear

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

Chain AW, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select /AA:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain BA, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BB, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BX, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /AD:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain BC, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BD, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select /AE:10-40@CA

31 atoms, 31 residues, 1 model selected  

Chain AE, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BE, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

Chain AE, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ignore ~se;

Expected a residues specifier or a keyword  

Chain AE, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ignore ~sel

ISOLDE: currently ignoring 5370 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

Chain AE, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BG, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> select clear

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BG, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select ~protein

32000 atoms, 32888 bonds, 14 pseudobonds, 295 residues, 39 models selected  

> select clear

> hide #!6 models

> hide #!8.1 models

> hide protein

> ~cartoon

> show ~HC

> show #!8.1 models

> cartoon

> select clear

> close #6

> select #8

111861 atoms, 114181 bonds, 14 pseudobonds, 5371 residues, 22 models selected  

> select clear

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #5 inPlace false

> close #5

> select clear

> select clear

Chain AW, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5371 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  
Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2727, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__  
self._prepare_mdff_managers()  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
_prepare_mdff_managers  
focus = False)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 982, in
isolate_and_cover_selection  
extra_padding=extra_padding)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> isolde ~ignore

> show ~HC

> color bychain

> color byhetero

> cartoon

Chain AW, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5372 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain AW, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

Chain AW, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ~ignore

Chain AW, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BV, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BW, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select :LMT

9072 atoms, 9184 bonds, 112 residues, 1 model selected  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5373 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

Chain AT, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BT, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ~ignore

Chain AT, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ~ignore

> isolde ignore ~sel

ISOLDE: currently ignoring 5374 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain AT, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select ~protein

32324 atoms, 33216 bonds, 14 pseudobonds, 299 residues, 39 models selected  

> select clear

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5375 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

Chain AQ, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5376 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BN, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BL, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5377 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BM, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5378 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ~ignore

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BK, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 5378 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5379 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5380 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ~ignore

Chain BH, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BI, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5381 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5382 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain AE, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 5382 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ignore ~sel

ISOLDE: currently ignoring 5382 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5383 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain AE, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BC, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BD, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AE, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BC, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BD, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> setattr #8 bonds radius 0.05

Assigning radius attribute to 115247 items  

> setattr #8 bonds radius 0.2

Assigning radius attribute to 115247 items  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> close #6

> select #8

112914 atoms, 115247 bonds, 14 pseudobonds, 5384 residues, 22 models selected  

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #5

> close #5

> select clear

Chain AQ, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5384 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain AQ, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> delete sel

Chain AQ, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BQ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand PEE

Deleted the following atoms from residue PEE AQ63: H83  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5384 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

Chain AQ, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> select ~protein

33267 atoms, 34168 bonds, 14 pseudobonds, 310 residues, 39 models selected  

> select clear

> isolde add ligand P5S

Deleted the following atoms from residue P5S M705: HXT, HO15  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5386 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> hide #!6 models

> select up

135 atoms, 134 bonds, 1 residue, 1 model selected  

> delete sel

> isolde add ligand PSF

Fetching CCD PSF from http://ligand-expo.rcsb.org/reports/P/PSF/PSF.cif  
Deleted the following atoms from residue PSF M705: HO3, HXT  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5386 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde add ligand PSF

Deleted the following atoms from residue PSF ai68: HO3, HXT  

> isolde ignore ~sel

ISOLDE: currently ignoring 5387 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> ui mousemode right "translate selected atoms"

> isolde ~ignore

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select up

62 atoms, 61 bonds, 1 residue, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> show #!6 models

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 5387 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ~ignore

> isolde ignore se

Expected a residues specifier or a keyword  

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BJ, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde ~ignore

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AK, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> isolde add ligand LMT

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 5388 residues in model 8.2  
ISOLDE: currently ignoring 1 residues in model 2  
ISOLDE: currently ignoring 1 residues in model 1.2  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde ~ignore

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select ~protein

33472 atoms, 34372 bonds, 14 pseudobonds, 313 residues, 39 models selected  

> select clear

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain AN, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Chain AW, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BA, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain BX, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear

Chain AH, residue 62 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> save working.cif #8

Not saving entity_poly_seq for non-authoritative sequences  

> select #1

256 atoms, 255 bonds, 1 residue, 8 models selected  

> select #8

113333 atoms, 115665 bonds, 14 pseudobonds, 5389 residues, 22 models selected  

> select clear

> view sel

> select /ak:67&~protein

140 atoms, 148 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> view sel

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> save working.cif #8

Not saving entity_poly_seq for non-authoritative sequences  

> select ~H

55527 atoms, 116032 bonds, 14 pseudobonds, 5391 residues, 39 models selected  

> save working_noh.cif #8 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> select clear

> save working.pdb #8

> view /CG:1

> select /C

4865 atoms, 4968 bonds, 4 pseudobonds, 303 residues, 2 models selected  

> select up

78 atoms, 81 bonds, 4 residues, 1 model selected  

> view /MG:MAN

> select up

78 atoms, 81 bonds, 4 residues, 1 model selected  

> save working.cif #8

Not saving entity_poly_seq for non-authoritative sequences  

> select clear

> hide #!6 models

> select up

78 atoms, 81 bonds, 4 residues, 1 model selected  

> save working.cif #8

Not saving entity_poly_seq for non-authoritative sequences  

> ui mousemode right "translate selected atoms"

> select /C:1010-1020

78 atoms, 81 bonds, 4 residues, 1 model selected  

> delete sel

> select /C:1010-1020

78 atoms, 81 bonds, 4 residues, 1 model selected  

> delete sel

> select /M:20-50

435 atoms, 440 bonds, 31 residues, 1 model selected  

> select /D:20-50

Nothing selected  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif  
---  
warnings | Unknown polymer entity '1' near line 475  
Unknown polymer entity '2' near line 2593  
Unknown polymer entity '3' near line 5781  
Unknown polymer entity '4' near line 26370  
Unknown polymer entity '5' near line 27136  
10 messages similar to the above omitted  
Atom H is not in the residue template for MET /AA:1  
Atom C1 is not in the residue template for GPC /AA:60  
Atom H is not in the residue template for MET /AB:1  
Atom C1 is not in the residue template for GPC /AB:60  
Atom H is not in the residue template for MET /AC:1  
Atom C1 is not in the residue template for GPC /AC:60  
Atom H is not in the residue template for MET /AD:1  
Atom C1 is not in the residue template for GPC /AD:60  
Atom H is not in the residue template for MET /AE:1  
Atom C1 is not in the residue template for GPC /AE:60  
Atom H is not in the residue template for MET /AF:1  
Atom C1 is not in the residue template for GPC /AF:60  
Atom H is not in the residue template for MET /AG:1  
Atom C1 is not in the residue template for GPC /AG:60  
Atom H is not in the residue template for MET /AH:1  
Atom C1 is not in the residue template for GPC /AH:60  
Atom H is not in the residue template for MET /AI:1  
Atom C1 is not in the residue template for GPC /AI:60  
Atom H is not in the residue template for MET /AJ:1  
Atom C1 is not in the residue template for GPC /AJ:60  
Atom H is not in the residue template for MET /AK:1  
Atom C1 is not in the residue template for GPC /AK:60  
Atom C26 is not in the residue template for PEX /AK:62  
Atom H is not in the residue template for MET /AL:1  
Atom C1 is not in the residue template for GPC /AL:60  
Atom H is not in the residue template for MET /AM:1  
Atom C1 is not in the residue template for GPC /AM:60  
Atom H is not in the residue template for MET /AN:1  
Atom C1 is not in the residue template for GPC /AN:60  
Atom H is not in the residue template for MET /AO:1  
Atom C1 is not in the residue template for GPC /AO:60  
Atom H is not in the residue template for MET /AP:1  
Atom C1 is not in the residue template for GPC /AP:60  
Atom H is not in the residue template for MET /AQ:1  
Atom C1 is not in the residue template for GPC /AQ:60  
Atom H is not in the residue template for MET /AR:1  
Atom C1 is not in the residue template for GPC /AR:60  
Atom H is not in the residue template for MET /AS:1  
Atom C1 is not in the residue template for GPC /AS:60  
Atom H is not in the residue template for MET /AT:1  
Atom C1 is not in the residue template for GPC /AT:60  
Atom H is not in the residue template for MET /AU:1  
Atom C1 is not in the residue template for GPC /AU:60  
Atom H is not in the residue template for MET /AV:1  
Atom C1 is not in the residue template for GPC /AV:60  
Atom H is not in the residue template for MET /AW:1  
Atom C1 is not in the residue template for GPC /AW:60  
Atom H is not in the residue template for MET /AX:1  
Atom C1 is not in the residue template for GPC /AX:60  
Atom H is not in the residue template for GLY /BQ:5  
Atom H is not in the residue template for GLY /BR:5  
Atom H is not in the residue template for GLY /BS:5  
Atom H is not in the residue template for GLY /BT:5  
Atom H11 is not in the residue template for BPH /L:606  
Atom H11 is not in the residue template for BPH /M:605  
Atom C1 is not in the residue template for RCC /M:701  
Atom HN2 is not in the residue template for ARG /ak:71  
Atom H is not in the residue template for GLY /C1:32  
Atom C1 is not in the residue template for GPC /Ba:60  
Atom C1 is not in the residue template for GPC /Bb:60  
Atom C1 is not in the residue template for GPC /Bc:60  
Atom C1 is not in the residue template for GPC /Bd:60  
Atom C1 is not in the residue template for GPC /Be:60  
11 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model1a.cif #5  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?  
AC AD | ?  
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
bm bo bp | ?  
BB BD BE BI BQ BR BS BT BV BW bn | ?  
C | ?  
C1 | ?  
H1 | ?  
H2 | ?  
L | ?  
M | ?  
aa | ?  
ab ad ae af ag ah ai aj al am an ao ap | ?  
ac | ?  
ak | ?  
  

> cartoon #5

> hide #5

> select /M:20-50

736 atoms, 744 bonds, 2 pseudobonds, 52 residues, 3 models selected  

> view /C:1010

No objects specified.  

> view /C:1001

> dssp

> select :BCL

25620 atoms, 26748 bonds, 336 pseudobonds, 183 residues, 3 models selected  

> close #5

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> select /ak

1347 atoms, 1369 bonds, 73 residues, 2 models selected  

> view /C:117

> select #8&~protein

33103 atoms, 34005 bonds, 14 pseudobonds, 311 residues, 22 models selected  

> select LMG

Expected an objects specifier or a keyword  

> select :LMG

141 atoms, 141 bonds, 1 residue, 1 model selected  

> view :LMG

> select :LMX

129 atoms, 129 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  
opened ChimeraX session  

> show #!6 models

> volume #6 level 0.03545

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select #6

4 models selected  

> select :HOH

15 atoms, 10 bonds, 5 residues, 1 model selected  

> hide #!6 models

> select :HOH

3309 atoms, 2206 bonds, 1103 residues, 2 models selected  

> delete sel

> select :HOH

2505 atoms, 1670 bonds, 835 residues, 1 model selected  

> show #!6 models

> hide #!6 models

> delete :HOH

> select :HOH

498 atoms, 332 bonds, 166 residues, 1 model selected  

> show #!6 models

> hide #!6 models

> select :HOH

498 atoms, 332 bonds, 166 residues, 1 model selected  

> show #!6 models

> delete :HOH

> select :HOH

1497 atoms, 998 bonds, 499 residues, 1 model selected  

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> select :HOH

1926 atoms, 1284 bonds, 642 residues, 1 model selected  

> hide #!6 models

Loading residue template for LMG from internal database  
Loading residue template for PEE from internal database  
Loading residue template for PEX from internal database  
Loading residue template for PSF from internal database  

> select :HOH

1926 atoms, 1284 bonds, 642 residues, 1 model selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> select clear

> select clear

> select :HOH

1926 atoms, 1284 bonds, 642 residues, 1 model selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> select #8.1.1.1

3 models selected  

> select clear

> select :HOH

2085 atoms, 1390 bonds, 695 residues, 1 model selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> close #6

> select #1

256 atoms, 255 bonds, 1 residue, 8 models selected  
Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2580, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2589, in _xtal_mask_to_atoms  
atoms, 0, context, cutoff, focus=focus)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 982, in
isolate_and_cover_selection  
extra_padding=extra_padding)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> select #8

115418 atoms, 117055 bonds, 14 pseudobonds, 6084 residues, 22 models selected  

> select clear

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #5

> close #5

> select clear

> select clear

> select :HOH

2085 atoms, 1390 bonds, 695 residues, 1 model selected  

> select clear

> hide #!6 models

> show #!6 models

> select clear

> select #6

4 models selected  

> select :HOH

1494 atoms, 996 bonds, 498 residues, 1 model selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> hide #!6 models

> select clear

> select :HOH

1494 atoms, 996 bonds, 498 residues, 1 model selected  

> isolde add water

> isolde sim start sel

> select :HOH

1095 atoms, 730 bonds, 365 residues, 1 model selected  

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> delete sel

> delete sel

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> delete sel

> setattr sel atoms name H

Assigning name attribute to 1 item  

> isolde add water

> isolde sim start sel

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> isolde add water simSettle false

> isolde add water simSettle false

> show #!6 models

> hide #!6 models

> show #!6 models

> isolde add water

> isolde sim start sel

> hide #!6 models

> isolde add water

> isolde sim start sel

> isolde add water simSettle false

> isolde add water simSettle false

> isolde add water simSettle false

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> isolde add water simSettle false

> isolde add water simSettle false

> isolde add water simSettle false

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> isolde add water simSettle false

> isolde add water simSettle false

> isolde add water

> isolde sim start sel

> show #!6 models

> volume #6 level 0.02957

> volume #6 level 0.02196

> volume #6 level 0.02872

> hide #!6 models

> isolde add water

> isolde sim start sel

> isolde add water

> isolde sim start sel

> isolde add water simSettle false

> isolde add water simSettle false

> select /ak

1380 atoms, 1391 bonds, 84 residues, 2 models selected  

> isolde add water simSettle false

> select /ak

1380 atoms, 1391 bonds, 84 residues, 2 models selected  

> select up

114625 atoms, 116562 bonds, 5784 residues, 2 models selected  

> select clear

> isolde add water simSettle false

> select /ak

1383 atoms, 1393 bonds, 85 residues, 2 models selected  

> select /ak

1383 atoms, 1393 bonds, 85 residues, 2 models selected  

> isolde add water simSettle false

> isolde add water simSettle false

> isolde add water simSettle false

> isolde add water simSettle false

> select clear

> isolde add water simSettle false

> select clear

> view /aa:45

> view /ab:45

> isolde add water simSettle false

> isolde add water simSettle false

> view /ac:45

> select clear

> view /ad:45

> view /ae:45

> view /af:45

> view /ag:45

> view /ah:45

> isolde add water simSettle false

> select clear

> view /ai:45

> view /aj:45

> view /ak:45

> view /al:45

> isolde add water simSettle false

> isolde add water simSettle false

> select clear

> view /am:45

> isolde add water simSettle false

> select clear

> view /an:45

> isolde add water simSettle false

> select clear

> view /ao:45

> view /ap:45

> isolde add water simSettle false

> select clear

> view /aa:5

> view /AA:45

> view /AB:4

> view /AB:43

> view /AC:43

> view /AD:43

> view /AE:43

> select clear

> view /AF:43

> view /AG:43

> view /AH:43

> view /AI:43

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> close #8.1

> clipper associate #3 toModel #8

> volume gaussian #8 bfactor 50

> clipper associate #3 toModel #1

> close #1.1

> volume gaussian #8 bfactor 50

> clipper associate #3 toModel #8

> clipper set contourSensitivity 0.25

> select /D1

Nothing selected  

> delete /C2

> select /H1

1580 atoms, 1586 bonds, 75 residues, 1 model selected  

> select /M

6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected  

> select clear

> isolde restrain distances #8

> select :HOH

1218 atoms, 812 bonds, 406 residues, 1 model selected  

> select /M

6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected  

> select clear

> select /M:20-50

435 atoms, 440 bonds, 31 residues, 1 model selected  

> isolde release distances sel

> select clear

> select #8

112951 atoms, 114855 bonds, 14 pseudobonds, 5695 residues, 22 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> close #8.2.10

> select clear

> select /M:20-50

435 atoms, 440 bonds, 31 residues, 1 model selected  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif  
---  
warnings | Unknown polymer entity '1' near line 475  
Unknown polymer entity '2' near line 2593  
Unknown polymer entity '3' near line 5781  
Unknown polymer entity '4' near line 26370  
Unknown polymer entity '5' near line 27136  
10 messages similar to the above omitted  
Atom H is not in the residue template for MET /AA:1  
Atom C1 is not in the residue template for GPC /AA:60  
Atom H is not in the residue template for MET /AB:1  
Atom C1 is not in the residue template for GPC /AB:60  
Atom H is not in the residue template for MET /AC:1  
Atom C1 is not in the residue template for GPC /AC:60  
Atom H is not in the residue template for MET /AD:1  
Atom C1 is not in the residue template for GPC /AD:60  
Atom H is not in the residue template for MET /AE:1  
Atom C1 is not in the residue template for GPC /AE:60  
Atom H is not in the residue template for MET /AF:1  
Atom C1 is not in the residue template for GPC /AF:60  
Atom H is not in the residue template for MET /AG:1  
Atom C1 is not in the residue template for GPC /AG:60  
Atom H is not in the residue template for MET /AH:1  
Atom C1 is not in the residue template for GPC /AH:60  
Atom H is not in the residue template for MET /AI:1  
Atom C1 is not in the residue template for GPC /AI:60  
Atom H is not in the residue template for MET /AJ:1  
Atom C1 is not in the residue template for GPC /AJ:60  
Atom H is not in the residue template for MET /AK:1  
Atom C1 is not in the residue template for GPC /AK:60  
Atom C26 is not in the residue template for PEX /AK:62  
Atom H is not in the residue template for MET /AL:1  
Atom C1 is not in the residue template for GPC /AL:60  
Atom H is not in the residue template for MET /AM:1  
Atom C1 is not in the residue template for GPC /AM:60  
Atom H is not in the residue template for MET /AN:1  
Atom C1 is not in the residue template for GPC /AN:60  
Atom H is not in the residue template for MET /AO:1  
Atom C1 is not in the residue template for GPC /AO:60  
Atom H is not in the residue template for MET /AP:1  
Atom C1 is not in the residue template for GPC /AP:60  
Atom H is not in the residue template for MET /AQ:1  
Atom C1 is not in the residue template for GPC /AQ:60  
Atom H is not in the residue template for MET /AR:1  
Atom C1 is not in the residue template for GPC /AR:60  
Atom H is not in the residue template for MET /AS:1  
Atom C1 is not in the residue template for GPC /AS:60  
Atom H is not in the residue template for MET /AT:1  
Atom C1 is not in the residue template for GPC /AT:60  
Atom H is not in the residue template for MET /AU:1  
Atom C1 is not in the residue template for GPC /AU:60  
Atom H is not in the residue template for MET /AV:1  
Atom C1 is not in the residue template for GPC /AV:60  
Atom H is not in the residue template for MET /AW:1  
Atom C1 is not in the residue template for GPC /AW:60  
Atom H is not in the residue template for MET /AX:1  
Atom C1 is not in the residue template for GPC /AX:60  
Atom H is not in the residue template for GLY /BQ:5  
Atom H is not in the residue template for GLY /BR:5  
Atom H is not in the residue template for GLY /BS:5  
Atom H is not in the residue template for GLY /BT:5  
Atom H11 is not in the residue template for BPH /L:606  
Atom H11 is not in the residue template for BPH /M:605  
Atom C1 is not in the residue template for RCC /M:701  
Atom HN2 is not in the residue template for ARG /ak:71  
Atom H is not in the residue template for GLY /C1:32  
Atom C1 is not in the residue template for GPC /Ba:60  
Atom C1 is not in the residue template for GPC /Bb:60  
Atom C1 is not in the residue template for GPC /Bc:60  
Atom C1 is not in the residue template for GPC /Bd:60  
Atom C1 is not in the residue template for GPC /Be:60  
11 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model1a.cif #3  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?  
AC AD | ?  
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
bm bo bp | ?  
BB BD BE BI BQ BR BS BT BV BW bn | ?  
C | ?  
C1 | ?  
H1 | ?  
H2 | ?  
L | ?  
M | ?  
aa | ?  
ab ad ae af ag ah ai aj al am an ao ap | ?  
ac | ?  
ak | ?  
  

> delete #3&~/M

> select #3/M

5881 atoms, 5992 bonds, 16 pseudobonds, 333 residues, 3 models selected  

> style sel stick

Changed 5881 atom styles  

> hide HC

> color sel green

> color sel byhetero

> select clear

> select #8/M:20-50

435 atoms, 440 bonds, 31 residues, 1 model selected  

> select clear

> hide #!3 models

> select #8/M:20-50

435 atoms, 440 bonds, 31 residues, 1 model selected  

> delete #8/M:22-35

> select #8/M:20-50

242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select #8/M:20-50

242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected  

> isolde add water simSettle false

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> close #6

> close #4

> close #3

> close #2

> close #1

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select #8

112761 atoms, 114661 bonds, 15 pseudobonds, 5682 residues, 23 models selected  

> select clear

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #1

> close #1

> select /M:4-12

162 atoms, 163 bonds, 9 residues, 1 model selected  

> select clear

> select up

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

215 atoms, 216 bonds, 12 residues, 1 model selected  

> select clear

> select clear

> select /AA/AX:BCL

1311 atoms, 1345 bonds, 57 residues, 1 model selected  

> select /AA-AX:BCL

5460 atoms, 5772 bonds, 39 residues, 1 model selected  

> select /AA-AX:BCL

5460 atoms, 5772 bonds, 39 residues, 1 model selected  

> isolde add water sel f

Expected a keyword  

> isolde add water simSettle false

> select /AA-AX:BCL

5460 atoms, 5772 bonds, 39 residues, 1 model selected  

> select /AA-AX:BCL

5460 atoms, 5772 bonds, 39 residues, 1 model selected  

> select /AA-AX:BCL

5460 atoms, 5772 bonds, 39 residues, 1 model selected  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> select /AD:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AB:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AB

1212 atoms, 1234 bonds, 53 residues, 1 model selected  

> select /AA-AX:BCL

5600 atoms, 5920 bonds, 40 residues, 1 model selected  

> select clear

> select /AB

1352 atoms, 1382 bonds, 54 residues, 1 model selected  

> select /AA-AX:BCL

5600 atoms, 5920 bonds, 40 residues, 1 model selected  

> select /AX:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AX

1302 atoms, 1322 bonds, 57 residues, 1 model selected  

> delete /AX:73

> select /AX:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AA-AX:BCL

5740 atoms, 6068 bonds, 41 residues, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select /AA-AX:BCL

5740 atoms, 6068 bonds, 41 residues, 1 model selected  

> select /AU:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AU

1218 atoms, 1238 bonds, 55 residues, 1 model selected  

> select /AA-AX:BCL

5880 atoms, 6216 bonds, 42 residues, 1 model selected  

> select /AA-AX:BCL

5880 atoms, 6216 bonds, 42 residues, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select /AA-AX:BCL

5880 atoms, 6216 bonds, 42 residues, 1 model selected  

> select /AR:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AR

1215 atoms, 1236 bonds, 54 residues, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AA-AX:BCL

6020 atoms, 6364 bonds, 43 residues, 1 model selected  

> select /AA-AX:BCL

6020 atoms, 6364 bonds, 43 residues, 1 model selected  

> select /AA-AX:BCL

6020 atoms, 6364 bonds, 43 residues, 1 model selected  

> select /Ao:10-40@CA

Nothing selected  

> select /AO:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AO

1134 atoms, 1154 bonds, 53 residues, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select /AO

1274 atoms, 1302 bonds, 54 residues, 1 model selected  

> select /AA-AX:BCL

6160 atoms, 6512 bonds, 44 residues, 1 model selected  

> select /AL:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AL

1305 atoms, 1324 bonds, 58 residues, 1 model selected  

> select /AL:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AA-AX:BCL

6300 atoms, 6660 bonds, 45 residues, 1 model selected  

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select /AA-AX:BCL

6300 atoms, 6660 bonds, 45 residues, 1 model selected  

> select /AA-AX:BCL

6300 atoms, 6660 bonds, 45 residues, 1 model selected  

> select clear

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> delete sel

> select /AF:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AF

1389 atoms, 1408 bonds, 60 residues, 1 model selected  

> select clear

> select /AA-AX:BCL

6440 atoms, 6808 bonds, 46 residues, 1 model selected  

> select /AA-AX:BCL

6440 atoms, 6808 bonds, 46 residues, 1 model selected  

> select /AI:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AI

1464 atoms, 1486 bonds, 59 residues, 1 model selected  

> select up

81 atoms, 82 bonds, 1 residue, 1 model selected  

> delete sel

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AA-AX:BCL

6580 atoms, 6956 bonds, 47 residues, 1 model selected  

> select /AC:10-40@CA

31 atoms, 31 residues, 1 model selected  

> select /AC

1207 atoms, 1225 bonds, 55 residues, 1 model selected  

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 8.2  

> isolde ~ignore

> select /AA-AX:BCL

6720 atoms, 7104 bonds, 48 residues, 1 model selected  

> select /AA-AX:BCL

6720 atoms, 7104 bonds, 48 residues, 1 model selected  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select /AA-AX:BCL

6720 atoms, 7104 bonds, 48 residues, 1 model selected  

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> select /ba-bp:BCL

2240 atoms, 2368 bonds, 16 residues, 1 model selected  

> select /ba-bp,aa-ap:BCL

4480 atoms, 4736 bonds, 32 residues, 1 model selected  

> select clear

> select clear

> isolde add water simSettle false

> view /aa:26

> view /ab:26

> select clear

> view /ac:26

> view /ad:26

> view /ae:26

> view /af:26

> view /ag:26

> view /ah:26

> view /ai:26

> view /ap:26

> view /aj:26

> select clear

> select clear

> save working.cxs

Taking snapshot of stepper: working_2.pdb  

> isolde add water simSettle false

> select :HOH

1218 atoms, 812 bonds, 406 residues, 1 model selected  

> select #8.1.1.1

3 models selected  

> select clear

> close #2

> select #8

113595 atoms, 115653 bonds, 15 pseudobonds, 5601 residues, 23 models selected  

> volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true

> volume subtract #8.1.1.1 #1

> close #1

> select clear

> select #2

4 models selected  

> select clear

> select :HOH

2655 atoms, 1770 bonds, 885 residues, 1 model selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> select clear

> select :HOH

2655 atoms, 1770 bonds, 885 residues, 1 model selected  

> select clear

> select :HOH

2799 atoms, 1866 bonds, 933 residues, 1 model selected  

> select clear

> style sel sphere

Changed 672 atom styles  

> select :HOH

2799 atoms, 1866 bonds, 933 residues, 1 model selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> select :HOH

2799 atoms, 1866 bonds, 933 residues, 1 model selected  

> style sel stick

Changed 2799 atom styles  

> select :HOH

2334 atoms, 1556 bonds, 778 residues, 1 model selected  

> select clear

> hide #!2 models

> select ~:HOH&~H

55004 atoms, 115015 bonds, 15 pseudobonds, 5282 residues, 27 models selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select up

9 atoms, 6 bonds, 3 residues, 1 model selected  

> delete sel

> delete sel

> select up

9 atoms, 6 bonds, 3 residues, 1 model selected  

> delete sel

> select #8

114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected  

> select clear

> select #8

114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected  

> select clear

> select #8

114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected  

> select clear

> select clear

> select #8

114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected  

> select clear

> select up

405 atoms, 410 bonds, 5 residues, 1 model selected  

> style sel sphere

Changed 405 atom styles  

> style sel ball

Changed 405 atom styles  

> style sel stick

Changed 405 atom styles  

> color sel lightgreen

> color sel byhetero

> color ~sel lightgrey

> color ~sel byhetero

> color sel green

> color sel byhetero

> select clear

> hide :HOH

> select clear

> save sideways_detergents.jpg

> save sideways_detergents.jpg

> color bychain

> color byhetero

> save working.cxs

Taking snapshot of stepper: working_2.pdb  
Restoring stepper: working_2.pdb  
opened ChimeraX session  

> close #8.1

> close #2

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class2a_26A.mrc

Opened class2a_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
0.0249, step 2, values float32  

> volume gaussian #1 bfactor 50

> clipper associate #1,2 toModel #8

Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2615, in
_set_map_to_transparent_surface  
volumecommand.volume(self.session, [v], **map_style_settings[style])  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/volumecommand.py", line 410, in volume  
apply_volume_options(v, dsettings, rsettings, session)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/volumecommand.py", line 444, in apply_volume_options  
v.set_display_style(doptions['style'])  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
line 660, in set_display_style  
self._drawings_need_update()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
line 742, in _drawings_need_update  
s._volume_update_manager = vm = VolumeUpdateManager(s)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
line 3950, in __init__  
t = session.triggers  
AttributeError: 'NoneType' object has no attribute 'triggers'  
  
AttributeError: 'NoneType' object has no attribute 'triggers'  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
line 3950, in __init__  
t = session.triggers  
  
See log for complete Python traceback.  
  

> clipper set contourSensitivity 0.25

> select #8

114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 22 models selected  

> isolde restrain distances #8

> select clear

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/working.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/working.cif  
---  
warnings | Unknown polymer entity '1' near line 609  
Unknown polymer entity '2' near line 3150  
Unknown polymer entity '3' near line 7200  
Unknown polymer entity '4' near line 33507  
Unknown polymer entity '5' near line 34519  
5 messages similar to the above omitted  
Unable to fetch template for 'LMX': might have incorrect bonds  
Unknown polymer entity '11' near line 75429  
Unknown polymer entity '12' near line 81996  
Unknown polymer entity '13' near line 83073  
Unknown polymer entity '14' near line 93894  
Unknown polymer entity '15' near line 113722  
Atom H is not in the residue template for MET /AA:1  
Atom C1 is not in the residue template for GPC /AA:60  
Atom H is not in the residue template for MET /AB:1  
Atom C1 is not in the residue template for GPC /AB:60  
Atom C26 is not in the residue template for PEX /AB:62  
Atom H is not in the residue template for MET /AC:1  
Atom C1 is not in the residue template for GPC /AC:60  
Atom C26 is not in the residue template for PEX /AC:62  
Atom H is not in the residue template for MET /AD:1  
Atom C1 is not in the residue template for GPC /AD:60  
Atom H is not in the residue template for MET /AE:1  
Atom C1 is not in the residue template for GPC /AE:60  
Atom C26 is not in the residue template for PEX /AE:62  
Atom H is not in the residue template for MET /AF:1  
Atom C1 is not in the residue template for GPC /AF:60  
Atom C26 is not in the residue template for PEX /AF:62  
Atom H is not in the residue template for MET /AG:1  
Atom C1 is not in the residue template for GPC /AG:60  
Atom H is not in the residue template for MET /AH:1  
Atom C1 is not in the residue template for GPC /AH:60  
Atom C26 is not in the residue template for PEX /AH:62  
Atom H is not in the residue template for MET /AI:1  
Atom C1 is not in the residue template for GPC /AI:60  
Atom C26 is not in the residue template for PEX /AI:62  
Atom H is not in the residue template for MET /AJ:1  
Atom C1 is not in the residue template for GPC /AJ:60  
Atom H is not in the residue template for MET /AK:1  
Atom C1 is not in the residue template for GPC /AK:60  
Atom C26 is not in the residue template for PEX /AK:62  
Atom H is not in the residue template for MET /AL:1  
Atom C1 is not in the residue template for GPC /AL:60  
Atom C26 is not in the residue template for PEX /AL:62  
Atom H is not in the residue template for MET /AM:1  
Atom C1 is not in the residue template for GPC /AM:60  
Atom H is not in the residue template for MET /AN:1  
Atom C1 is not in the residue template for GPC /AN:60  
Atom C26 is not in the residue template for PEX /AN:62  
Atom H is not in the residue template for MET /AO:1  
Atom C1 is not in the residue template for GPC /AO:60  
Atom C26 is not in the residue template for PEX /AO:62  
Atom H is not in the residue template for MET /AP:1  
Atom C1 is not in the residue template for GPC /AP:60  
Atom H is not in the residue template for MET /AQ:1  
Atom C1 is not in the residue template for GPC /AQ:60  
Atom C26 is not in the residue template for PEX /AQ:62  
Atom H is not in the residue template for MET /AR:1  
Atom C1 is not in the residue template for GPC /AR:60  
Atom C26 is not in the residue template for PEX /AR:62  
Atom H is not in the residue template for MET /AS:1  
Atom C1 is not in the residue template for GPC /AS:60  
Atom H is not in the residue template for MET /AT:1  
Atom C1 is not in the residue template for GPC /AT:60  
Atom C26 is not in the residue template for PEX /AT:62  
Atom H is not in the residue template for MET /AU:1  
Atom C1 is not in the residue template for GPC /AU:60  
Atom C26 is not in the residue template for PEX /AU:62  
Atom H is not in the residue template for MET /AV:1  
Atom C1 is not in the residue template for GPC /AV:60  
Atom H is not in the residue template for MET /AW:1  
Atom C1 is not in the residue template for GPC /AW:60  
Atom C26 is not in the residue template for PEX /AW:62  
Atom H is not in the residue template for MET /AX:1  
Atom C1 is not in the residue template for GPC /AX:60  
Atom C26 is not in the residue template for PEX /AX:62  
Atom H is not in the residue template for GLY /BQ:5  
Atom H is not in the residue template for GLY /BR:5  
Atom H is not in the residue template for GLY /BS:5  
Atom H is not in the residue template for GLY /BT:5  
Atom H is not in the residue template for ALA /C:15  
Atom H6 is not in the residue template for P5S /H1:1001  
Atom H11 is not in the residue template for BPH /L:606  
Atom H11 is not in the residue template for BPH /M:605  
Atom C1 is not in the residue template for RCC /M:701  
Atom HN2 is not in the residue template for ARG /ak:71  
Atom H is not in the residue template for GLY /C1:32  
Atom C1 is not in the residue template for GPC /Ba:60  
Atom C1 is not in the residue template for GPC /Bb:60  
Atom C1 is not in the residue template for GPC /Bc:60  
Atom C1 is not in the residue template for GPC /Bd:60  
Atom C1 is not in the residue template for GPC /Be:60  
11 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for working.cif #1  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?  
AC AD | ?  
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
bm bo bp | ?  
BB BD BE BI BQ BR BS BT BV BW bn | ?  
C | ?  
C1 | ?  
H1 | ?  
H2 | ?  
L | ?  
M | ?  
aa | ?  
ab ad ae af ag ah ai aj al am an ao ap | ?  
ac | ?  
ak | ?  
  

> select #1

114906 atoms, 116079 bonds, 464 pseudobonds, 6038 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> select #8/C,H2,L,M,C1

22623 atoms, 22703 bonds, 15 pseudobonds, 1551 residues, 3 models selected  

> select #8/C,H2,L,M,C1&protein

18620 atoms, 18935 bonds, 1 pseudobond, 1192 residues, 2 models selected  

> select #8/C,H2,L,M,C1&protein&@CA

1192 atoms, 1192 residues, 1 model selected  

> delete #1&~/C,H2,L,M,C1

> fitmap #1 inMap #8.1.1.1

Fit molecule working.cif (#1) to map class2a_26A.mrc (#8.1.1.1) using 22623
atoms  
average map value = 0.05124, steps = 144  
shifted from previous position = 0.474  
rotated from previous position = 22.5 degrees  
atoms outside contour = 17046, contour level = 0.070771  
  
Position of working.cif (#1) relative to class2a_26A.mrc (#8.1.1.1)
coordinates:  
Matrix rotation and translation  
0.92374096 0.38273145 -0.01480832 -58.21505213  
-0.38287530 0.92376145 -0.00844378 93.76317888  
0.01044766 0.01346961 0.99985470 -4.82454281  
Axis 0.02859500 -0.03295677 -0.99904763  
Axis point 206.42003168 193.23813197 0.00000000  
Rotation angle (degrees) 22.53007222  
Shift along axis 0.06515675  
  

> hide #!8.2 models

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cif  
---  
warnings | Unknown polymer entity '1' near line 564  
Unknown polymer entity '2' near line 2935  
Unknown polymer entity '3' near line 6791  
Unknown polymer entity '4' near line 31845  
Unknown polymer entity '5' near line 32854  
6 messages similar to the above omitted  
Unable to fetch template for 'LMX': might have incorrect bonds  
Unknown polymer entity '12' near line 74416  
Unknown polymer entity '13' near line 80927  
Unknown polymer entity '14' near line 81989  
Unknown polymer entity '15' near line 92567  
Unknown polymer entity '16' near line 112107  
Atom H is not in the residue template for MET /AA:1  
Atom C1 is not in the residue template for GPC /AA:60  
Atom H is not in the residue template for MET /AB:1  
Atom C1 is not in the residue template for GPC /AB:60  
Atom C26 is not in the residue template for PEX /AB:62  
Atom H is not in the residue template for MET /AC:1  
Atom C1 is not in the residue template for GPC /AC:60  
Atom C26 is not in the residue template for PEX /AC:62  
Atom H is not in the residue template for MET /AD:1  
Atom C1 is not in the residue template for GPC /AD:60  
Atom H is not in the residue template for MET /AE:1  
Atom C1 is not in the residue template for GPC /AE:60  
Atom C26 is not in the residue template for PEX /AE:62  
Atom H is not in the residue template for MET /AF:1  
Atom C1 is not in the residue template for GPC /AF:60  
Atom C26 is not in the residue template for PEX /AF:62  
Atom H is not in the residue template for MET /AG:1  
Atom C1 is not in the residue template for GPC /AG:60  
Atom H is not in the residue template for MET /AH:1  
Atom C1 is not in the residue template for GPC /AH:60  
Atom C26 is not in the residue template for PEX /AH:62  
Atom H is not in the residue template for MET /AI:1  
Atom C1 is not in the residue template for GPC /AI:60  
Atom C26 is not in the residue template for PEX /AI:62  
Atom H is not in the residue template for MET /AJ:1  
Atom C1 is not in the residue template for GPC /AJ:60  
Atom H is not in the residue template for MET /AK:1  
Atom C1 is not in the residue template for GPC /AK:60  
Atom C26 is not in the residue template for PEX /AK:62  
Atom H is not in the residue template for MET /AL:1  
Atom C1 is not in the residue template for GPC /AL:60  
Atom C26 is not in the residue template for PEX /AL:62  
Atom H is not in the residue template for MET /AM:1  
Atom C1 is not in the residue template for GPC /AM:60  
Atom H is not in the residue template for MET /AN:1  
Atom C1 is not in the residue template for GPC /AN:60  
Atom C26 is not in the residue template for PEX /AN:62  
Atom H is not in the residue template for MET /AO:1  
Atom C1 is not in the residue template for GPC /AO:60  
Atom C26 is not in the residue template for PEX /AO:62  
Atom H is not in the residue template for MET /AP:1  
Atom C1 is not in the residue template for GPC /AP:60  
Atom H is not in the residue template for MET /AQ:1  
Atom C1 is not in the residue template for GPC /AQ:60  
Atom C26 is not in the residue template for PEX /AQ:62  
Atom H is not in the residue template for MET /AR:1  
Atom C1 is not in the residue template for GPC /AR:60  
Atom C26 is not in the residue template for PEX /AR:62  
Atom H is not in the residue template for MET /AS:1  
Atom C1 is not in the residue template for GPC /AS:60  
Atom H is not in the residue template for MET /AT:1  
Atom C1 is not in the residue template for GPC /AT:60  
Atom C26 is not in the residue template for PEX /AT:62  
Atom H is not in the residue template for MET /AU:1  
Atom C1 is not in the residue template for GPC /AU:60  
Atom C26 is not in the residue template for PEX /AU:62  
Atom H is not in the residue template for MET /AV:1  
Atom C1 is not in the residue template for GPC /AV:60  
Atom H is not in the residue template for MET /AW:1  
Atom C1 is not in the residue template for GPC /AW:60  
Atom C26 is not in the residue template for PEX /AW:62  
Atom H is not in the residue template for MET /AX:1  
Atom C1 is not in the residue template for GPC /AX:60  
Atom C26 is not in the residue template for PEX /AX:62  
Atom H is not in the residue template for GLY /BQ:5  
Atom H is not in the residue template for GLY /BR:5  
Atom H is not in the residue template for GLY /BS:5  
Atom H is not in the residue template for GLY /BT:5  
Atom H6 is not in the residue template for P5S /H1:1001  
Atom H11 is not in the residue template for BPH /L:606  
Atom H11 is not in the residue template for BPH /M:605  
Atom C1 is not in the residue template for RCC /M:701  
Atom HN2 is not in the residue template for ARG /ak:71  
Atom H is not in the residue template for GLY /C1:32  
Atom C1 is not in the residue template for GPC /Ba:60  
Atom C1 is not in the residue template for GPC /Bb:60  
Atom C1 is not in the residue template for GPC /Bc:60  
Atom C1 is not in the residue template for GPC /Bd:60  
Atom C1 is not in the residue template for GPC /Be:60  
11 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for working.cif #2  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?  
AC AD | ?  
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
bm bo bp | ?  
BB BD BE BI BQ BR BS BT BV BW bn | ?  
C | ?  
C1 | ?  
C2 | ?  
H1 | ?  
H2 | ?  
L | ?  
M | ?  
aa | ?  
ab ad ae af ag ah ai aj al am an ao ap | ?  
ac | ?  
ak | ?  
  

> cartoon #2

> hide #2

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker working.cif, chain M (#1) with working.cif, chain M (#2), sequence
alignment score = 1682.6  
RMSD between 291 pruned atom pairs is 0.195 angstroms; (across all 323 pairs:
4.491)  
  

> color #1 red

> color #2 green

> delete #2&~/C,H2,L,M,C1,H1

> hide #!1 models

> show #!8.2 models

> select clear

> delete #2/M:22-36

> delete #2/M:22-52

> select #2

22948 atoms, 23331 bonds, 47 pseudobonds, 1275 residues, 3 models selected  

> select #2&protein

19393 atoms, 19722 bonds, 1 pseudobond, 1237 residues, 2 models selected  

> hide #!2 models

> select #8

114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 22 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

> select #8:C,H2,L,M,C1,H1

Nothing selected  

> select #8/C,H2,L,M,C1,H1

24224 atoms, 24303 bonds, 15 pseudobonds, 1633 residues, 3 models selected  

> isolde release distances sel externalOnly true

> select clear

> select #8/C,H2,L,M,C1,H1

24224 atoms, 24303 bonds, 15 pseudobonds, 1633 residues, 3 models selected  

> isolde adjust distances sel kappa 40

> select clear

> select clear

> select /ak

1282 atoms, 1289 bonds, 88 residues, 1 model selected  

> close #8.2.10

> delete :HOH

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

267 atoms, 271 bonds, 21 residues, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

267 atoms, 271 bonds, 21 residues, 1 model selected  

> select clear

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> select clear

> select up

20 atoms, 19 bonds, 2 residues, 1 model selected  

> delete sel

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

253 atoms, 255 bonds, 20 residues, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 20 residues in model 8.2  

> select /ak:59-71

175 atoms, 177 bonds, 13 residues, 1 model selected  

> setattr sel residues chain_id al

Assigning chain_id attribute to 13 items  
Cannot set attribute 'chain_id' to 'al'  

> save working.cxs

Taking snapshot of stepper: working_2.pdb  
opened ChimeraX session  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> close #1-2

> isolde start

> set selectionWidth 4

Done loading forcefield  
Loading residue template for LMG from internal database  
Loading residue template for PSF from internal database  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> select /al:5-65

923 atoms, 934 bonds, 61 residues, 1 model selected  

Chain al, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> cartoon

> select clear

> ~cartoon

> cartoon

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

92 atoms, 93 bonds, 8 residues, 1 model selected  

> select up

1234 atoms, 1257 bonds, 72 residues, 1 model selected  

> ~cartoon

> cartoon

Chain al, residue 67 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select clear




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        6.7G         43G        183M         12G         55G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Async: 0.1
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.0.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-Phenix: 0.1
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    graphviz: 0.14.1
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    objgraph: 3.4.1
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.17
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    versioneer: 0.18
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

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