id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3125 glBlitFramebuffer() error drawing selection outline florejo@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.3.11-100.fc29.x86_64-x86_64-with-fedora-29-Twenty_Nine ChimeraX Version: 0.93 (2020-04-03) Description Starting up the ISOLDE tutorial ""intro to cryoem model building"" 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 > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > clipper associate #2 toModel #1 > isolde start > set bgColor white > addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records Termini for 6out.pdb (#1.2) chain B determined from SEQRES records Termini for 6out.pdb (#1.2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 Missing OXT added to C-terminal residue /A SER 520 1438 hydrogen bonds Adding 'H' to /A ASP 29 Adding 'H' to /C ASP 29 /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11439 hydrogens added > hide HC > isolde restrain ligands #1 > select #1 22945 atoms, 23062 bonds, 14 models selected 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 ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 235, in _draw_scene r.outline.set_outline_mask() # copy depth to outline framebuffer File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 1734, in set_outline_mask cfb.copy_to_framebuffer(mfb, color=False) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 2167, in copy_to_framebuffer GL.glBlitFramebuffer(0, 0, w, h, 0, 0, w, h, what, GL.GL_NEAREST) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/platform/baseplatform.py"", line 415, in __call__ return self( *args, **named ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glBlitFramebuffer, cArguments = ( 0, 0, 669, 610, 0, 0, 669, 610, 256, GL_NEAREST, ) ) OpenGL version: 3.3 (Core Profile) Mesa 18.3.6 OpenGL renderer: llvmpipe (LLVM 7.0, 256 bits) OpenGL vendor: VMware, Inc. Manufacturer: Supermicro Model: SYS-7048A-T OS: Fedora 29 Architecture: 64bit ELF CPU: 48 Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz Cache Size: 30720 KB Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1) Subsystem: ASUSTeK Computer Inc. Device [1043:85aa] Kernel driver in use: nvidia }}} " defect closed normal Graphics fixed all ChimeraX