Context Navigation

← Previous Ticket
Next Ticket →

#5354 closed defect (fixed)

Crystal Contacts: name 'm' is not defined

Reported by:	macbas@…	Owned by:	Tom Goddard
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:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\Maciek\\\Desktop\\\k-turn.cxs

Log from Tue Oct 5 12:34:16 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4cs1

Summary of feedback from opening 4cs1 fetched from pdb  
---  
note | Fetching compressed mmCIF 4cs1 from
http://files.rcsb.org/download/4cs1.cif  
  
4cs1 title:  
Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg bound. [more
info...]  
  
Chain information for 4cs1 #1  
---  
Chain | Description  
A | 5'-(*GP*GP*CP*GP*ap*ap*GP*ap*ap*CP*CP*GP*GP*GP *GP*ap*GP*CP*CP)-3'  
  
Non-standard residues in 4cs1 #1  
---  
MG — magnesium ion  
  
4cs1 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> sym #1 assembly 1

> view

> hide #!2.1 models

> show #!2.1 models

> color #1 green

> color #2.1 green

> color #2.2 red

> delete solvent

> delete mg

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete MG

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete atoms MG

Expected a keyword  

> delete magnesiu

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete magnesium

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete metal

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete ions

> color #!2.1-2 bynucleotide

> nucleotides #!2.1-2 fill

> style nucleic & #!2.1-2 stick

Changed 834 atom styles  

> hbonds

87 hydrogen bonds found  

> select clear

> hbonds

87 hydrogen bonds found  

> select clear

> select clear

> !hbonds

Unknown command: !hbonds  

> ~hbonds

> select up

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show #!1 models

> hide #!2 models

> hide #!2.2 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2 models

> hide #!1 models

> select #2.1

417 atoms, 468 bonds, 19 residues, 1 model selected  

> select #2

834 atoms, 936 bonds, 38 residues, 3 models selected  

> ~select #2

Nothing selected  

> show #!2 models

> select #2.1/A:6

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #2.1/A:5

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select clear

> select #2.1/A:4

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #2.1/A:5

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add #2.1/A:6

67 atoms, 73 bonds, 3 residues, 1 model selected  

> color sel blue

> select clear

> hbonds

87 hydrogen bonds found  

> contacts

5823 contacts  

> ~contacts

> color @@color=blue purple

> select #2.1/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2.1/A:2

43 atoms, 46 bonds, 2 residues, 1 model selected  

> color sel yellow

> select clear

> select #2.1/A:7

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2.1/A:8

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #2.1/A:7

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color sel green

> select clear

> ui tool show H-Bonds

> hbonds reveal true

87 hydrogen bonds found  

> hbonds reveal true

87 hydrogen bonds found  

> hbonds reveal true

87 hydrogen bonds found  

> hbonds reveal true

87 hydrogen bonds found  

> hbonds dashes 6 reveal true retainCurrent true

87 hydrogen bonds found  

> hbonds twoColors true reveal true

87 hydrogen bonds found  
59 strict hydrogen bonds found  

> select #2.1/A:11

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hbonds twoColors true reveal true

87 hydrogen bonds found  
59 strict hydrogen bonds found  

> hbonds twoColors true reveal true

87 hydrogen bonds found  
59 strict hydrogen bonds found  

> hbonds twoColors true reveal true

87 hydrogen bonds found  
59 strict hydrogen bonds found  

> show #!2.2 models

> hide #!2 models

> hide #1.1 models

> show #1.1 models

> show #!2 models

> hide #!1 models

> hide #1.1 models

> hide #3 models

> show #3 models

> hide #3 models

> save C:/Users/Maciek/Desktop/k-turn.cxs

——— End of log from Tue Oct 5 12:34:16 2021 ———

opened ChimeraX session  

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!2.1 models

> show #!2.2 models

> select #2.1/A:4

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2.1/A:5

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #2.1/A:6

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select add #2.1/A:4

67 atoms, 73 bonds, 3 residues, 1 model selected  

> show sel atms

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show atoms sel

Expected ',' or a keyword  

> color sel cpk

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> select #2.1/A:3

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2.1/A:2

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #2.1/A:4

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #2.1/A:5

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select add #2.1/A:6

110 atoms, 119 bonds, 5 residues, 1 model selected  

> select add #2.1/A:7

133 atoms, 144 bonds, 6 residues, 1 model selected  

> select add #2.1/A:8

155 atoms, 168 bonds, 7 residues, 1 model selected  

> select add #2.1/A:9

177 atoms, 192 bonds, 8 residues, 1 model selected  

> color ~sel grey

> select clear

> select clear

> select #2.1/A:7

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2.2/A:16

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 210 atoms, 15 residues, 235 bonds, 39 shapes  

> hide ~sel

> hide ~sel cartoons

> select clear

> save C:/Users/Maciek/Desktop/k-turn.cxs

> tool show si

> contacts

5823 contacts  

> hbonds

87 hydrogen bonds found  

> ~contacts

> crystalcontacts

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalcmd.py", line 59, in crystalcontacts  
show_crystal_contacts(m, distance,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
NameError: name 'm' is not defined  
  
NameError: name 'm' is not defined  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
  
See log for complete Python traceback.  
  

> crystalcontacts

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalcmd.py", line 59, in crystalcontacts  
show_crystal_contacts(m, distance,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
NameError: name 'm' is not defined  
  
NameError: name 'm' is not defined  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
  
See log for complete Python traceback.  
  

> ui tool show "Crystal Contacts"

> crystalcontacts #2.1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalgui.py", line 130, in _show_contacts  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalcmd.py", line 59, in crystalcontacts  
show_crystal_contacts(m, distance,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
NameError: name 'm' is not defined  
  
NameError: name 'm' is not defined  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
  
See log for complete Python traceback.  
  

> crystalcontacts #2.2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalgui.py", line 130, in _show_contacts  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalcmd.py", line 59, in crystalcontacts  
show_crystal_contacts(m, distance,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
NameError: name 'm' is not defined  
  
NameError: name 'm' is not defined  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
  
See log for complete Python traceback.  
  

> crystalcontacts #2.2 distance 5

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalgui.py", line 130, in _show_contacts  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalcmd.py", line 59, in crystalcontacts  
show_crystal_contacts(m, distance,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
NameError: name 'm' is not defined  
  
NameError: name 'm' is not defined  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
  
See log for complete Python traceback.  
  

> crystalcontacts #2.2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalgui.py", line 130, in _show_contacts  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystalcmd.py", line 59, in crystalcontacts  
show_crystal_contacts(m, distance,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
NameError: name 'm' is not defined  
  
NameError: name 'm' is not defined  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\crystal_contacts\crystal.py", line 36, in
show_crystal_contacts  
raise UserError('No unit cell parameters for %s' % m.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 8,361,283,584
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
OSLanguage: pl-PL
Locale: ('pl_PL', 'cp1250')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    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: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    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: 2.0.1
    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-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Structure Analysis
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crystal Contacts: name 'm' is not defined

comment:2 by Tom Goddard, 4 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

The crystalcontacts command was trying to report that "No unit cell parameters available for <molecule-name>" but there was a typo in the error message variable to get the molecule name.

Since you are looking at a structure 4cs1 from the PDB the unit cell parameters should be available. But apparently there is another bug in ChimeraX where it did not save those unit cell parameters in the session file. So to get crystal contacts to work right now you need to use "open 4cs1" instead of opening it from a ChimeraX session file. I've reported the session file bug as #5358 (https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5358).

Note: See TracTickets for help on using tickets.

Download in other formats: