Opened 4 years ago

Closed 4 years ago

#4848 closed defect (duplicate)

AddH: name 'chain' is not defined

Reported by: jamess.davies@… Owned by: Eric Pettersen
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:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202106180200 (2021-06-18 02:00:22 UTC)
Description
Computing electrostatic surface when chains of model are "exploded" in interface gui. Thanks..

Log:
UCSF ChimeraX version: 1.3.dev202106180200 (2021-06-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/dobsongroup/Desktop/JD2/Figure1_PpSiaQM_JD/Interface/Master-
> session.cxs format session

Log from Thu Jul 1 10:59:21 2021UCSF ChimeraX version: 1.3.dev202106180200
(2021-06-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/dobsongroup/Desktop/JD2/Figure1_PpSiaQM_JD/Interface/Interface-
> session-coloured.cxs format session

Log from Thu Jul 1 09:17:09 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/dobsongroup/Desktop/PpSiaQM_EM/PpSiaQM_TopModel_2406.pdb

Chain information for PpSiaQM_TopModel_2406.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> set bgColor white

> lighting simple

> lighting soft

> lighting simple

> style ball

Changed 4473 atom styles  

> style sphere

Changed 4473 atom styles  

> style ball

Changed 4473 atom styles  

> show atoms

> hide cartoons

> hide atoms

> show atoms

> style sphere

Changed 4473 atom styles  

> color byhetero

> color bychain

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /A ILE 154 OXT  

> save /Users/dobsongroup/Desktop/JD2/Figure1_PpSiaQM_JD/Interface/Interface-
> session.cxs

> hide atoms

> set bgColor white

> show cartoons

> transparency surface 0.5

Missing or invalid "percent" argument: Expected a number  

> transparency surface 50%

Missing or invalid "percent" argument: Expected a number  

> transparency surface 0.5 a

Missing or invalid "percent" argument: Expected a number  

> transparency surface 50 a

Missing or invalid "percent" argument: Expected a number  

> transparency a 50 surface

Missing or invalid "percent" argument: Expected a number  

> transparency 50 surfaces

> open /Users/dobsongroup/Downloads/PpSiaQM_TopModel_2406out.pdb

Summary of feedback from opening
/Users/dobsongroup/Downloads/PpSiaQM_TopModel_2406out.pdb  
---  
warnings | Duplicate atom serial number found: 1575  
Duplicate atom serial number found: 1575  
Duplicate atom serial number found: 1576  
Duplicate atom serial number found: 1576  
Duplicate atom serial number found: 1577  
2546 messages similar to the above omitted  
  
Chain information for PpSiaQM_TopModel_2406out.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> 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 PpSiaQM_TopModel_2406.pdb, chain B (#1) with
PpSiaQM_TopModel_2406out.pdb, chain B (#2), sequence alignment score = 2183  
RMSD between 427 pruned atom pairs is 0.000 angstroms; (across all 427 pairs:
0.000)  
  

> hide #!1 models

> show #2 atoms

> select #2/A

1265 atoms, 1298 bonds, 154 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #2/B

3208 atoms, 3278 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #!1 models

> rainbow sel

> rainbow sel

> hide sel surfaces

> hide sel surfaces

> hide sel surfaces

> hide sel surfaces

> select #2

7115 atoms, 4576 bonds, 1902 residues, 1 model selected  

> select #1

4473 atoms, 4576 bonds, 581 residues, 1 model selected  

> select #2

7115 atoms, 4576 bonds, 1902 residues, 1 model selected  

> ~select #2

Nothing selected  

> select #1

4473 atoms, 4576 bonds, 581 residues, 1 model selected  

> hide sel surfaces

> rainbow sel

> show sel surfaces

> coulombic sel

Alignment identifier is 1/A  
Alignment identifier is 1/B  

> interfaces sel & ~solvent

1 buried areas: B A 2427  

> hide sel surfaces

> select helix

6570 atoms, 6644 bonds, 852 residues, 2 models selected  

> color (#!1 & sel) #6bac3fff

> color (#!1 & sel) #6bac3fff

> color (#!1 & sel) #7a7a2bff

> color (#!1 & sel) #4cb96aff

> color (#!1 & sel) #3abf9cff

> color (#!1 & sel) #346622ff

> color (#!1 & sel) #412b84ff

> color (#!1 & sel) #5c5cd6ff

> color (#!1 & sel) #d15d90ff

> color (#!1 & sel) #b45e1cff

> color (#!1 & sel) #b45e1cff

> color (#!1 & sel) #b45e1cff

> color (#!1 & sel) #b45e1cff

> color (#!1 & sel) #b45e1cff

> color (#!1 & sel) #3abf9cff

> color (#!1 & sel) #3abf9cff

> color (#!1 & sel) #4e78cdff

> select clear

> color (#!1 & sel) #5c5cd6ff

> color (#!1 & sel) #3abf9cff

> color (#!1 & sel) #4cb96aff

> select clear

> color (#!1 & sel) #c12d7aff

> color (#!1 & sel) #c89939ff

Empty filename passed to function  

> save /Users/dobsongroup/Desktop/JD2/Figure1_PpSiaQM_JD/Interface/Interface-
> session-coloured.cxs

——— End of log from Thu Jul 1 09:17:09 2021 ———

opened ChimeraX session  

> interfaces sel & ~solvent

0 buried areas:  

> close #2

> close #1

> open /Users/dobsongroup/Downloads/PpSiaQM_TopModel_2406out.pdb format pdb

Summary of feedback from opening
/Users/dobsongroup/Downloads/PpSiaQM_TopModel_2406out.pdb  
---  
warnings | Duplicate atom serial number found: 1575  
Duplicate atom serial number found: 1575  
Duplicate atom serial number found: 1576  
Duplicate atom serial number found: 1576  
Duplicate atom serial number found: 1577  
2546 messages similar to the above omitted  
  
Chain information for PpSiaQM_TopModel_2406out.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close

> open /Users/dobsongroup/Downloads/PpSiaQM_TopModel_2406out.pdb

Summary of feedback from opening
/Users/dobsongroup/Downloads/PpSiaQM_TopModel_2406out.pdb  
---  
warnings | Duplicate atom serial number found: 1575  
Duplicate atom serial number found: 1575  
Duplicate atom serial number found: 1576  
Duplicate atom serial number found: 1576  
Duplicate atom serial number found: 1577  
2546 messages similar to the above omitted  
  
Chain information for PpSiaQM_TopModel_2406out.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> show atoms

> select /A

1265 atoms, 1298 bonds, 154 residues, 1 model selected  

> select /B

3208 atoms, 3278 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select /A

1265 atoms, 1298 bonds, 154 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> open /Users/dobsongroup/Desktop/PpSiaQM_EM/PpSiaQM_TopModel_2406.pdb

Chain information for PpSiaQM_TopModel_2406.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /Users/dobsongroup/Desktop/PpSiaQM_EM/PpSiaQM_TopModel_2406.pdb

Chain information for PpSiaQM_TopModel_2406.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #1 to #2

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 PpSiaQM_TopModel_2406.pdb, chain B (#2) with
PpSiaQM_TopModel_2406out.pdb, chain B (#1), sequence alignment score = 2183  
RMSD between 427 pruned atom pairs is 0.000 angstroms; (across all 427 pairs:
0.000)  
  

> matchmaker #1 to #3

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 PpSiaQM_TopModel_2406.pdb, chain B (#3) with
PpSiaQM_TopModel_2406out.pdb, chain B (#1), sequence alignment score = 2183  
RMSD between 427 pruned atom pairs is 0.000 angstroms; (across all 427 pairs:
0.000)  
  

> select #2

4473 atoms, 4576 bonds, 581 residues, 1 model selected  

> select #3

4473 atoms, 4576 bonds, 581 residues, 1 model selected  

> select #1

7115 atoms, 4576 bonds, 1902 residues, 1 model selected  

> select #2

4473 atoms, 4576 bonds, 581 residues, 1 model selected  

> select #3

4473 atoms, 4576 bonds, 581 residues, 1 model selected  

> view orient

> save /Users/dobsongroup/Desktop/JD2/Figure1_PpSiaQM_JD/Interface/Master-
> session.cxs

——— End of log from Thu Jul 1 10:59:21 2021 ———

opened ChimeraX session  

> coulombic sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1287, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run  
f(s)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2854, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/coulombic.py", line 79, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 168, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, template, **prot_schemes)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 423, in _prep_add  
real_N, real_C, fake_N, fake_C, fake_5p = determine_termini(session,
structures)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/util.py", line 73, in determine_termini  
rn, rc, fn, fc, f5p = guess_termini(chain)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/util.py", line 140, in guess_termini  
if chain.polymer_type == Residue.PT_AMINO:  
NameError: name 'chain' is not defined  
  
NameError: name 'chain' is not defined  
  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/util.py", line 140, in guess_termini  
if chain.polymer_type == Residue.PT_AMINO:  
  
See log for complete Python traceback.  
  

> interfaces sel & ~solvent

1 buried areas: B A 2427  

> hide #1 models

> hide #2 models

> color sel gray

> lighting simple

> lighting soft

> select clear

[Repeated 3 time(s)]

> show sel atoms

> color sel byhetero

Drag select of 2 atoms, 2 residues, 1 bonds  

> select #3/B:237@CD

1 atom, 1 residue, 1 model selected  

> select clear

> select #3/B:329@CD

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 2 time(s)]Drag select of 2 residues  

> select clear

Drag select of 2 residues  

> select clear

> select #3/B:281@SD

1 atom, 1 residue, 1 model selected  

> distance

Missing or invalid "objects" argument: empty atom specifier  

> select add #3/B:281@SD

1 atom, 1 bond, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts

191355 contacts  

> undo

> ui tool show Contacts

> hide #4 models

> show #4 models

> hide #3 models

> show #3 models

> close #4

Drag select of 3 residues  

> select #3/A:99

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

> select clear

[Repeated 2 time(s)]

> ui dockable false "Chain Contacts"

> ui dockable true "Chain Contacts"

> select #3/A

1265 atoms, 1298 bonds, 154 residues, 1 model selected  

> color sel #7cb750ff

> select #3/B

3208 atoms, 3278 bonds, 427 residues, 1 model selected  

> color sel #544096ff

> color sel byhetero

> style sel stick

Changed 348 atom styles  

> ui tool show Distances

> select clear

> select add #3/B:281@SD

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #3/A:100@SD

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

> select clear

> select #3/A:100@SD

1 atom, 1 residue, 1 model selected  

> select #3/B:281@SD

1 atom, 1 residue, 1 model selected  

> select add #3/A:100@SD

2 atoms, 2 residues, 1 model selected  

> distance #3/B:281@SD #3/A:100@SD

Distance between PpSiaQM_TopModel_2406.pdb #3/B MET 281 SD and /A MET 100 SD:
5.159Å  

> select clear

> select #3/B:45@SD

1 atom, 1 residue, 1 model selected  

> select add #3/A:100@SD

2 atoms, 2 residues, 1 model selected  

> distance #3/B:45@SD #3/A:100@SD

Distance between PpSiaQM_TopModel_2406.pdb #3/B MET 45 SD and /A MET 100 SD:
4.403Å  

> select clear

Drag select of 13 atoms  

> select #3/B:20@CE1

1 atom, 1 residue, 1 model selected  

> select #3/A:100@SD

1 atom, 1 residue, 1 model selected  

> select add #3/B:20@CE1

2 atoms, 2 residues, 1 model selected  

> distance #3/A:100@SD #3/B:20@CE1

Distance between PpSiaQM_TopModel_2406.pdb #3/A MET 100 SD and /B PHE 20 CE1:
5.442Å  

> select add #3/B:23@CD1

3 atoms, 3 residues, 1 model selected  

> select subtract #3/A:100@SD

2 atoms, 2 residues, 1 model selected  

> distance #3/B:20@CE1 #3/B:23@CD1

Distance between PpSiaQM_TopModel_2406.pdb #3/B PHE 20 CE1 and ILE 23 CD1:
5.450Å  

> select add #3/A:100@SD

3 atoms, 3 residues, 1 model selected  

> select subtract #3/B:23@CD1

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 348 atom styles  

> select clear

> hide #3 atoms

> show #3 cartoons

> style sel sphere

Changed 348 atom styles  

> style sel sphere

Changed 348 atom styles  

> show sel atoms

> color sel bychain

> color sel byhetero

> style sel sphere

Changed 389 atom styles  

> show sel atoms

Must select one or more distances in the table  
[Repeated 1 time(s)]

> ~distance #3/A:100@SD #3/B:20@CE1

> ~distance #3/B:20@CE1 #3/B:23@CD1

> ~distance #3/B:45@SD #3/A:100@SD

> ~distance #3/B:281@SD #3/A:100@SD

> color sel bychain

> color sel byhetero

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.99518,-0.092729,0.031821,6.089,0.089319,0.9914,0.095623,-19.8,-0.040415,-0.09232,0.99491,14.143

> view matrix models
> #3,0.99969,-0.023463,0.0087329,1.3662,0.023595,0.9996,-0.015422,-0.58207,-0.0083676,0.015623,0.99984,-0.68654

> select clear

Drag select of 1 atoms  

> hide #3 models

> show #3 models

> show #2 models

> hide #2 models

> show #2 models

> select #2/A

1265 atoms, 1298 bonds, 154 residues, 1 model selected  

> select #1/B

3208 atoms, 3278 bonds, 427 residues, 1 model selected  

> select #2/B

3208 atoms, 3278 bonds, 427 residues, 1 model selected  

> hide target m

> show #3 models

> show #2 models

> hide sel cartoons

> select #2/B

3208 atoms, 3278 bonds, 427 residues, 1 model selected  

> select #2/A

1265 atoms, 1298 bonds, 154 residues, 1 model selected  

> color sel #7cb750ff

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> color sel #608ed6ff

> hide #2 models

> show sel cartoons

> color sel byhetero

> save /Users/dobsongroup/Desktop/JD2/Figure1_PpSiaQM_JD/Interface/Interface-
> coloured-sandwich.cxs

> select clear

> style sel sphere

Changed 737 atom styles  

> select clear

> color sel #b0b737ff

> undo

> select clear

> color sel #b0b737ff

[Repeated 2 time(s)]

> color sel byhetero

> color sel #cc7fd1ff

> color sel #db75a1ff

> color sel byhetero

[Repeated 1 time(s)]

> select clear

> style sel stick

Changed 348 atom styles  

> select clear

> turn #3A y 45

Expected an axis vector or a keyword  

> turn y #3A 45

Expected a number or a keyword  

> turn y #3A 45

Expected a number or a keyword  

> turn y 45 #3a

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 45 #3

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 45

[Repeated 7 time(s)]Drag select of 221 atoms, 154 residues, 186 bonds  

> turn selection y 45

Expected an axis vector or a keyword  

> turn y 45 selected

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 45

[Repeated 7 time(s)]

> turn y 45, sel

Expected a number or a keyword  

> view matrix models
> #3,0.92902,-0.3285,0.17034,20.255,0.36958,0.84663,-0.38292,22.621,-0.018424,0.41869,0.90794,-29.369

> view matrix models
> #3,0.99115,-0.12964,0.028627,10.603,0.11489,0.94562,0.30432,-42.8,-0.066522,-0.29834,0.95214,42.769

> select #3/B

3208 atoms, 3278 bonds, 427 residues, 1 model selected  

> color sel #7075deff

> color sel #7cb750ff

> color sel #544096ff

> color sel #543f96ff

> color sel #5e448cff

> color sel #543f96ff

> color sel #7c516dff

> color sel #724d77ff

> color sel #684881ff

> color sel #5e448cff

> color sel #543f96ff

> color sel #544096ff

> color sel #7075deff

> color sel #608ed6ff

> color sel #544096ff

> color sel #5440968c

> color sel #5440968d

> color sel #5440968f

[Repeated 1 time(s)]

> color sel #54409690

> color sel #54409693

> color sel #544096a6

> color sel #544096d3

> color sel #544096fa

> color sel #544096fb

> color sel #544096ff

> color sel #005493ff

> color sel #009193ff

> color sel #009051ff

> color sel #008f00ff

> color sel #4f8f00ff

> color sel #7cb750ff

> color sel #544096ff

> color sel #db75a1ff

> color sel byhetero

> style sel sphere

Changed 389 atom styles  

> style sel sphere

Changed 389 atom styles  

> style sel sphere

Changed 348 atom styles  

> color sel #7075deff

> color sel #608ed6ff

> color sel byhetero

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel atoms

> show sel surfaces

> hide sel atoms

> coulombic sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1287, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run  
f(s)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2854, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/coulombic.py", line 79, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 168, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, template, **prot_schemes)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 423, in _prep_add  
real_N, real_C, fake_N, fake_C, fake_5p = determine_termini(session,
structures)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/util.py", line 73, in determine_termini  
rn, rc, fn, fc, f5p = guess_termini(chain)  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/util.py", line 140, in guess_termini  
if chain.polymer_type == Residue.PT_AMINO:  
NameError: name 'chain' is not defined  
  
NameError: name 'chain' is not defined  
  
File
"/Applications/ChimeraX-1.3-daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/util.py", line 140, in guess_termini  
if chain.polymer_type == Residue.PT_AMINO:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.21
OpenGL renderer: AMD Radeon HD - FirePro D500 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: Mac Pro
      Model Identifier: MacPro6,1
      Processor Name: 6-Core Intel Xeon E5
      Processor Speed: 3.5 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: MP61.0123.B00
      SMC Version (system): 2.20f18
      Panel Illumination Version: 1.4a6

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1217)
      Kernel Version: Darwin 19.6.0
      Time since boot: 14 days 17:21

Graphics/Displays:

    AMD FirePro D500:

      Chipset Model: AMD FirePro D500
      Type: GPU
      Bus: PCIe
      Slot: Slot-1
      PCIe Lane Width: x16
      VRAM (Total): 3 GB
      Vendor: AMD (0x1002)
      Device ID: 0x679e
      Revision ID: 0x0000
      ROM Revision: 113-C3861J-687
      VBIOS Version: 113-C3861LA-029
      EFI Driver Version: 01.0D.687
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.11 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Connection Type: No Display Connected

    AMD FirePro D500:

      Chipset Model: AMD FirePro D500
      Type: GPU
      Bus: PCIe
      Slot: Slot-2
      PCIe Lane Width: x16
      VRAM (Total): 3 GB
      Vendor: AMD (0x1002)
      Device ID: 0x679e
      Revision ID: 0x0000
      ROM Revision: 113-C3861J-687
      VBIOS Version: 113-C3861LB-029
      EFI Driver Version: 01.0D.687
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.11 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        LED Cinema Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2A0512Y86JL 
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort
        HP E243:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: CNK018145X  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.7
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.23
    ChimeraX-AtomicLibrary: 3.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202106180200
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.3
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.6
    ChimeraX-PDB: 2.4.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.10
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.6.7.dev1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.5
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddH: name 'chain' is not defined

comment:2 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Jim,

Thanks for reporting this problem. It was fixed roughly a week ago, so slightly after the version you're currently using. If you update to the latest daily build then things should work. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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