crystalcontacts traceback on 1g74 schematic

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202103070148 (2021-03-07 01:48:03 UTC)
Description
open 1g74
crystalcontacts #1 copies false schematic true

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> 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

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

executed startup.cxc  
UCSF ChimeraX version: 1.2.dev202103070148 (2021-03-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1g74 format mmcif fromDatabase pdb

1g74 title:  
Toward changing specificity: adipocyte lipid binding protein mutant, oleic
acid bound form [more info...]  
  
Chain information for 1g74 #1  
---  
Chain | Description  
A | adipocyte lipid-binding protein  
  
Non-standard residues in 1g74 #1  
---  
OLA — oleic acid  
PO4 — phosphate ion  
  

> ui tool show "Crystal Contacts"

> crystalcontacts #1 copies false schematic true

10 pairs of asymmetric units of 1g74 contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
      1160     0      0      0  0  0      0         1
        12     0      3     -1  0 -1      0         1
        12     0      3     -1 -1 -1      0         1
        11     0      0      0  0 -1      0         1
        10     0      0      0  1  0      0         1
        10     0      0      0  0  1      0         1
         9     0      3     -1  0  0      0         1
         9     0      3     -1 -1  0      0         1
         9     0      0      0 -1  0      0         1
         6     0      1     -1  0  0      0         1
    

  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/crystal_contacts/crystalgui.py", line 130, in _show_contacts  
run(self.session, cmd)  
File
"/Users/meng/Desktop/ChimeraX_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
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/crystal_contacts/crystalcmd.py", line 59, in crystalcontacts  
show_crystal_contacts(m, distance,  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/crystal_contacts/crystal.py", line 58, in
show_crystal_contacts  
marker_set = contact_marker_model(molecule, crystal, clist, asu_list)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/crystal_contacts/crystal.py", line 171, in
contact_marker_model  
links = create_clash_links(clist, n, link_radius, link_rgba, markers)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/crystal_contacts/crystal.py", line 225, in
create_clash_links  
m1 = markers[(a1.ncs_index, a1.smtry_index, a1.unit_cell_index)]  
KeyError: (0, None, (0, 0, 0))  
  
KeyError: (0, None, (0, 0, 0))  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/crystal_contacts/crystal.py", line 225, in
create_clash_links  
m1 = markers[(a1.ncs_index, a1.smtry_index, a1.unit_cell_index)]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.12
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 426.0.0.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H524)
      Kernel Version: Darwin 19.6.0
      Time since boot: 7:20

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[Elaine Meng]

works fine showing atomic copies, must be something about the schematic

[Tom Goddard]

Fixed.

Crystal symmetries changed the identity symmetry to have small non-zero 1e-16 components so it was not treated as the identity leading to this error. Fixed the coordinate system transform to preserve identity matrix.

Then 1g74 mmcif unit cell is still not right, 2 of the 4 copies exactly overlap each other. In PDB format it works correctly. Looking into that problem.

[Tom Goddard]

Fixed 1g74 wrong unit cell - was caused by a mistake in the fix I made for this bug, used tested is_identity instead of is_identity().