Opened 6 years ago

Closed 6 years ago

#1907 closed defect (can't reproduce)

OpenGL buffer problem

Reported by: Elaine Meng 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-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-01)
Description
RuntimeError when Ctrl-click , Shift-Ctrl-click selecting

was showing part of 1bna as ribbon/ladder in case that matters... not sure if the error happened when I was using Shift or not

Log:
UCSF ChimeraX version: 0.9 (2019-05-01)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/meng/Desktop/icons/colorbyicon.cxs

opened ChimeraX session  

> close

> open 6cmn

Summary of feedback from opening 6cmn fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for G #18 in chain D  
  
6cmn title:  
Co-Crystal Structure of HIV-1 TAR Bound to Lab-Evolved RRM TBP6.7 [more
info...]  
  
Chain information for 6cmn #1  
---  
Chain | Description  
A | TAR-Binding Protein 6.7  
D | Trans-Activation Response RNA Element  
  
  

> delete protein

> label residues

> label /a residues

Invalid "target" argument: Character 'l' is not an allowed target, must be one
of acrsbpf  

> label color red

> nucleotides selAtoms tube/slab shape box

> nucleotides selAtoms fill

> set bgColor black

> close

> open /Users/meng/Desktop/icons/colorbyicon.cxs

opened ChimeraX session  

> close

> open 6cmn

Summary of feedback from opening 6cmn fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for G #18 in chain D  
  
6cmn title:  
Co-Crystal Structure of HIV-1 TAR Bound to Lab-Evolved RRM TBP6.7 [more
info...]  
  
Chain information for 6cmn #1  
---  
Chain | Description  
A | TAR-Binding Protein 6.7  
D | Trans-Activation Response RNA Element  
  
  

> label /d residues

> delete protein

> zoom 5

> delete ~:27,28,37,38

Unknown command: ~longbond  

> close #1.3

Expected keyword "depthBias", "depthCue", "depthCueColor", "depthCueEnd", or
"depthCueStart"  

> lighting depthCue false

> set silhouetteDepthJump .2

> set silhouetteDepthJump .1

> close

> open 1bna

1bna title:  
Structure of A B-DNA dodecamer. Conformation and dynamics [more info...]  
  
Chain information for 1bna #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*TP*CP*GP*CP*G)-3')  
  
  

> delete ~/a:4,5/b:20,21

> view

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands: 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; cartoon style protein modeh default arrows f x round width 1 thick 1;
cartoon style nucleic x round width 1.6 thick 1.6; nucleotides tube/slab shape
ellipsoid  

> close

> open 1bna

1bna title:  
Structure of A B-DNA dodecamer. Conformation and dynamics [more info...]  
  
Chain information for 1bna #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*TP*CP*GP*CP*G)-3')  
  
  

> nucleotides selAtoms ladder

> lighting depthCue false

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands: 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; cartoon style protein modeh default arrows f x round width 1 thick 1;
cartoon style nucleic x round width 1.6 thick 1.6; nucleotides tube/slab shape
ellipsoid  

> nucleotides selAtoms ladder

> color selAtoms bynucleotide

> color tan target ar

> color gray target ar

> color lightgray target ar

> color silver target ar

> nucleotides stubs

> hide ~:4,5,20,21

> zoom 1.2

> show :6,19

> show :3,22

> zoom .98

> zoom .98

> zoom .98

> zoom .98

> nucleotides ladder

> nucleotides stubs

> zoom 1.01

> zoom 1.01

> ~ribbon ~:1-6,20-25

> ribbon

> ~ribbon :2-7,18-24

> ribbon

> ~ribbon ~:2-7,18-24

> ~ribbon :17

> ~ribbon :18

> ~ribbon :19

> ribbon :19

> ~ribbon :3,24

> ribbon :3

> ~ribbon :2

> zoom 1.01

> zoom 1.01

> zoom 1.01

> zoom 1.01

> move y -.1

> move y -.1

> move y -.1

> move x .1

> move x .1

> save icons/nuc-ladder-icon.cxs

> save nuc-stubs.png width 128

> nucleotides ladder

> save nuc-ladder.png width 128

Exception ignored in: <function Buffer.__del__ at 0x117e83a60>  
Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2393, in __del__  
% self.shader_variable_name)  
RuntimeError: OpenGL buffer "None" was not deleted before core.graphics.Buffer
destroyed  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Component: UnassignedGraphics
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionOpenGL buffer problem

comment:2 by Elaine Meng, 6 years ago

unfortunately not easily reproduced... tried a couple of times

comment:3 by Tom Goddard, 6 years ago

Resolution: can't reproduce
Status: assignedclosed

Could not find the cause of this error. Could not reproduce it. The error message means an OpenGL element buffer was not deleted properly by some Python object, either a Drawing or TextureWindow. I studied the code and could not find any way this can happen.

If this happens again report it. It will be hard to debug without a reproducible case.

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