id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1907 OpenGL buffer problem Elaine Meng Tom Goddard "{{{ 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: 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 }}} " defect closed normal Graphics can't reproduce all ChimeraX