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#3119 closed defect (duplicate)

pseudobond's atoms pb_scene_coord is None(?)

Reported by:	jeremy.force@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Graphics	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-14)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3ZBF format mmCIF fromDatabase pdb

3zbf title:  
Structure of Human ROS1 Kinase Domain in Complex with Crizotinib [more
info...]  
  
Chain information for 3zbf #1  
---  
Chain | Description  
A | proto-oncogene tyrosine-protein kinase ros  
  
Non-standard residues in 3zbf #1  
---  
VGH —
3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine
(crizotinib)  
  
  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select ::name="HOH"::name="VGH"

167 atoms, 33 bonds, 1 model selected  

> delete atoms sel

> delete bonds sel

> color bynucleotide

> color bynucleotide

> select /A

2260 atoms, 2311 bonds, 2 pseudobonds, 2 models selected  

> rainbow sel

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> undo

> redo

> select

2260 atoms, 2311 bonds, 2 pseudobonds, 2 models selected  

> undo

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> show sel cartoons

> show sel cartoons

> show sel surfaces

> hide sel surfaces

> hide sel cartoons

> hide sel cartoons

> show sel cartoons

> show sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> ~select #1

1 model selected  

> select #1

2260 atoms, 2311 bonds, 2 pseudobonds, 2 models selected  

> ~select #1

1 model selected  

> color bychain

> color bychain

> rainbow

> hbonds

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 2230 N  

263 hydrogen bonds found  

> hide atoms

> show atoms

> hide atoms

> show atoms

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> undo

> rainbow

> select

2260 atoms, 2311 bonds, 265 pseudobonds, 3 models selected  

> show sel atoms

> hide sel surfaces

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> rainbow sel

> show sel atoms

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 2230 N  

263 hydrogen bonds found  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 2230 N  

263 hydrogen bonds found  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 2230 N  

263 hydrogen bonds found  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 2230 N  

263 hydrogen bonds found  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 2230 N  

263 hydrogen bonds found  

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select

2260 atoms, 2311 bonds, 265 pseudobonds, 3 models selected  

> ~select #1

1 model selected  

> set bgColor black

> set bgColor white

Empty filename passed to function  

Empty filename passed to function  

> save2 "/Users/jf119/Downloads/ROS1_no criz.pdb"

> open2 /Users/jf119/Desktop/ROS1_ATP.pdb

> close session

> open2 "/Users/jf119/Desktop/ROS1 ATP/ROS1 ATP V1.pdb"

Chain information for ROS1 ATP V1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open2 "/Users/jf119/Desktop/ROS1 ATP/ROS1_model 1.pdb"

> open2 "/Users/jf119/Desktop/ROS1 ATP/ROS1_model 7.pdb"

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> undo

> show #3 models

> select #1/A

2753 atoms, 2804 bonds, 4 pseudobonds, 2 models selected  

> select clear

> select clear

> hide #3 models

> show #3 models

> select #1/A

2753 atoms, 2804 bonds, 4 pseudobonds, 2 models selected  

> select ~sel

84 atoms, 88 bonds, 2 models selected  

> delete atoms sel

> delete bonds sel

> open2 "/Users/jf119/Desktop/ROS1 ATP/ROS1_model 1.pdb"

> cartoon

> select #1/A

2753 atoms, 2804 bonds, 4 pseudobonds, 2 models selected  

> cartoon style sel xsection oval modeHelix default

> cartoon sel

> show (sel-residues & sidechain) target ab

> cartoon style sel xsection rectangle modeHelix default

> cartoon style sel xsection oval modeHelix default

> cartoon style sel xsection rectangle modeHelix default

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> show (sel-residues & sidechain) target ab

> hide sel target a

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (single color)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "ghostly white"

Changed 2753 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> rainbow sel

> color sel bynucleotide

> mlp sel

Map values for surface "ROS1 ATP V1.pdb_A SES surface": minimum -29.32, mean
-3.722, maximum 22.64  

> select clear

> toolshed show Rotamers

No residues selected  
Alignment identifier is 1.A  

> toolshed show Rotamers

> show (sel-residues & sidechain) target ab

> toolshed show Rotamers

> swapaa interactive sel GLY rotLib Richardson.mode

> swapaa sel GLY rotLib Richardson.mode

Using Richardson.mode library  
Swapping ROS1 ATP V1.pdb #1/A SER 1953 to GLY  
  

> toolshed show Rotamers

> swapaa interactive sel SER rotLib Richardson.mode

ROS1 ATP V1.pdb #1/A GLY 1953: phi -128.8, psi none trans  
Changed 9 bond radii  

> swapaa #1/A:1953 SER criteria 1 rotLib Richardson.mode

Using Richardson.mode library  
ROS1 ATP V1.pdb #1/A GLY 1953: phi -128.8, psi none trans  
Applying SER rotamer (chi angles: 64.0) to ROS1 ATP V1.pdb #1/A SER 1953  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: ROS1 ATP V1.pdb #1/A ARG 2230 N  

0 hydrogen bonds found  

> select #1/A

2751 atoms, 2802 bonds, 4 pseudobonds, 2 models selected  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: ROS1 ATP V1.pdb #1/A ARG 2230 N  

227 hydrogen bonds found  
Traceback (most recent call last):  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 754, 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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 754, 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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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.  
  

> ~select #3

2751 atoms, 2802 bonds, 4 pseudobonds, 3 models selected  

> hide #3 models

Traceback (most recent call last):  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 754, 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
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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 "model display changed":  
TypeError: Cannot multiply Place times "None"  
  
File
"/private/var/folders/h3/jpj8bdk14xng5pcdjzwhtjt40f6t51/T/AppTranslocation/66F26260-83A1-4E18-A9DB-8C7810C80931/d/ChimeraX_Daily.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 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Graphics
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → pseudobond's atoms pb_scene_coord is None(?)

comment:2 by Eric Pettersen, 5 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Hi Jeremy,

Thanks for reporting this problem. It was fixed two days after the build you have, so if you download the latest build you won't run into it anymore. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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