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#2713 closed defect (fixed)

Clashes: "Include intramolecule" option throws error

Reported by:	Elaine Meng	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Structure Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2019-12-24)
Description
trying to use Clashes dialog after unchecking "Include intramolecule" gives traceback

Log:
UCSF ChimeraX version: 0.92 (2019-12-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6bkl

Summary of feedback from opening 6bkl fetched from pdb  
---  
notes | Fetching compressed mmCIF 6bkl from
http://files.rcsb.org/download/6bkl.cif  
Fetching CCD EU7 from http://ligand-expo.rcsb.org/reports/E/EU7/EU7.cif  
Fetching CCD RIM from http://ligand-expo.rcsb.org/reports/R/RIM/RIM.cif  
  
6bkl title:  
Influenza A M2 transmembrane domain bound to rimantadine [more info...]  
  
Chain information for 6bkl #1  
---  
Chain | Description  
A B C D E F G H | Matrix protein 2  
  
Non-standard residues in 6bkl #1  
---  
EU7 — (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine
(S-rimantadine)  
RIM — rimantadine (1-(1-adamantyl)ethanamine)  
  
6bkl mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> sym #1 assembly 2

> view

> show #2 atoms

> style #2 stick

Changed 767 atom styles  

> mlp

Map values for surface "6bkl_A SES surface": minimum -21.78, mean 1.875,
maximum 22.14  
Map values for surface "6bkl_B SES surface": minimum -21.11, mean 2.503,
maximum 22.49  
Map values for surface "6bkl_C SES surface": minimum -21.15, mean 2.547,
maximum 21.52  
Map values for surface "6bkl_D SES surface": minimum -20.92, mean 2.507,
maximum 21.14  
Map values for surface "6bkl_E SES surface": minimum -21.29, mean 1.889,
maximum 21.9  
Map values for surface "6bkl_F SES surface": minimum -21.19, mean 2.543,
maximum 21.97  
Map values for surface "6bkl_G SES surface": minimum -21.61, mean 2.499,
maximum 21.53  
Map values for surface "6bkl_H SES surface": minimum -21.17, mean 2.462,
maximum 21.51  
Map values for surface "6bkl assembly 2_E SES surface": minimum -21.29, mean
1.889, maximum 21.9  
Map values for surface "6bkl assembly 2_F SES surface": minimum -21.19, mean
2.543, maximum 21.97  
Map values for surface "6bkl assembly 2_G SES surface": minimum -21.61, mean
2.499, maximum 21.53  
Map values for surface "6bkl assembly 2_H SES surface": minimum -21.17, mean
2.462, maximum 21.51  

> select #2/E:32@CG2

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 2 models selected  

> select up

180 atoms, 183 bonds, 2 models selected  

> hide sel surfaces

> select #2/F:39@N

1 atom, 1 model selected  

> select #2/F:39@N

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 2 models selected  

> select up

172 atoms, 175 bonds, 2 models selected  

> hide sel surfaces

Expected an objects specifier or a keyword  

> select ligand

78 atoms, 90 bonds, 2 models selected  

> hbonds sel

36 hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 model selected  

> select up

7 atoms, 6 bonds, 2 models selected  

> select up

180 atoms, 183 bonds, 2 models selected  

> select up

188 atoms, 189 bonds, 2 models selected  

> hide sel surfaces

> lighting shadows false

> close #2,3

> show #!1 models

> style stick

Changed 1536 atom styles  

> delete /a-d

> ~surface

> close

> open 6bkl

6bkl title:  
Influenza A M2 transmembrane domain bound to rimantadine [more info...]  
  
Chain information for 6bkl #1  
---  
Chain | Description  
A B C D E F G H | Matrix protein 2  
  
Non-standard residues in 6bkl #1  
---  
EU7 — (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine
(S-rimantadine)  
RIM — rimantadine (1-(1-adamantyl)ethanamine)  
  
6bkl mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> delete /e-h

> style stick

Changed 769 atom styles  

> lighting shadows false

> close

> open 6bkl format mmCIF fromDatabase pdb

6bkl title:  
Influenza A M2 transmembrane domain bound to rimantadine [more info...]  
  
Chain information for 6bkl #1  
---  
Chain | Description  
A B C D E F G H | Matrix protein 2  
  
Non-standard residues in 6bkl #1  
---  
EU7 — (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine
(S-rimantadine)  
RIM — rimantadine (1-(1-adamantyl)ethanamine)  
  
6bkl mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> style stick

Changed 1536 atom styles  

> preset "initial styles" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select ::name="EU7"

26 atoms, 30 bonds, 1 model selected  

> hide protein

> ~select

Nothing selected  

> hide :eu7

> show :eu7

> close

> open 1gta format mmCIF fromDatabase pdb

1gta title:  
Crystal structures of A schistosomal drug and vaccine target: glutathione
S-transferase from schistosoma japonica and its complex with the leading
antischistosomal drug praziquantel [more info...]  
  
Chain information for 1gta #1  
---  
Chain | Description  
A | glutathione S-transferase  
  
1gta mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> close

> open 6nec

Summary of feedback from opening 6nec fetched from pdb  
---  
notes | Fetching compressed mmCIF 6nec from
http://files.rcsb.org/download/6nec.cif  
Fetching CCD XIN from http://ligand-expo.rcsb.org/reports/X/XIN/XIN.cif  
Fetching CCD FMT from http://ligand-expo.rcsb.org/reports/F/FMT/FMT.cif  
  
6nec title:  
Structure of ret protein tyrosine kinase domain In complex with nintedanib
[more info...]  
  
Chain information for 6nec #1  
---  
Chain | Description  
A C | Proto-oncogene tyrosine-protein kinase receptor Ret  
  
Non-standard residues in 6nec #1  
---  
FMT — formic acid  
XIN — methyl
(3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate  
  
6nec mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
  

> sym #1 assembly 1

> view

> sym #1 assembly 2

> view

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> show #!1 models

> close #2,3

> delete /c

> select :xin

40 atoms, 44 bonds, 1 model selected  

Unknown command: start H-Bonds  

> open startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

executed startup.cxc  

> start H-Bonds

> hbonds sel interModel false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6nec
    
    4 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LYS 758 NZ   /A XIN 1101 O26  no hydrogen  2.805  N/A
    /A ALA 807 N    /A XIN 1101 O10  no hydrogen  2.865  N/A
    /A ASP 892 N    /A XIN 1101 O26  no hydrogen  3.073  N/A
    /A XIN 1101 N9  /A GLU 805 O     no hydrogen  2.801  N/A
    

  
4 hydrogen bonds found  

> mlp

Map values for surface "6nec_A SES surface": minimum -27.86, mean -4.635,
maximum 24.27  

> surface hide

> open 6nja

Summary of feedback from opening 6nja fetched from pdb  
---  
notes | Fetching compressed mmCIF 6nja from
http://files.rcsb.org/download/6nja.cif  
Fetching CCD ADE from http://ligand-expo.rcsb.org/reports/A/ADE/ADE.cif  
  
6nja title:  
Structure of WT RET protein tyrosine kinase domain at 1.92A resolution. [more
info...]  
  
Chain information for 6nja #2  
---  
Chain | Description  
A | Proto-oncogene tyrosine-protein kinase receptor Ret  
  
Non-standard residues in 6nja #2  
---  
FMT — formic acid  
  
  

> mmaker #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 6nec, chain A (#1) with 6nja, chain A (#2), sequence alignment
score = 1521.2  
RMSD between 271 pruned atom pairs is 0.396 angstroms; (across all 280 pairs:
1.290)  
  

> show :ade

> hide #!2 models

> hide #!1 models

> show #!2 models

> select :ade

10 atoms, 11 bonds, 1 model selected  

> hbonds sel interModel false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	2 6nja
    
    5 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6nja #2/A ALA 807 N    6nja #2/A ADE 1101 N1  no hydrogen  2.912  N/A
    6nja #2/A ADE 1101 N6  6nja #2/A GLU 805 O    no hydrogen  3.139  N/A
    6nja #2/A ADE 1101 N6  6nja #2/A HOH 1302 O   no hydrogen  3.165  N/A
    6nja #2/A HOH 1302 O   6nja #2/A ADE 1101 N7  no hydrogen  3.429  N/A
    6nja #2/A HOH 1345 O   6nja #2/A ADE 1101 N3  no hydrogen  3.345  N/A
    

  
5 hydrogen bonds found  

> cartoon suppressBackboneDisplay false

> close #2

> open 6ne7

Summary of feedback from opening 6ne7 fetched from pdb  
---  
note | Fetching compressed mmCIF 6ne7 from
http://files.rcsb.org/download/6ne7.cif  
  
6ne7 title:  
Structure of G810A mutant of RET protein tyrosine kinase domain. [more
info...]  
  
Chain information for 6ne7 #2  
---  
Chain | Description  
A | Proto-oncogene tyrosine-protein kinase receptor Ret  
  
Non-standard residues in 6ne7 #2  
---  
AMP — adenosine monophosphate  
FMT — formic acid  
  
  

> mmaker #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 6nec, chain A (#1) with 6ne7, chain A (#2), sequence alignment
score = 1511  
RMSD between 272 pruned atom pairs is 0.362 angstroms; (across all 281 pairs:
1.524)  
  

> show #!1 models

> hide #!1 models

> mlp

Map values for surface "6nec_A SES surface": minimum -27.86, mean -4.635,
maximum 24.27  
Map values for surface "6ne7_A SES surface": minimum -26.8, mean -4.409,
maximum 23.73  

> surface hide

> mmaker #1 to #2 show t

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 6ne7, chain A (#2) with 6nec, chain A (#1), sequence alignment
score = 1511  
Alignment identifier is 1  
RMSD between 272 pruned atom pairs is 0.362 angstroms; (across all 281 pairs:
1.524)  
  
Seqview [ID: 1] region 6ne7, chain A..6nec, chain A [111] RMSD: 0.433  
  

> show #!1 models

> show sel

> cartoon suppressBackboneDisplay false

> select :xin

40 atoms, 44 bonds, 1 model selected  

> hbonds sel intraModel false reveal true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6nec
    	2 6ne7
    
    4 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6nec #1/A XIN 1101 N9  6ne7 #2/A GLU 805 O     no hydrogen  2.927  N/A
    6ne7 #2/A LYS 758 NZ   6nec #1/A XIN 1101 O26  no hydrogen  2.348  N/A
    6ne7 #2/A ALA 807 N    6nec #1/A XIN 1101 O10  no hydrogen  2.847  N/A
    6ne7 #2/A ASP 892 N    6nec #1/A XIN 1101 O26  no hydrogen  3.103  N/A
    

  
4 hydrogen bonds found  

> hbonds sel interModel false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6nec
    
    4 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6nec #1/A LYS 758 NZ   6nec #1/A XIN 1101 O26  no hydrogen  2.805  N/A
    6nec #1/A ALA 807 N    6nec #1/A XIN 1101 O10  no hydrogen  2.865  N/A
    6nec #1/A ASP 892 N    6nec #1/A XIN 1101 O26  no hydrogen  3.073  N/A
    6nec #1/A XIN 1101 N9  6nec #1/A GLU 805 O     no hydrogen  2.801  N/A
    

  
4 hydrogen bonds found  

> close

> open 6bkk

Summary of feedback from opening 6bkk fetched from pdb  
---  
notes | Fetching compressed mmCIF 6bkk from
http://files.rcsb.org/download/6bkk.cif  
Fetching CCD 308 from http://ligand-expo.rcsb.org/reports/3/308/308.cif  
  
6bkk title:  
Influenza A M2 transmembrane domain bound to amantadine [more info...]  
  
Chain information for 6bkk #1  
---  
Chain | Description  
A B C D E F G H | Matrix protein 2  
  
Non-standard residues in 6bkk #1  
---  
308 — (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine (Amantadine)  
ACE — acetyl group  
CL — chloride ion  
  
6bkk mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> delete /e-h

> style stick

Changed 833 atom styles  

> select ligand

11 atoms, 13 bonds, 1 model selected  

> hbonds sel interModel false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6bkk
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /B 308 101 N1  /A HOH 103 O  no hydrogen  3.202  N/A
    

  
1 hydrogen bonds found  

> close

> open 6nec

6nec title:  
Structure of ret protein tyrosine kinase domain In complex with nintedanib
[more info...]  
  
Chain information for 6nec #1  
---  
Chain | Description  
A C | Proto-oncogene tyrosine-protein kinase receptor Ret  
  
Non-standard residues in 6nec #1  
---  
FMT — formic acid  
XIN — methyl
(3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate  
  
6nec mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
Associated 6nec chain A to 6nec, chain A with 0 mismatches  
Associated 6nec chain C to 6nec, chain A with 0 mismatches  
  

> mlp

Map values for surface "6nec_A SES surface": minimum -27.86, mean -4.635,
maximum 24.27  
Map values for surface "6nec_C SES surface": minimum -26.84, mean -4.353,
maximum 22.31  

> delete /c

> select :810

4 atoms, 3 bonds, 1 model selected  

> transparency 50

> show sel

> show :810

> select :810

4 atoms, 3 bonds, 1 model selected  

> label sel

> open 6ne7

6ne7 title:  
Structure of G810A mutant of RET protein tyrosine kinase domain. [more
info...]  
  
Chain information for 6ne7 #2  
---  
Chain | Description  
A | Proto-oncogene tyrosine-protein kinase receptor Ret  
  
Non-standard residues in 6ne7 #2  
---  
AMP — adenosine monophosphate  
FMT — formic acid  
  
Associated 6ne7 chain A to 6ne7, chain A with 0 mismatches  
  

> mmaker #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 6nec, chain A (#1) with 6ne7, chain A (#2), sequence alignment
score = 1511  
RMSD between 272 pruned atom pairs is 0.362 angstroms; (across all 281 pairs:
1.524)  
  

> show :810

> mlp

Map values for surface "6nec_A SES surface": minimum -27.86, mean -4.635,
maximum 24.27  
Map values for surface "6ne7_A SES surface": minimum -26.8, mean -4.409,
maximum 23.73  

> select :xin

40 atoms, 44 bonds, 1 model selected  

> start Clashes

> clashes sel intraMol false

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 22, in cmd_clashes  
return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff,
"clashes", color, radius, **kw)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 127, in _cmd  
intra_mol=intra_mol, res_separation=res_separation, restrict=restrict)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/clashes.py", line 140, in find_clashes  
if not intra_mol and a.molecule.rootForAtom(a,  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Atom' object has no attribute 'molecule'  
  
AttributeError: 'Atom' object has no attribute 'molecule'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> clashes sel

80 clashes  

> hide #1 & protein

> hide surfaces

> ~cartoon #1

> clashes sel intraMol false

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 22, in cmd_clashes  
return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff,
"clashes", color, radius, **kw)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 127, in _cmd  
intra_mol=intra_mol, res_separation=res_separation, restrict=restrict)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/clashes.py", line 140, in find_clashes  
if not intra_mol and a.molecule.rootForAtom(a,  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Atom' object has no attribute 'molecule'  
  
AttributeError: 'Atom' object has no attribute 'molecule'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> start Contacts

> clashes sel intraMol false

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 22, in cmd_clashes  
return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff,
"clashes", color, radius, **kw)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 127, in _cmd  
intra_mol=intra_mol, res_separation=res_separation, restrict=restrict)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/clashes.py", line 140, in find_clashes  
if not intra_mol and a.molecule.rootForAtom(a,  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Atom' object has no attribute 'molecule'  
  
AttributeError: 'Atom' object has no attribute 'molecule'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Change History (3)

in reply to: 1 ; follow-up: 1 comment:1 by Elaine Meng, 6 years ago

Also I find myself wishing for an “intraModel” option to clashes and contacts in the GUIs.  Use case is that I am looking at drug-resistant mutants as possible demo systems for the tutorial, so I superimpose the mutant and the wild-type (which has drug bound), and then I want to find clashes or contacts between the drug in the wild-type structure and the mutant protein only.  I.e I want to turn OFF intramodel.

Currently “hbonds” has “intraModel” but clashes and contacts do not.  Obviously you can specify only the other model in the “restrict” atomspec in the commands, but there is no way to do it in the GUIs.

However, not likely to be available before the class, so file that one as desired.

comment:2 by Eric Pettersen, 6 years ago

Component:	Unassigned → Structure Analysis
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Clashes: "Include intramolecule" option throws error

comment:3 by Eric Pettersen, 6 years ago

Resolution:	→ fixed
Status:	accepted → closed

Fix available in next build.

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