Changes between Initial Version and Version 1 of Ticket #4152, comment 1


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Timestamp:
Jan 22, 2021, 3:31:53 PM (5 years ago)
Author:
Eric Pettersen

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  • Ticket #4152, comment 1

    initial v1  
    1 {{{
    21Also, occupancies are filled with uninitialised values and B-factors are zero. Would be better if the new altlocs inherited all the properties of the parent, and even better if the occupancies were automatically divided in two (a pretty reasonable starting point in most cases).
    3 ________________________________
    4 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
    5 Sent: 21 January 2021 18:27
    6 To: Tristan Croll <tic20@cam.ac.uk>
    7 Subject: [ChimeraX] #4152: ChimeraX bug report submission
    8 
    9 #4152: ChimeraX bug report submission
    10 ---------------------------+-----------------------------
    11  Reporter:  Tristan Croll  |                Type:  defect
    12    Status:  new            |            Priority:  normal
    13 Component:  Unassigned     |          Blocked By:
    14  Blocking:                 |  Notify when closed:
    15 ---------------------------+-----------------------------
    16  {{{
    17  The following bug report has been submitted:
    18  Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-
    19  centos-7.8.2003-Core
    20  ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
    21  Description
    22  If I try to create new altlocs for a set of atoms by:
    23 
    24  {{{
    25  for a in selected_atoms(session)
    26  a.set_alt_loc('A', True)
    27  }}}
    28 
    29  ... then all the coordinates for the new altlocs (or the master
    30  coordinates if there were no previous altlocs) are set to (0,0,0). I think
    31  it would be more sensible if the new ones inherited the existing
    32  coordinates as a starting point.
    33 
    34  Log:
    35  > alias preview_toolshed toolshed url https://cxtoolshed-
    36  > preview.rbvi.ucsf.edu; toolshed reload available
    37 
    38  > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
    39  > toolshed reload available
    40 
    41  > alias st isolde step $*
    42 
    43  > alias aw isolde add water $*
    44 
    45  > alias awsf isolde add water sim false
    46 
    47  UCSF ChimeraX version: 1.1 (2020-09-09)
    48  © 2016-2020 Regents of the University of California. All rights reserved.
    49  How to cite UCSF ChimeraX
    50 
    51  > open working.pdb
    52 
    53  Summary of feedback from opening working.pdb
    54  ---
    55  warnings | Ignored bad PDB record found on line 243
    56  LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN
    57 
    58  Ignored bad PDB record found on line 244
    59  LINKR TYR L 184 LEU L 186 gap
    60 
    61  Ignored bad PDB record found on line 245
    62  LINKR VAL L 210 GLU L 212 gap
    63 
    64  Ignored bad PDB record found on line 246
    65  LINKR PRO A 140 GLY A 148 gap
    66 
    67  working.pdb title:
    68  \--- [more info...]
    69 
    70  Chain information for working.pdb #1
    71  ---
    72  Chain | Description
    73  A | No description available
    74  B | No description available
    75  H | No description available
    76  L | No description available
    77  R | No description available
    78 
    79  Non-standard residues in working.pdb #1
    80  ---
    81  CL — (CL)
    82  GOL — (GOL)
    83  NAG — (NAG)
    84  POL — (POL)
    85  SO4 — (SO4)
    86 
    87 
    88  > isolde start
    89 
    90  > set selectionWidth 4
    91 
    92  working.pdb title:
    93  \--- [more info...]
    94 
    95  Chain information for working.pdb
    96  ---
    97  Chain | Description
    98  1.2/A | No description available
    99  1.2/B | No description available
    100  1.2/H | No description available
    101  1.2/L | No description available
    102  1.2/R | No description available
    103 
    104  Non-standard residues in working.pdb #1.2
    105  ---
    106  CL — (CL)
    107  GOL — (GOL)
    108  NAG — (NAG)
    109  POL — (POL)
    110  SO4 — (SO4)
    111 
    112  Done loading forcefield
    113  Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
    114  Y
    115  Reflection data provided as intensities. Performing French & Wilson
    116  scaling to
    117  convert to amplitudes...
    118 
    119  > view /B:92
    120 
    121  Loading residue template for GOL from internal database
    122  Loading residue template for SO4 from internal database
    123  Updating bulk solvent parameters...
    124 
    125  > select clear
    126 
    127  > select clear
    128 
    129  Updating bulk solvent parameters...
    130 
    131  > view /A:59
    132 
    133  > select clear
    134 
    135  Updating bulk solvent parameters...
    136 
    137  > view /A:213
    138 
    139  > select clear
    140 
    141  Updating bulk solvent parameters...
    142 
    143  > view /A:179
    144 
    145  > view /H:179
    146 
    147  > ui tool show Shell
    148 
    149  /opt/UCSF/ChimeraX/lib/python3.7/site-
    150  packages/IPython/core/history.py:226:
    151  UserWarning: IPython History requires SQLite, your history will not be
    152  saved
    153  warn("IPython History requires SQLite, your history will not be saved")
    154 
    155  > select clear
    156 
    157  > select clear
    158 
    159  Updating bulk solvent parameters...
    160 
    161  > save working.pdb #1
    162 
    163  > close #1
    164 
    165  Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
    166  Deleting (LIVE) 2mFo-DFc
    167  Deleting (LIVE) mFo-DFc
    168  Deleting (LIVE) 2mFo-DFc_smooth_18
    169  Deleting (LIVE) MDFF potential
    170 
    171  > open working_refine_001.pdb
    172 
    173  Chain information for working_refine_001.pdb #1
    174  ---
    175  Chain | Description
    176  A | No description available
    177  B | No description available
    178  H | No description available
    179  L | No description available
    180  R | No description available
    181 
    182  Chain information for working_refine_001.pdb
    183  ---
    184  Chain | Description
    185  1.2/A | No description available
    186  1.2/B | No description available
    187  1.2/H | No description available
    188  1.2/L | No description available
    189  1.2/R | No description available
    190 
    191  Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
    192  Y
    193  Reflection data provided as intensities. Performing French & Wilson
    194  scaling to
    195  convert to amplitudes...
    196 
    197  > open
    198  >
    199  /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb
    200 
    201  Summary of feedback from opening
    202  /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb
    203  ---
    204  warnings | Ignored bad PDB record found on line 243
    205  LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN
    206 
    207  Ignored bad PDB record found on line 244
    208  LINKR TYR L 184 LEU L 186 gap
    209 
    210  Ignored bad PDB record found on line 245
    211  LINKR VAL L 210 GLU L 212 gap
    212 
    213  Ignored bad PDB record found on line 246
    214  LINKR PRO A 140 GLY A 148 gap
    215 
    216  working.pdb title:
    217  \--- [more info...]
    218 
    219  Chain information for working.pdb #2
    220  ---
    221  Chain | Description
    222  A | No description available
    223  B | No description available
    224  H | No description available
    225  L | No description available
    226  R | No description available
    227 
    228  Non-standard residues in working.pdb #2
    229  ---
    230  CL — (CL)
    231  GOL — (GOL)
    232  NAG — (NAG)
    233  POL — (POL)
    234  SO4 — (SO4)
    235 
    236 
    237  > close #2
    238 
    239  > close #1
    240 
    241  Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
    242  Deleting (LIVE) 2mFo-DFc
    243  Deleting (LIVE) mFo-DFc
    244  Deleting (LIVE) 2mFo-DFc_smooth_18
    245  Deleting (LIVE) MDFF potential
    246 
    247  > open
    248  >
    249  /run/media/tic20/storage/structure_dump/papers/2020_study_weekend/examples/3fyj_ref_3fhr/ref_to_isolde_rebuild/Refine_56/3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
    250  > format pdb
    251 
    252  Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb #1
    253  ---
    254  Chain | Description
    255  X | No description available
    256 
    257  Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
    258  ---
    259  Chain | Description
    260  1.2/X | No description available
    261 
    262 
    263  > close #1
    264 
    265  > open working.pdb
    266 
    267  Summary of feedback from opening working.pdb
    268  ---
    269  warnings | Ignored bad PDB record found on line 243
    270  LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN
    271 
    272  Ignored bad PDB record found on line 244
    273  LINKR TYR L 184 LEU L 186 gap
    274 
    275  Ignored bad PDB record found on line 245
    276  LINKR VAL L 210 GLU L 212 gap
    277 
    278  Ignored bad PDB record found on line 246
    279  LINKR PRO A 140 GLY A 148 gap
    280 
    281  working.pdb title:
    282  \--- [more info...]
    283 
    284  Chain information for working.pdb #1
    285  ---
    286  Chain | Description
    287  A | No description available
    288  B | No description available
    289  H | No description available
    290  L | No description available
    291  R | No description available
    292 
    293  Non-standard residues in working.pdb #1
    294  ---
    295  CL — (CL)
    296  GOL — (GOL)
    297  NAG — (NAG)
    298  POL — (POL)
    299  SO4 — (SO4)
    300 
    301  working.pdb title:
    302  \--- [more info...]
    303 
    304  Chain information for working.pdb
    305  ---
    306  Chain | Description
    307  1.2/A | No description available
    308  1.2/B | No description available
    309  1.2/H | No description available
    310  1.2/L | No description available
    311  1.2/R | No description available
    312 
    313  Non-standard residues in working.pdb #1.2
    314  ---
    315  CL — (CL)
    316  GOL — (GOL)
    317  NAG — (NAG)
    318  POL — (POL)
    319  SO4 — (SO4)
    320 
    321 
    322  > view /R:449
    323 
    324  > delete /R:616
    325 
    326  Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
    327  Y
    328  Reflection data provided as intensities. Performing French & Wilson
    329  scaling to
    330  convert to amplitudes...
    331 
    332  > set bgColor white
    333 
    334  Loading residue template for POL from internal database
    335 
    336  > select clear
    337 
    338  Updating bulk solvent parameters...
    339 
    340  > open 6m0j
    341 
    342  6m0j title:
    343  Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with
    344  ACE2
    345  [more info...]
    346 
    347  Chain information for 6m0j #2
    348  ---
    349  Chain | Description
    350  A | Angiotensin-converting enzyme 2
    351  E | Spike receptor binding domain
    352 
    353  Non-standard residues in 6m0j #2
    354  ---
    355  CL — chloride ion
    356  NAG — N-acetyl-D-glucosamine
    357  ZN — zinc ion
    358 
    359 
    360  > matchmaker #2 to #1/R
    361 
    362  Parameters
    363  ---
    364  Chain pairing | bb
    365  Alignment algorithm | Needleman-Wunsch
    366  Similarity matrix | BLOSUM-62
    367  SS fraction | 0.3
    368  Gap open (HH/SS/other) | 18/18/6
    369  Gap extend | 1
    370  SS matrix |  |  | H | S | O
    371  ---|---|---|---
    372  H | 6 | -9 | -6
    373  S |  | 6 | -6
    374  O |  |  | 4
    375  Iteration cutoff | 2
    376 
    377  Matchmaker working.pdb, chain R (#1.2) with 6m0j, chain E (#2), sequence
    378  alignment score = 1012.9
    379  RMSD between 192 pruned atom pairs is 0.602 angstroms; (across all 194
    380  pairs:
    381  0.726)
    382 
    383 
    384  > show #2
    385 
    386  > close #2
    387 
    388  > view /R:604
    389 
    390  > select up
    391 
    392  3 atoms, 2 bonds, 1 residue, 1 model selected
    393 
    394  > delete sel
    395 
    396  > select :HOH
    397 
    398  1284 atoms, 856 bonds, 428 residues, 1 model selected
    399 
    400  > clipper isolate sel contextDistance 0
    401 
    402  > clipper isolate sel contextDistance 0
    403 
    404  > select up
    405 
    406  3 atoms, 2 bonds, 1 residue, 1 model selected
    407 
    408  > delete sel
    409 
    410  > select clear
    411 
    412  Updating bulk solvent parameters...
    413 
    414  > select :HOH
    415 
    416  1281 atoms, 854 bonds, 427 residues, 1 model selected
    417 
    418  > delete sel
    419 
    420  > close #1
    421 
    422  Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
    423  Deleting (LIVE) 2mFo-DFc
    424  Deleting (LIVE) mFo-DFc
    425  Deleting (LIVE) 2mFo-DFc_smooth_18
    426  Deleting (LIVE) MDFF potential
    427 
    428  > open working.pdb
    429 
    430  Summary of feedback from opening working.pdb
    431  ---
    432  warnings | Ignored bad PDB record found on line 243
    433  LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN
    434 
    435  Ignored bad PDB record found on line 244
    436  LINKR TYR L 184 LEU L 186 gap
    437 
    438  Ignored bad PDB record found on line 245
    439  LINKR VAL L 210 GLU L 212 gap
    440 
    441  Ignored bad PDB record found on line 246
    442  LINKR PRO A 140 GLY A 148 gap
    443 
    444  working.pdb title:
    445  \--- [more info...]
    446 
    447  Chain information for working.pdb #1
    448  ---
    449  Chain | Description
    450  A | No description available
    451  B | No description available
    452  H | No description available
    453  L | No description available
    454  R | No description available
    455 
    456  Non-standard residues in working.pdb #1
    457  ---
    458  CL — (CL)
    459  GOL — (GOL)
    460  NAG — (NAG)
    461  POL — (POL)
    462  SO4 — (SO4)
    463 
    464  working.pdb title:
    465  \--- [more info...]
    466 
    467  Chain information for working.pdb
    468  ---
    469  Chain | Description
    470  1.2/A | No description available
    471  1.2/B | No description available
    472  1.2/H | No description available
    473  1.2/L | No description available
    474  1.2/R | No description available
    475 
    476  Non-standard residues in working.pdb #1.2
    477  ---
    478  CL — (CL)
    479  GOL — (GOL)
    480  NAG — (NAG)
    481  POL — (POL)
    482  SO4 — (SO4)
    483 
    484  Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
    485  Y
    486  Reflection data provided as intensities. Performing French & Wilson
    487  scaling to
    488  convert to amplitudes...
    489 
    490  > select up
    491 
    492  6 atoms, 4 bonds, 2 residues, 1 model selected
    493 
    494  > delete sel
    495 
    496  > select clear
    497 
    498  > select up
    499 
    500  3 atoms, 2 bonds, 1 residue, 1 model selected
    501 
    502  > delete sel
    503 
    504  > select clear
    505 
    506  > select #1
    507 
    508  17592 atoms, 17354 bonds, 2 pseudobonds, 1532 residues, 30 models selected
    509  Map is too large for fast cubic interpolation on the GPU! Switching to
    510  slower,
    511  more memory-efficient implementation.
    512 
    513  > select clear
    514 
    515  Updating bulk solvent parameters...
    516 
    517  > view /R:449
    518 
    519  > select up
    520 
    521  21 atoms, 21 bonds, 1 residue, 1 model selected
    522 
    523  > select clear
    524 
    525  > select clear
    526 
    527  Updating bulk solvent parameters...
    528 
    529  > select up
    530 
    531  3 atoms, 2 bonds, 1 residue, 1 model selected
    532 
    533  > delete sel
    534 
    535  > view /R:449
    536 
    537  > awsf
    538 
    539  > awsf
    540 
    541  > awsf
    542 
    543  > awsf
    544 
    545  > awsf
    546 
    547  > select clear
    548 
    549  Updating bulk solvent parameters...
    550 
    551  > st first
    552 
    553  > st
    554 
    555  > st interp 2
    556 
    557  > st
    558 
    559  > st
    560 
    561  > st
    562 
    563  > st
    564 
    565  > st
    566 
    567  > st
    568 
    569  > st
    570 
    571  > st
    572 
    573  > st
    574 
    575  > st
    576 
    577  > st
    578 
    579  > st
    580 
    581  > st
    582 
    583  > st
    584 
    585  > st
    586 
    587  > aw
    588 
    589  > isolde sim start sel
    590 
    591  Updating bulk solvent parameters...
    592 
    593  > st
    594 
    595  > st
    596 
    597  > st
    598 
    599  > st
    600 
    601  > aw
    602 
    603  > isolde sim start sel
    604 
    605  > select clear
    606 
    607  Updating bulk solvent parameters...
    608 
    609  > aw
    610 
    611  > isolde sim start sel
    612 
    613  Updating bulk solvent parameters...
    614 
    615  > st
    616 
    617  > st
    618 
    619  > st
    620 
    621  > st
    622 
    623  > st
    624 
    625  > aw
    626 
    627  > isolde sim start sel
    628 
    629  > select clear
    630 
    631  Updating bulk solvent parameters...
    632 
    633  > st
    634 
    635  > aw
    636 
    637  > isolde sim start sel
    638 
    639  > select clear
    640 
    641  Updating bulk solvent parameters...
    642 
    643  > st
    644 
    645  > st
    646 
    647  > st
    648 
    649  > st
    650 
    651  > st
    652 
    653  > st
    654 
    655  > st
    656 
    657  > st
    658 
    659  > st
    660 
    661  > st
    662 
    663  > st
    664 
    665  > st
    666 
    667  > aw
    668 
    669  > isolde sim start sel
    670 
    671  Updating bulk solvent parameters...
    672 
    673  > awsf
    674 
    675  > awsf
    676 
    677  > awsf
    678 
    679  > select clear
    680 
    681  Updating bulk solvent parameters...
    682 
    683  > select up
    684 
    685  9 atoms, 6 bonds, 3 residues, 1 model selected
    686 
    687  > delete sel
    688 
    689  > st
    690 
    691  > st
    692 
    693  > st
    694 
    695  > st
    696 
    697  > st
    698 
    699  > st
    700 
    701  > aw
    702 
    703  > isolde sim start sel
    704 
    705  > select clear
    706 
    707  Updating bulk solvent parameters...
    708 
    709  > select up
    710 
    711  3 atoms, 2 bonds, 1 residue, 1 model selected
    712 
    713  > delete sel
    714 
    715  > alias al isolde add ligand $*
    716 
    717  > alias so setattr sel atoms occupancy $*
    718 
    719  > al SO4
    720 
    721  > so 0.7
    722 
    723  Assigning occupancy attribute to 5 items
    724 
    725  > select up
    726 
    727  5 atoms, 4 bonds, 1 residue, 1 model selected
    728  Updating bulk solvent parameters...
    729 
    730  > select up
    731 
    732  5 atoms, 4 bonds, 1 residue, 1 model selected
    733 
    734  > so 0.5
    735 
    736  Assigning occupancy attribute to 5 items
    737 
    738  > st
    739 
    740  > st
    741 
    742  > st
    743 
    744  > st
    745 
    746  > st
    747 
    748  > awsf
    749 
    750  > awsf
    751 
    752  Updating bulk solvent parameters...
    753 
    754  > st
    755 
    756  > st
    757 
    758  > st
    759 
    760  > al GOL
    761 
    762  > select clear
    763 
    764  Updating bulk solvent parameters...
    765 
    766  > st
    767 
    768  > aw
    769 
    770  > isolde sim start sel
    771 
    772  Updating bulk solvent parameters...
    773 
    774  > awsf
    775 
    776  > awsf
    777 
    778  Updating bulk solvent parameters...
    779 
    780  > select up
    781 
    782  9 atoms, 6 bonds, 3 residues, 1 model selected
    783 
    784  > delete sel
    785 
    786  > select up
    787 
    788  3 atoms, 2 bonds, 1 residue, 1 model selected
    789 
    790  > delete sel
    791 
    792  > al BMA
    793 
    794  Deleted the following atoms from residue BMA R710: HO1, O1
    795 
    796  > show sel
    797 
    798  > ui mousemode right "translate selected atoms"
    799 
    800  > delete sel
    801 
    802  Traceback (most recent call last):
    803  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py",
    804  line
    805  1574, in <lambda>
    806  action.triggered.connect(lambda arg, cb = callback: cb())
    807  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    808  packages/chimerax/isolde/menu/menu.py", line 58, in f
    809  module.run_script(session)
    810  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    811  packages/chimerax/isolde/menu/model_building/make_bond.py", line 22, in
    812  run_script
    813  add_bond(*sel)
    814  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    815  packages/chimerax/atomic/struct_edit.py", line 225, in add_bond
    816  \+ all_residues[i1+1:i2] + all_residues[end_range+1:]
    817  TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'
    818 
    819  TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'
    820 
    821  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    822  packages/chimerax/atomic/struct_edit.py", line 225, in add_bond
    823  \+ all_residues[i1+1:i2] + all_residues[end_range+1:]
    824 
    825  See log for complete Python traceback.
    826 
    827 
    828  > select clear
    829 
    830  > select up
    831 
    832  22 atoms, 22 bonds, 1 residue, 1 model selected
    833  Updating bulk solvent parameters...
    834 
    835  > al MAN
    836 
    837  Deleted the following atoms from residue MAN R711: HO1, O1
    838 
    839  > show sel
    840 
    841  > ui mousemode right "translate selected atoms"
    842 
    843  > delete sel
    844 
    845  > select clear
    846 
    847  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    848  bonded heavy atom.
    849 
    850  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    851  bonded heavy atom.
    852 
    853  Updating bulk solvent parameters...
    854 
    855  > select up
    856 
    857  22 atoms, 22 bonds, 1 residue, 1 model selected
    858 
    859  > delete sel
    860 
    861  Updating bulk solvent parameters...
    862 
    863  > delete sel
    864 
    865  > save working_2.pdb #1
    866 
    867  > view /R:449
    868 
    869  > select up
    870 
    871  21 atoms, 21 bonds, 1 residue, 1 model selected
    872 
    873  > select sel&sideonly
    874 
    875  15 atoms, 15 bonds, 1 residue, 1 model selected
    876 
    877 
    878 
    879 
    880  OpenGL version: 3.3.0 NVIDIA 455.32.00
    881  OpenGL renderer: TITAN Xp/PCIe/SSE2
    882  OpenGL vendor: NVIDIA Corporation
    883  Manufacturer: Dell Inc.
    884  Model: Precision T5600
    885  OS: CentOS Linux 7 Core
    886  Architecture: 64bit ELF
    887  CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
    888  Cache Size: 20480 KB
    889  Memory:
    890                        total        used        free      shared
    891  buff/cache   available
    892          Mem:            62G         12G         36G        303M
    893  13G         49G
    894          Swap:          4.9G          0B        4.9G
    895 
    896  Graphics:
    897          03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102
    898  [TITAN Xp] [10de:1b02] (rev a1)
    899          Subsystem: NVIDIA Corporation Device [10de:11df]
    900          Kernel driver in use: nvidia
    901  PyQt version: 5.12.3
    902  Compiled Qt version: 5.12.4
    903  Runtime Qt version: 5.12.9
    904  Installed Packages:
    905      alabaster: 0.7.12
    906      appdirs: 1.4.4
    907      Babel: 2.8.0
    908      backcall: 0.2.0
    909      blockdiag: 2.0.1
    910      certifi: 2020.6.20
    911      chardet: 3.0.4
    912      ChimeraX-AddH: 2.1.1
    913      ChimeraX-AlignmentAlgorithms: 2.0
    914      ChimeraX-AlignmentHdrs: 3.2
    915      ChimeraX-AlignmentMatrices: 2.0
    916      ChimeraX-Alignments: 2.1
    917      ChimeraX-Arrays: 1.0
    918      ChimeraX-Async: 0.1
    919      ChimeraX-Atomic: 1.6.1
    920      ChimeraX-AtomSearch: 2.0
    921      ChimeraX-AxesPlanes: 2.0
    922      ChimeraX-BasicActions: 1.1
    923      ChimeraX-BILD: 1.0
    924      ChimeraX-BlastProtein: 1.0.1
    925      ChimeraX-BondRot: 2.0
    926      ChimeraX-BugReporter: 1.0
    927      ChimeraX-BuildStructure: 2.0
    928      ChimeraX-Bumps: 1.0
    929      ChimeraX-BundleBuilder: 1.0
    930      ChimeraX-ButtonPanel: 1.0
    931      ChimeraX-CageBuilder: 1.0
    932      ChimeraX-CellPack: 1.0
    933      ChimeraX-Centroids: 1.1
    934      ChimeraX-ChemGroup: 2.0
    935      ChimeraX-Clashes: 2.0
    936      ChimeraX-Clipper: 0.15.0
    937      ChimeraX-ColorActions: 1.0
    938      ChimeraX-ColorGlobe: 1.0
    939      ChimeraX-CommandLine: 1.1.3
    940      ChimeraX-ConnectStructure: 2.0
    941      ChimeraX-Contacts: 1.0
    942      ChimeraX-Core: 1.1
    943      ChimeraX-CoreFormats: 1.0
    944      ChimeraX-coulombic: 1.0.1
    945      ChimeraX-Crosslinks: 1.0
    946      ChimeraX-Crystal: 1.0
    947      ChimeraX-DataFormats: 1.0
    948      ChimeraX-Dicom: 1.0
    949      ChimeraX-DistMonitor: 1.1
    950      ChimeraX-DistUI: 1.0
    951      ChimeraX-Dssp: 2.0
    952      ChimeraX-EMDB-SFF: 1.0
    953      ChimeraX-ExperimentalCommands: 1.0
    954      ChimeraX-FileHistory: 1.0
    955      ChimeraX-FunctionKey: 1.0
    956      ChimeraX-Geometry: 1.1
    957      ChimeraX-gltf: 1.0
    958      ChimeraX-Graphics: 1.0
    959      ChimeraX-Hbonds: 2.0
    960      ChimeraX-Help: 1.0
    961      ChimeraX-HKCage: 1.3
    962      ChimeraX-IHM: 1.0
    963      ChimeraX-ImageFormats: 1.0
    964      ChimeraX-IMOD: 1.0
    965      ChimeraX-IO: 1.0
    966      ChimeraX-ISOLDE: 1.1.0
    967      ChimeraX-Label: 1.0
    968      ChimeraX-LinuxSupport: 1.0
    969      ChimeraX-ListInfo: 1.0
    970      ChimeraX-Log: 1.1.1
    971      ChimeraX-LookingGlass: 1.1
    972      ChimeraX-Map: 1.0.1
    973      ChimeraX-MapData: 2.0
    974      ChimeraX-MapEraser: 1.0
    975      ChimeraX-MapFilter: 2.0
    976      ChimeraX-MapFit: 2.0
    977      ChimeraX-MapSeries: 2.0
    978      ChimeraX-Markers: 1.0
    979      ChimeraX-Mask: 1.0
    980      ChimeraX-MatchMaker: 1.1
    981      ChimeraX-MDcrds: 2.0
    982      ChimeraX-MedicalToolbar: 1.0.1
    983      ChimeraX-Meeting: 1.0
    984      ChimeraX-MLP: 1.0
    985      ChimeraX-mmCIF: 2.2
    986      ChimeraX-MMTF: 2.0
    987      ChimeraX-Modeller: 1.0
    988      ChimeraX-ModelPanel: 1.0
    989      ChimeraX-ModelSeries: 1.0
    990      ChimeraX-Mol2: 2.0
    991      ChimeraX-Morph: 1.0
    992      ChimeraX-MouseModes: 1.0
    993      ChimeraX-Movie: 1.0
    994      ChimeraX-Neuron: 1.0
    995      ChimeraX-Nucleotides: 2.0
    996      ChimeraX-OpenCommand: 1.2.1
    997      ChimeraX-PDB: 2.1
    998      ChimeraX-PDBBio: 1.0
    999      ChimeraX-Phenix: 0.1
    1000      ChimeraX-PickBlobs: 1.0
    1001      ChimeraX-Positions: 1.0
    1002      ChimeraX-PresetMgr: 1.0
    1003      ChimeraX-PubChem: 2.0
    1004      ChimeraX-Read-Pbonds: 1.0
    1005      ChimeraX-Registration: 1.1
    1006      ChimeraX-RemoteControl: 1.0
    1007      ChimeraX-ResidueFit: 1.0
    1008      ChimeraX-RestServer: 1.0
    1009      ChimeraX-RNALayout: 1.0
    1010      ChimeraX-RotamerLibMgr: 2.0
    1011      ChimeraX-RotamerLibsDunbrack: 2.0
    1012      ChimeraX-RotamerLibsDynameomics: 2.0
    1013      ChimeraX-RotamerLibsRichardson: 2.0
    1014      ChimeraX-SaveCommand: 1.2
    1015      ChimeraX-SchemeMgr: 1.0
    1016      ChimeraX-SDF: 2.0
    1017      ChimeraX-Segger: 1.0
    1018      ChimeraX-Segment: 1.0
    1019      ChimeraX-SeqView: 2.2
    1020      ChimeraX-Shape: 1.0.1
    1021      ChimeraX-Shell: 1.0
    1022      ChimeraX-Shortcuts: 1.0
    1023      ChimeraX-ShowAttr: 1.0
    1024      ChimeraX-ShowSequences: 1.0
    1025      ChimeraX-SideView: 1.0
    1026      ChimeraX-Smiles: 2.0
    1027      ChimeraX-SmoothLines: 1.0
    1028      ChimeraX-SpaceNavigator: 1.0
    1029      ChimeraX-StdCommands: 1.0.4
    1030      ChimeraX-STL: 1.0
    1031      ChimeraX-Storm: 1.0
    1032      ChimeraX-Struts: 1.0
    1033      ChimeraX-Surface: 1.0
    1034      ChimeraX-SwapAA: 2.0
    1035      ChimeraX-SwapRes: 2.0
    1036      ChimeraX-TapeMeasure: 1.0
    1037      ChimeraX-Test: 1.0
    1038      ChimeraX-Toolbar: 1.0
    1039      ChimeraX-ToolshedUtils: 1.0
    1040      ChimeraX-Tug: 1.0
    1041      ChimeraX-UI: 1.2.3
    1042      ChimeraX-uniprot: 2.0
    1043      ChimeraX-ViewDockX: 1.0
    1044      ChimeraX-Vive: 1.1
    1045      ChimeraX-VolumeMenu: 1.0
    1046      ChimeraX-VTK: 1.0
    1047      ChimeraX-WavefrontOBJ: 1.0
    1048      ChimeraX-WebCam: 1.0
    1049      ChimeraX-WebServices: 1.0
    1050      ChimeraX-Zone: 1.0
    1051      colorama: 0.4.3
    1052      comtypes: 1.1.7
    1053      cxservices: 1.0
    1054      cycler: 0.10.0
    1055      Cython: 0.29.20
    1056      decorator: 4.4.2
    1057      distlib: 0.3.1
    1058      distro: 1.5.0
    1059      docutils: 0.16
    1060      filelock: 3.0.12
    1061      funcparserlib: 0.3.6
    1062      grako: 3.16.5
    1063      graphviz: 0.14.1
    1064      h5py: 2.10.0
    1065      html2text: 2020.1.16
    1066      idna: 2.10
    1067      ihm: 0.16
    1068      imagecodecs: 2020.5.30
    1069      imagecodecs-lite: 2020.1.31
    1070      imagesize: 1.2.0
    1071      ipykernel: 5.3.0
    1072      ipython: 7.15.0
    1073      ipython-genutils: 0.2.0
    1074      jedi: 0.17.2
    1075      Jinja2: 2.11.2
    1076      jupyter-client: 6.1.3
    1077      jupyter-core: 4.6.3
    1078      kiwisolver: 1.2.0
    1079      line-profiler: 2.1.2
    1080      lxml: 4.5.1
    1081      MarkupSafe: 1.1.1
    1082      matplotlib: 3.2.1
    1083      msgpack: 1.0.0
    1084      netifaces: 0.10.9
    1085      networkx: 2.4
    1086      numexpr: 2.7.1
    1087      numpy: 1.18.5
    1088      numpydoc: 1.0.0
    1089      objgraph: 3.4.1
    1090      openvr: 1.12.501
    1091      packaging: 20.4
    1092      ParmEd: 3.2.0
    1093      parso: 0.7.1
    1094      pexpect: 4.8.0
    1095      pickleshare: 0.7.5
    1096      Pillow: 7.1.2
    1097      pip: 20.2.2
    1098      pkginfo: 1.5.0.1
    1099      prompt-toolkit: 3.0.7
    1100      psutil: 5.7.0
    1101      ptyprocess: 0.6.0
    1102      pycollada: 0.7.1
    1103      pydicom: 2.0.0
    1104      Pygments: 2.6.1
    1105      PyOpenGL: 3.1.5
    1106      PyOpenGL-accelerate: 3.1.5
    1107      pyparsing: 2.4.7
    1108      PyQt5-commercial: 5.12.3
    1109      PyQt5-sip: 4.19.19
    1110      PyQtWebEngine-commercial: 5.12.1
    1111      python-dateutil: 2.8.1
    1112      pytz: 2020.1
    1113      pyzmq: 19.0.2
    1114      qtconsole: 4.7.4
    1115      QtPy: 1.9.0
    1116      RandomWords: 0.3.0
    1117      requests: 2.24.0
    1118      scipy: 1.4.1
    1119      Send2Trash: 1.5.0
    1120      SEQCROW: 0.20
    1121      setuptools: 49.4.0
    1122      sfftk-rw: 0.6.6.dev0
    1123      six: 1.15.0
    1124      snowballstemmer: 2.0.0
    1125      sortedcontainers: 2.2.2
    1126      Sphinx: 3.1.1
    1127      sphinxcontrib-applehelp: 1.0.2
    1128      sphinxcontrib-blockdiag: 2.0.0
    1129      sphinxcontrib-devhelp: 1.0.2
    1130      sphinxcontrib-htmlhelp: 1.0.3
    1131      sphinxcontrib-jsmath: 1.0.1
    1132      sphinxcontrib-qthelp: 1.0.3
    1133      sphinxcontrib-serializinghtml: 1.1.4
    1134      suds-jurko: 0.6
    1135      tables: 3.6.1
    1136      tifffile: 2020.6.3
    1137      tinyarray: 1.2.2
    1138      tornado: 6.0.4
    1139      traitlets: 5.0.4
    1140      urllib3: 1.25.10
    1141      versioneer: 0.18
    1142      wcwidth: 0.2.5
    1143      webcolors: 1.11.1
    1144      wheel: 0.34.2
    1145 
    1146  }}}
    1147 
    1148 --
    1149 Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4152>
    1150 ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    1151 ChimeraX Issue Tracker
    1152 }}}