The following bug report has been submitted:
Platform: Linux-4.18.0-348.2.1.el8_5.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
pbond not working 'unknown command'
example:
pbond #1/A:1601@CL01 #1/A:796@O2'
output: 'unknown command: pbond'
I could not find any bug report online, any idea?
(https://www.cgl.ucsf.edu/chimerax/docs/user/commands/pbond.html)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open complex3_body_J266.pdb
Chain information for complex3_body_J266.pdb #1
---
Chain | Description
A | No description available
D | No description available
E | No description available
F | No description available
H | No description available
K | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
U | No description available
> set bgColor white
> style stick
Changed 35257 atom styles
> view #1:1601
> lighting soft
> view #1:1601
> ui tool show "Side View"
> select #1:1601
45 atoms, 46 bonds, 2 residues, 1 model selected
> show #1:1601
> show #1:@A:1601
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1@A:1601
> show #1@2:32
> getcrd #1@2:32
Atom /1:32@O 237.408 213.349 161.516
Atom /2:32@K 224.948 251.118 179.276
Atom /3:32@MG 229.135 183.751 117.370
Atom /A:32@P 188.564 200.971 133.396
Atom /A:32@OP1 187.122 200.867 133.725
Atom /A:32@OP2 188.999 201.043 131.980
Atom /A:32@O5' 189.149 202.241 134.154
Atom /A:32@C5' 188.346 202.971 135.063
Atom /A:32@C4' 188.961 203.027 136.437
Atom /A:32@O4' 190.344 203.457 136.343
Atom /A:32@C3' 188.318 204.019 137.390
Atom /A:32@O3' 187.174 203.482 138.029
Atom /A:32@C2' 189.451 204.361 138.347
Atom /A:32@O2' 189.604 203.344 139.325
Atom /A:32@C1' 190.660 204.317 137.414
Atom /A:32@N9 190.999 205.636 136.844
Atom /A:32@C8 191.208 205.871 135.510
Atom /A:32@N7 191.509 207.107 135.222
Atom /A:32@C5 191.505 207.736 136.453
Atom /A:32@C6 191.755 209.066 136.808
Atom /A:32@N6 192.057 210.008 135.918
Atom /A:32@N1 191.679 209.395 138.111
Atom /A:32@C2 191.372 208.440 138.998
Atom /A:32@N3 191.117 207.149 138.780
Atom /A:32@C4 191.200 206.850 137.470
Atom /D:32@N 180.817 240.501 105.792
Atom /D:32@CA 181.191 240.810 107.167
Atom /D:32@C 182.502 241.580 107.155
Atom /D:32@O 183.224 241.609 106.155
Atom /D:32@CB 181.326 239.544 108.022
Atom /D:32@SG 182.811 238.568 107.672
Atom /E:32@N 217.710 249.380 132.915
Atom /E:32@CA 218.206 249.348 131.556
Atom /E:32@C 217.785 248.035 130.916
Atom /E:32@O 217.361 247.093 131.594
Atom /E:32@CB 219.715 249.519 131.527
Atom /E:32@OG 220.211 248.861 130.398
Atom /F:32@N 293.332 201.478 176.475
Atom /F:32@CA 292.329 200.882 175.606
Atom /F:32@C 292.752 200.795 174.138
Atom /F:32@O 291.886 200.544 173.296
Atom /F:32@CB 291.023 201.666 175.714
Atom /H:32@N 252.737 197.125 119.519
Atom /H:32@CA 251.368 197.621 119.382
Atom /H:32@C 251.375 199.100 119.039
Atom /H:32@O 250.594 199.561 118.195
Atom /H:32@CB 250.565 197.379 120.665
Atom /H:32@CG 249.089 197.814 120.678
Atom /H:32@CD1 248.353 197.164 119.519
Atom /H:32@CD2 248.398 197.477 121.993
Atom /K:32@N 263.961 256.178 191.551
Atom /K:32@CA 265.383 256.504 191.472
Atom /K:32@C 265.986 256.284 192.852
Atom /K:32@O 265.536 256.893 193.831
Atom /K:32@CB 265.613 257.951 191.008
Atom /K:32@CG1 267.016 258.114 190.440
Atom /K:32@CG2 264.555 258.367 189.999
Atom /L:32@N 186.162 210.248 155.158
Atom /L:32@CA 186.491 210.439 156.549
Atom /L:32@C 185.444 211.230 157.305
Atom /L:32@O 184.600 211.921 156.727
Atom /O:32@N 267.531 192.065 155.324
Atom /O:32@CA 266.366 192.583 156.036
Atom /O:32@C 266.180 191.872 157.370
Atom /O:32@O 265.909 192.512 158.396
Atom /O:32@CB 265.114 192.456 155.168
Atom /O:32@CG 265.045 193.469 154.025
Atom /O:32@CD1 263.755 193.373 153.211
Atom /O:32@CD2 265.254 194.889 154.550
Atom /P:32@N 198.399 174.848 121.868
Atom /P:32@CA 198.424 173.865 120.788
Atom /P:32@C 199.848 173.477 120.406
Atom /P:32@O 200.819 174.142 120.775
Atom /P:32@CB 197.737 174.441 119.542
Atom /P:32@CG 198.328 175.751 119.100
Atom /P:32@CD1 199.340 175.790 118.161
Atom /P:32@CD2 197.902 176.943 119.661
Atom /P:32@CE1 199.909 176.999 117.781
Atom /P:32@CE2 198.464 178.152 119.275
Atom /P:32@CZ 199.466 178.175 118.331
Atom /Q:32@N 226.463 193.220 132.924
Atom /Q:32@CA 225.277 193.625 132.150
Atom /Q:32@C 225.067 195.128 132.063
Atom /Q:32@O 224.472 195.584 131.080
Atom /Q:32@CB 224.111 192.975 132.906
Atom /Q:32@CG 224.706 192.026 133.837
Atom /Q:32@CD 226.085 192.480 134.140
Atom /R:32@N 281.339 237.936 164.404
Atom /R:32@CA 279.942 237.606 164.156
Atom /R:32@C 279.066 237.779 165.387
Atom /R:32@O 277.921 237.306 165.392
Atom /R:32@CB 279.836 236.178 163.619
Atom /R:32@CG 280.630 235.995 162.354
Atom /R:32@CD1 280.171 236.509 161.151
Atom /R:32@CD2 281.847 235.330 162.361
Atom /R:32@CE1 280.893 236.358 159.991
Atom /R:32@CE2 282.578 235.172 161.202
Atom /R:32@CZ 282.095 235.689 160.019
Atom /R:32@OH 282.812 235.541 158.854
Atom /T:32@N 207.228 138.037 150.288
Atom /T:32@CA 208.562 138.641 150.231
Atom /T:32@C 209.317 138.379 151.531
Atom /T:32@O 210.499 137.997 151.533
Atom /T:32@CB 208.458 140.150 149.947
Atom /T:32@CG1 207.761 140.398 148.611
Atom /T:32@CG2 209.836 140.802 149.996
Atom /T:32@CD1 208.424 139.729 147.453
Atom /U:32@N 261.487 243.871 175.323
Atom /U:32@CA 260.667 243.952 176.528
Atom /U:32@C 259.207 244.194 176.166
Atom /U:32@O 258.305 243.520 176.675
Atom /U:32@CB 261.203 245.043 177.471
Atom /U:32@CG1 260.171 245.386 178.533
Atom /U:32@CG2 262.498 244.588 178.119
> view #1:1601
> view #1:1498
[Repeated 1 time(s)]
> view #1:1601
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting flat
> lighting soft
> ui mousemode right "tape measure"
> ui mousemode right select
> select /A:1601@C15
1 atom, 1 residue, 1 model selected
> select /A:1601@C21
1 atom, 1 residue, 1 model selected
> select add /A:1601@N07
2 atoms, 1 residue, 1 model selected
> select add /A:1601@C22
3 atoms, 1 residue, 1 model selected
> select add /A:1601@N06
4 atoms, 1 residue, 1 model selected
> select add /A:1601@C15
5 atoms, 1 residue, 1 model selected
> ui mousemode right "mark center"
> measure center sel mark true radius 0.3 color cyan
Center of mass of 5 atoms = (234.22, 253.66, 181.10)
> hide #2 models
> show #2 models
> ui mousemode right select
> select clear
> select #1/A:693@N1
1 atom, 1 residue, 1 model selected
> select #1/A:693@C6
1 atom, 1 residue, 1 model selected
> select #1/A:693@N1
1 atom, 1 residue, 1 model selected
> select add #1/A:693@C6
2 atoms, 1 residue, 1 model selected
> select add #1/A:693@C5
3 atoms, 1 residue, 1 model selected
> select add #1/A:693@C4
4 atoms, 1 residue, 1 model selected
> select add #1/A:693@N3
5 atoms, 1 residue, 1 model selected
> select add #1/A:693@C2
6 atoms, 1 residue, 1 model selected
> measure center sel mark true radius 0.3 color cyan
Center of mass of 6 atoms = (237.23, 254.53, 183.02)
> select clear
[Repeated 1 time(s)]
> select add #1/A:1601@C23
1 atom, 1 residue, 1 model selected
> select add #1/A:1601@C19
2 atoms, 1 residue, 1 model selected
> select add #1/A:1601@N08
3 atoms, 1 residue, 1 model selected
> select add #1/A:1601@C24
4 atoms, 1 residue, 1 model selected
> select add #1/A:1601@N09
5 atoms, 1 residue, 1 model selected
> ui mousemode right "mark center"
> marker #2 position 239.3,249.7,177.6 color yellow radius 1
> hide #3 models
> show #3 models
> hide #2 models
> show #2 models
> ui mousemode right "delete markers"
> marker delete #2:2
> ui mousemode right select
> select #2/M:1@M
1 atom, 1 residue, 1 model selected
> select add #3/M:1@M
2 atoms, 2 residues, 2 models selected
> select clear
> select #2/M:1
1 atom, 1 residue, 1 model selected
> ui mousemode right "delete markers"
> distance #2/M:1 #3/M:1
Distance between complex3_body_J266.pdb center 5 atoms #2/M mark 1 M and
complex3_body_J266.pdb center 6 atoms #3/M mark 1 M: 3.673Å
> hide #3 models
> show #3 models
> hide #4.1 models
> hide #!4 models
> show #!4 models
> hide #2 models
> show #2 models
> distance style #2,3/M color grey
> distance style color grey
> distance style #2,3/M color grey70
Invalid "color" argument: Invalid color name or specifier
> color #4 #d3d7cfff models
> color #4 #888a85ff models
> color #4 #babdb6ff models
> color #4 #888a85ff models
> marker change #2/M:1 markers false
> marker change #2/M:1 radius 0.0
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/markers/cmd.py", line 74, in marker_change
m.radius = radius
^^^^^^^^
File "atomic_cpp/cymol.pyx", line 467, in
chimerax.atomic.cymol.CyAtom.radius.__set__
RuntimeError: radius must be positive
RuntimeError: radius must be positive
File "atomic_cpp/cymol.pyx", line 467, in
chimerax.atomic.cymol.CyAtom.radius.__set__
See log for complete Python traceback.
> marker change #2/M:1 radius 0.01
> marker change #2,3/M:1 radius 0.01
> marker change #2,3/M:1 radius 0.001
> ui mousemode right select
> select #1/A:1601@C23
1 atom, 1 residue, 1 model selected
> select add #1/A:1601@C19
2 atoms, 1 residue, 1 model selected
> select add #1/A:1601@N08
3 atoms, 1 residue, 1 model selected
> select add #1/A:1601@C24
4 atoms, 1 residue, 1 model selected
> select add #1/A:1601@N09
5 atoms, 1 residue, 1 model selected
> measure center sel mark true radius 0.3 color cyan modelId 4
Center of mass of 5 atoms = (240.16, 250.14, 177.78)
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 68, in measure_center
place_marker(session, xyz, rgba, r, mname, model_id)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 157, in place_marker
session.models.add([mset])
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 733, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 802, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model complex3_body_J266.pdb center 5 atoms #4 with
the same id as another model distances #4
ValueError: Tried to add model complex3_body_J266.pdb center 5 atoms #4 with
the same id as another model distances #4
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 802, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
See log for complete Python traceback.
> measure center sel mark true radius 0.3 color cyan modelId 5
Center of mass of 5 atoms = (240.16, 250.14, 177.78)
> measure center sel mark true radius 0.3 color cyan modelId 5
Center of mass of 5 atoms = (240.16, 250.14, 177.78)
> distance #2/M:1 #1/K:129@CB
Distance between complex3_body_J266.pdb center 5 atoms #2/M mark 1 M and
complex3_body_J266.pdb #1/K VAL 129 CB: 11.022Å
> hide #!4 models
> show #!4 models
> distance delete #1/K:129@CB
> distance delete #2/M:1 #1/K:129@CB
> distance #5/M:1 #1/K:129@CB
Distance between complex3_body_J266.pdb center 5 atoms #5/M mark 1 M and
complex3_body_J266.pdb #1/K VAL 129 CB: 3.690Å
> select clear
> select #1/A:1-1543
23172 atoms, 25951 bonds, 1 pseudobond, 1078 residues, 2 models selected
> hbonds /A:1601 restrict /A:1-1543 reveal true
4 hydrogen bonds found
> ui mousemode right select
> select clear
> select #1/A:1601@O01
1 atom, 1 residue, 1 model selected
> select #1/A:1601@N08
1 atom, 1 residue, 1 model selected
> select add #1/A:1601@O01
2 atoms, 1 residue, 1 model selected
> distance /A:1601@N08 /A:1601@O01 color yellow radius 0.2 dashes 9
Distance between complex3_body_J266.pdb #1/A GE8 1601 N08 and O01: 2.878Å
> distance /A:1601@N08 /A:1601@O01 color yellow radius 0.1 dashes 9
Distance already exists; modify distance properties with 'distance style'
> distance style /A:1601@N08 /A:1601@O01 color yellow radius 0.1 dashes 9
> distance style color yellow
> distance style /A:1601@N08 /A:1601@O01 color yellow radius 0.1 dashes 6
> distance style dashes 6
> distance /A:1601@CL01 #1/A:796@O2 color yellow radius 0.1 dashes 9
Distance between complex3_body_J266.pdb #1/A GE8 1601 CL01 and C 796 O2:
5.950Å
> distance delete /A:1601@CL01 #1/A:796@O2
> distance /A:1601@CL01 #1/A:796@O2' color yellow radius 0.1 dashes 9
Distance between complex3_body_J266.pdb #1/A GE8 1601 CL01 and C 796 O2':
3.630Å
> select clear
> distance style #5/M:1 #1/K:129@CB color light slate gray
> distance style color lightslategrey
> hide #!4 models
> show #!4 models
> distance delete /A:1601@CL01 #1/A:796@O2'
> pbond /A:1601@CL01 #1/A:796@O2' reveal true color yellow radius 0.1 dashes 6
Unknown command: pbond /A:1601@CL01 #1/A:796@O2' reveal true color yellow
radius 0.1 dashes 6
> pbond /A:1601@CL01 #1/A:796@O2'
Unknown command: pbond /A:1601@CL01 #1/A:796@O2'
> pbond /A:1601@CL01 #1/A:796@O2'
Unknown command: pbond /A:1601@CL01 #1/A:796@O2'
> pbond #2/M:1 #1/K:129@CB
Unknown command: pbond #2/M:1 #1/K:129@CB
> pbond
Unknown command: pbond
> distance
Missing or invalid "objects" argument: empty atom specifier
> pbond
Unknown command: pbond
> pbonds
Unknown command: pbonds
> pbond
Unknown command: pbond
> pbond
Unknown command: pbond
> pbond
Unknown command: pbond
> pbond
Unknown command: pbond
OpenGL version: 3.3.0 NVIDIA 460.84
OpenGL renderer: Quadro K620/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Hewlett-Packard
Model: HP Z440 Workstation
OS: CentOS Stream 8
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz
Cache Size: 10240 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 11Gi 338Mi 496Mi 3.4Gi 3.0Gi
Swap: 7.8Gi 1.4Gi 6.5Gi
Graphics:
02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107GL [Quadro K620] [10de:13bb] (rev a2)
Subsystem: Hewlett-Packard Company Device [103c:1098]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Andreas,
--Eric