pb_scene_coord returning None

[rohou.alexis@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

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  

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/TRPA1_3551_setup.cxc

> cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551

Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551  

> windowsize 1600 1600

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2.pdb
> name model

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2.pdb  
---  
warnings | Ignored bad PDB record found on line 3  
HELIX 1 1 PRO A 449 SER A 455 1 Generated by MOE 7  
  
Ignored bad PDB record found on line 4  
HELIX 2 2 ILE A 459 LEU A 465 1 Generated by MOE 7  
  
Ignored bad PDB record found on line 5  
HELIX 3 3 PRO A 485 ASN A 492 1 Generated by MOE 8  
  
Ignored bad PDB record found on line 6  
HELIX 4 4 ASP A 495 LYS A 504 1 Generated by MOE 10  
  
Ignored bad PDB record found on line 7  
HELIX 5 5 ALA A 517 GLY A 524 1 Generated by MOE 8  
  
148 messages similar to the above omitted  
  
Chain information for model #1  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/ResolveCryoEM_70/denmod_map_resample.mrc
> name map

Opened denmod_map_resample.mrc, grid size 324,324,324, pixel 1, shown at level
0.0393, step 2, values float32  

> open /Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif

Summary of feedback from opening
/Users/rohoua/work/Genentech/TRPA1/TRPA1_3551/6pqq_S448-T1078_ali.cif  
---  
warnings | Unknown polymer entity '1' near line 137  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 6pqq_S448-T1078_ali.cif #3  
---  
Chain | Description  
A B C D | ?  
  

> align #3:803-819,833-847@CA/B:877-891,935-946@CA toAtoms
> #1:803-819,833-847@CA/B:877-891,935-946@CA

RMSD between 155 atom pairs is 0.706 angstroms  

> ~show #3

> set bgColor white

> set silhouettes true

> lighting full

> lighting shadows false

> name ank #1:start-618

> name linker #1:619-701

> name preS1 #1:702-715

> name helixS1 #1:715-739

> name helixS2 #1:768-783

> name helixS3 #1:804-822

> name helixS4 #1:830-853

> name S4S5Linker #1:854-875

> name helixS5 #1:876-891

> name poreH1 #1:901-911

> name poreH2 #1:919-928

> name helixS6 #1:933-967

> name TRPlike #1:972-990

> name betaSheet #1:991-1031

> name coiledCoil #1:1032-end

> name membraneDomain #1:715-967

> color #1,3/A rgb(212,130,97)

> color #1,3/D rgb(137,187,206)

> color #1,3/C rgb(248,238,166)

> color #1,3/B rgb(147,186,128)

> color :LXY gold

> style :LXY ball

Changed 180 atom styles  

> color zone #2 near #1 distance 6.0

> surface dust #2

> ~show (#1 & ~ :LXY)

> volume #2 step 1 level 0.326 color #9999CC

> display #2

> volume #2 symmetry C4

> volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10

> volume #10 step 1 level 0.126 color rgb(255,255,153)

> transparency #10 70 target s

> color :LXY byhetero

> volume gaussian #2 sDev 1.8 modelId 100

> volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20

> close #100

> volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212

> transparency #20 90 target s

executed TRPA1_3551_setup.cxc  

> hide #!3 models

> hide #!10 models

> hide #!20 models

> view /L

> help hbonds

> hbonds reveal true

6198 hydrogen bonds found  
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
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update  
self._update_graphics()  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "changes":  
TypeError: Cannot multiply Place times "None"  
  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  
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
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 185, in _update_graphics_if_needed  
self._update_graphics(gc)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "graphics update":  
TypeError: Cannot multiply Place times "None"  
  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  
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
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update  
self._update_graphics()  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "changes":  
TypeError: Cannot multiply Place times "None"  
  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.17
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.

[Tom Goddard]

Error showing pseudobonds fixed a month ago. Use a ChimeraX daily build. If you need ISOLDE we expect a new ISOLDE version that works with the daily build later this week. If you use the 0.93 version then using the hbonds command which creates pseudobonds may cause this error.