openmm/swig: type object 'object' has no attribute '__getattr__'

[iche4489@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-10-10)
Description
(Describe the actions that caused this problem to occur here)
Clicked start on ISOLDE

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-10-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/zdvs1995/Documents/Cryo-
EM/Data_processing/CtffindClass6_419/ISOLDE_Class6_1.cif format mmCIF

Summary of feedback from opening /Users/zdvs1995/Documents/Cryo-
EM/Data_processing/CtffindClass6_419/ISOLDE_Class6_1.cif  
---  
warnings | Unknown polymer entity '1' near line 110  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for ISOLDE_Class6_1.cif #1  
---  
Chain | Description  
A | ?  
  

> open /Users/zdvs1995/Documents/Cryo-
EM/Data_processing/CtffindClass6_419/Autosharpen_3/sharpened_map.ccp4

Opened sharpened_map.ccp4, grid size 256,256,256, pixel 0.986, shown at level
0.0746, step 1, values float32  

> clipper associate #2 toModel #1

Chain information for ISOLDE_Class6_1.cif  
---  
Chain | Description  
1.1/A | ?  
  

> select up

Nothing selected  

> isolde tutorial

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to ISOLDE_Class6_1.cif #1.1  
---  
notes | No usable SEQRES records for ISOLDE_Class6_1.cif (#1.1) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A LYS 6  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 416  
286 hydrogen bonds  
/A GLU 416 is not terminus, removing H atom from 'C'  
3252 hydrogens added  
  

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

> hide HC

QWidget::repaint: Recursive repaint detected  

> select #1

6294 atoms, 6347 bonds, 12 models selected  
Traceback (most recent call last):  
File "/Users/zdvs1995/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2676, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/zdvs1995/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "/Users/zdvs1995/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "/Users/zdvs1995/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "/Users/zdvs1995/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1500, in
_prepare_sim  
self.initialize_implicit_solvent(params)  
File "/Users/zdvs1995/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 2741, in
initialize_implicit_solvent  
gbforce.addParticles(params)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 9186, in <lambda>  
__getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 74, in _swig_getattr  
return _swig_getattr_nondynamic(self, class_type, name, 0)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 69, in _swig_getattr_nondynamic  
return object.__getattr__(self, name)  
AttributeError: type object 'object' has no attribute '__getattr__'  
  
AttributeError: type object 'object' has no attribute '__getattr__'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 69, in _swig_getattr_nondynamic  
return object.__getattr__(self, name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

[Tristan Croll]

Updating your ChimeraX installation to the 0.91 *release* build (Dec 23 - yours is Oct 10) or later should fix this. There was an update to OpenMM between the version you have and the release.

[pett]

Reported by Ichia Chen

[Tristan Croll]

Bug is fixed in more recent builds. Just for reference: the traceback here is somewhat misleading - it's due to SWIG bending over backwards to search for a method that isn't in one of its wrapped classes, and getting it wrong (due to using a deprecated part of the Python API). The real error is that ISOLDE's code is calling a method (gbforce.addParticles(params)) that didn't yet exist in the version of OpenMM you were using.