id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3148 pb_scene_coord returning None rohou.alexis@… Tom Goddard "{{{ 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. }}} " defect closed normal Graphics duplicate all ChimeraX