id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2952 Eventual failure in glDrawBuffer chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.4.3.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.92 (2020-02-11) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.92 (2020-02-11) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /nas/nsilvia/Trx_MsrAs/Refine_117/Trx_MsrAs_refine_117.pdb Summary of feedback from opening /nas/nsilvia/Trx_MsrAs/Refine_117/Trx_MsrAs_refine_117.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-12-10 Time 14:49:25 CET +0100 (1575985765.95 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /mnt/data1/Silvia/Xray/20190927/merge/TrxC35SMsrAC206_cut2_94A.mtz 48 messages similar to the above omitted Chain information for Trx_MsrAs_refine_117.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available > toolshed show ISOLDE > set selectionWidth 4 Chain information for Trx_MsrAs_refine_117.pdb --- Chain | Description 1.1/A | No description available 1.1/B | No description available 1.1/C | No description available 1.1/D | No description available 1.1/E | No description available 1.1/F | No description available 1.1/G | No description available Done loading forcefield Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Missing ""hbond"" keyword's argument > addh Summary of feedback from adding hydrogens to Trx_MsrAs_refine_117.pdb #1.1 --- warnings | Not adding hydrogens to /A LYS 6 CB because it is missing heavy- atom bond partners Not adding hydrogens to /B LYS 5 CB because it is missing heavy-atom bond partners Not adding hydrogens to /G PHE 12 CB because it is missing heavy-atom bond partners Not adding hydrogens to /G LYS 57 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for Trx_MsrAs_refine_117.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for Trx_MsrAs_refine_117.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for Trx_MsrAs_refine_117.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for Trx_MsrAs_refine_117.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for Trx_MsrAs_refine_117.pdb (#1.1) chain E; guessing termini instead 2 messages similar to the above omitted Chain-initial residues that are actual N termini: /A PHE 3, /B ASP 4, /C ALA 3, /D LYS 6, /E SER 1, /F SER 1, /G LYS 3 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ALA 211, /F ALA 108, /G ALA 108 Chain-final residues that are not actual C termini: /B GLU 210, /C GLU 210, /D CYS 206, /E LEU 103 937 hydrogen bonds /B GLU 210 is not terminus, removing H atom from 'C' /C GLU 210 is not terminus, removing H atom from 'C' /D CYS 206 is not terminus, removing H atom from 'C' /E LEU 103 is not terminus, removing H atom from 'C' 8437 hydrogens added > hide HC > select #1 17247 atoms, 17452 bonds, 26 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. Updating bulk solvent parameters... QWidget::repaint: Recursive repaint detected > select clear Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Unable to flip peptide bond after 50 rounds. Giving up. Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 248, in _draw_scene pixel_width = self._highlight_width) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1480, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 1756, in finish_rendering_outline r.pop_framebuffer() File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 644, in pop_framebuffer fb.activate() File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2137, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) OpenGL version: 3.3.0 NVIDIA 440.36 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Graphics duplicate Tristan Croll all ChimeraX