ChimeraX bug report submission

[eferri@…]

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
I am attempting to use ISOLDE on a large (8000 atoms) model and crystallographic data using a MacBook Pro. The interface says "simulation is running" but nothing moves. I tried to stop the simulation. I get this error.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open2 "/Users/elenaferri/Box/Antibody Research - Structural
> Biology/Structures/CoV2/RBD_S304_S309 Complex/almost_final.pdb"

Summary of feedback from opening <_io.textiowrapper
name="/Users/elenaferri/Box/Antibody Research - Structural
Biology/Structures/CoV2/RBD_S304_S309 Complex/almost_final.pdb" mode="rt"
encoding="utf-8">  
---  
warning | Ignored bad PDB record found on line 206  
LINKR ND2 ASN R 343 C1 NAG R 601 NAG-ASN  
  
almost_final.pdb title:  
\--- [more info...]  
  
Chain information for almost_final.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in almost_final.pdb #1  
---  
NAG — (NAG)  
  
almost_final.pdb title:  
\--- [more info...]  
  
Chain information for almost_final.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in almost_final.pdb #1.2  
---  
NAG — (NAG)  
  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> volume #!1.1.1.2-4 style surface

> transparency #1.1.1.2.1#1.1.1.3.1-2#1.1.1.4.1 0

> transparency #1.1.1.2.1#1.1.1.3.1-2#1.1.1.4.1 50

> volume #!1.1.1.2-4 showOutlineBox true

> volume #!1.1.1.2-4 showOutlineBox false

> addh

Summary of feedback from adding hydrogens to almost_final.pdb #1.2  
---  
notes | No usable SEQRES records for almost_final.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain H; guessing termini
instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain L; guessing termini
instead  
No usable SEQRES records for almost_final.pdb (#1.2) chain R; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLN 1, /B GLU 1, /H VAL
2, /L ASP 1, /R PRO 330  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 229, /B GLU 213, /H LYS
221, /L GLU 214, /R LYS 528  
Chain-final residues that are not actual C termini:  
980 hydrogen bonds  
7962 hydrogens added  
  

> hide HC

> select #1.2

16185 atoms, 16396 bonds, 5 models selected  

No template found for residue R601 (NAG)  

Excluding residue  
Updating bulk solvent parameters...  
Updating bulk solvent parameters...  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/elenaferri/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/delayed_reaction.py", line 64, in callback  
if self.tf is None or self.tf():  
File "/Users/elenaferri/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 241, in
thread_finished  
return f(self._c_pointer)  
AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'  
  
Error processing trigger "new frame":  
AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'  
  
File "/Users/elenaferri/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 241, in
thread_finished  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro Vega 16 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.