coulombic: KeyError: 'OXT'

[rihsan2@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
couldn't predict the electrosatic surfae charge

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

> open "C:\\\Users\\\amyee\\\OneDrive - University of Illinois -
> Urbana\\\UIUC\\\PhD\\\Lab
> Work\\\2021\\\2_February_2021\\\2_23_2021\\\BioI_3EJB\\\BioI.cxs"

Log from Wed Feb 24 12:28:46 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\amyee\\\OneDrive - University of Illinois -
> Urbana\\\UIUC\\\PhD\\\Lab
> Work\\\2021\\\February_2021\\\2_23_2021\\\BioI_3EJB\\\3ejd.pdb"

3ejd.pdb title:  
Crystal structure of P450BIOI In complex with hexadec-9Z-enoic acid ligated
acyl carrier protein [more info...]  
  
Chain information for 3ejd.pdb #1  
---  
Chain | Description  
A C E G | acyl carrier protein  
B | biotin biosynthesis cytochrome P450-like enzyme  
D | biotin biosynthesis cytochrome P450-like enzyme  
F | biotin biosynthesis cytochrome P450-like enzyme  
H | biotin biosynthesis cytochrome P450-like enzyme  
  
Non-standard residues in 3ejd.pdb #1  
---  
CL — chloride ion  
HEM — protoporphyrin IX containing Fe (HEME)  
HTG — heptyl 1-thio-β-D-glucopyranoside  
ZMQ —
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-β-alanyl}amino)ethyl]
(9Z)-hexadec-9-enethioate  
  

> select /B

3319 atoms, 3168 bonds, 9 pseudobonds, 603 residues, 3 models selected  

> select ~sel

12738 atoms, 12167 bonds, 27 pseudobonds, 2265 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select /B

3319 atoms, 3168 bonds, 9 pseudobonds, 603 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> rainbow sel

> select clear

> select /A

719 atoms, 670 bonds, 134 residues, 1 model selected  

> show sel cartoons

> select ::name="HEM"

172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected  

> show sel atoms

> show sel atoms

> style sel ball

Changed 9 atom styles  

> color sel byelement

> show sel atoms

> style sel ball

Changed 16 atom styles  

> color sel byelement

> show sel atoms

> style sel ball

Changed 6 atom styles  

> color sel byelement

> ui mousemode right select

> select /B:234

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:238

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

> select /B:237

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

> select /B:238

7 atoms, 6 bonds, 1 residue, 1 model selected  
Drag select of 43 atoms, 4 pseudobonds, 46 bonds  

> hide sel atoms

Drag select of 43 atoms, 4 pseudobonds, 46 bonds  

> hide sel atoms

Drag select of 43 atoms, 4 pseudobonds, 46 bonds  

> hide sel atoms

Drag select of 5 residues  

> select clear

> select ::name="HOH"

1010 atoms, 1010 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select ::name="HTG"

76 atoms, 72 bonds, 8 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select ::name="ZMQ"

152 atoms, 148 bonds, 4 residues, 1 model selected  

> show sel atoms

> select /A:56

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 6 atom styles  

> color sel byelement

> save "C:/Users/amyee/OneDrive - University of Illinois - Urbana/UIUC/PhD/Lab
> Work/2021/February_2021/2_23_2021/BioI_3EJB/BioI.cxs"

> lighting full

> lighting simple

> lighting soft

> lighting full

> select /B:238@CB

1 atom, 1 residue, 1 model selected  

> select /B:237

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

> select /B:238

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

> select /B:81

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

> select /B:92

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

> select /B:89

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

> select /B:88

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

> select /B:89

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

> select /B:92

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

> style sel ball

Changed 8 atom styles  

> show sel atoms

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> ui mousemode right pivot

> ui mousemode right select

> select /B:344@CA

1 atom, 1 residue, 1 model selected  

> select /B:344

6 atoms, 5 bonds, 1 residue, 1 model selected  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select /B:81

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

> select /B:80

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

> select /B:82

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

> show sel atoms

> style sel ball

Changed 11 atom styles  

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

Drag select of 38 atoms, 37 bonds  

> hide sel atoms

Drag select of 38 atoms, 37 bonds  

> hide sel atoms

Drag select of 38 atoms, 37 bonds  

> hide sel atoms

> save "C:/Users/amyee/OneDrive - University of Illinois - Urbana/UIUC/PhD/Lab
> Work/2021/February_2021/2_23_2021/BioI_3EJB/BioI.cxs"

> select /A

719 atoms, 670 bonds, 134 residues, 1 model selected  

> select clear

> style sel stick

Changed 8 atom styles  

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> show sel atoms

> style sel stick

Changed 11 atom styles  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> color sel byelement

> select /A:99@C8

1 atom, 1 residue, 1 model selected  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> label sel atoms

> select /A:99@C7

1 atom, 1 residue, 1 model selected  

> label sel atoms

> select /B:405@FE

1 atom, 1 residue, 1 model selected  

> label sel atoms

> select /B:237

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

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select /B:238

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

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select /B:81

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

> select /B:80

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

> select /B:88

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

> select /B:92

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

> select /B:88

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

> select /B:92

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

> select /B:306

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

> show sel atoms

> style sel stick

Changed 12 atom styles  

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select /B:62

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

> select /B:61

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

> select /B:63

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

> select /B:62

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select /B:36

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

> select /B:37

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

> select /B:36

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

> select /B:37

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

> select /B:38

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /B:302

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /B:303

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

> select /B:304

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

> select /B:303

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

> select /B:36

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

> select /B:37

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

> select /B:304

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

> select /B:302

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /B:34

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

> select /B:33

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

> select /B:35

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

> style sel stick

Changed 9 atom styles  

> show sel atoms

> color sel byelement

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> save "C:/Users/amyee/OneDrive - University of Illinois - Urbana/UIUC/PhD/Lab
> Work/2021/February_2021/2_23_2021/BioI_3EJB/BioI.cxs"

> save "C:/Users/amyee/OneDrive - University of Illinois - Urbana/UIUC/PhD/Lab
> Work/2021/February_2021/2_23_2021/BioI_3EJB/BioI.cxs"

opened ChimeraX session  

> select /B

3319 atoms, 3168 bonds, 9 pseudobonds, 603 residues, 3 models selected  

> show sel surfaces

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /B ASP 217 CG, /B ASP 217 OD1, /B ASP 217 OD2, and
/B GLU 394 OXT  

/B GLY 213 OXT  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 313, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 96, in assign_charges  
assign_residue_charges(charged_residues, his_scheme)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
KeyError: 'OXT'  
  
KeyError: 'OXT'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
  
See log for complete Python traceback.  
  

> surface style mesh

> mlp sel

Map values for surface "3ejd.pdb_B SES surface": minimum -28.84, mean -4.198,
maximum 24.5  

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /B ASP 217 CG, /B ASP 217 OD1, /B ASP 217 OD2, and
/B GLU 394 OXT  

/B GLY 213 OXT  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 313, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 96, in assign_charges  
assign_residue_charges(charged_residues, his_scheme)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
KeyError: 'OXT'  
  
KeyError: 'OXT'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 465.89
OpenGL renderer: NVIDIA GeForce RTX 2070 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: Zephyrus S GX531GW_GX531GW
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 17,022,173,184
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz"
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: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1file:///C:/Users/amyee/OneDrive - University of Illinois - Urbana/UIUC/PhD/Lab Work/2021/2_February_2021/2_23_2021/BioI_3EJB/BioI.cxs
    ChimeraX-Arrays: 1.0
    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-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: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 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-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
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
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    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
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    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
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    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
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    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
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    wheel: 0.34.2
    WMI: 1.5.1
File attachment: BioI.cxs

BioI.cxs​

[rihsan2@…]

Added by email2trac

[Eric Pettersen]

Hi Rayeed,

The 'coulombic' command has made significantly more robust since the 1.1 release. If you get the ChimeraX daily build then your coulombic command will work on your structure (I tested it).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab