id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3621 many labels == problems Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Trying to label all nucleotide residues in a ribosome kills the graphics. Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4bna 4bna title: Reversible bending and helix geometry In A B-DNA dodecamer: cgcgaattbrcgcg [more info...] Chain information for 4bna #1 --- Chain | Description A B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*TP*(CBR)P*GP*CP*G)-3') > style stick Changed 602 atom styles > nucleotides atoms > style nucleic stick Changed 488 atom styles > label nucleic > close #1 > open 6zm7 6zm7 title: SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex [more info...] Chain information for 6zm7 #1 --- Chain | Description CA | Proliferation-associated protein 2G4 CC | tRNA CE | Coiled-coil domain-containing protein 124 CF | Non-structural protein 1 L5 | 28S ribosomal RNA L7 | 5S ribosomal RNA L8 | 5.8S ribosomal RNA LA | 60S ribosomal protein L8 LB | 60S ribosomal protein L3 LC | 60S ribosomal protein L4 LD | 60S ribosomal protein L5 LE | 60S ribosomal protein L6 LF | 60S ribosomal protein L7 LG | 60S ribosomal protein L7a LH | 60S ribosomal protein L9 LI | 60S ribosomal protein L10-like LJ | 60S ribosomal protein L11 LL | 60S ribosomal protein L13 LM | 60S ribosomal protein L14 LN | 60S ribosomal protein L15 LO | 60S ribosomal protein L13a LP | 60S ribosomal protein L17 LQ | 60S ribosomal protein L18 LR | 60S ribosomal protein L19 LS | 60S ribosomal protein L18a LT | 60S ribosomal protein L21 LU | 60S ribosomal protein L22 LV | 60S ribosomal protein L23 LW | 60S ribosomal protein L24 LX | 60S ribosomal protein L23a LY | 60S ribosomal protein L26 LZ | 60S ribosomal protein L27 La | 60S ribosomal protein L27a Lb | 60S ribosomal protein L29 Lc | 60S ribosomal protein L30 Ld | 60S ribosomal protein L31 Le | 60S ribosomal protein L32 Lf | 60S ribosomal protein L35a Lg | 60S ribosomal protein L34 Lh | 60S ribosomal protein L35 Li | 60S ribosomal protein L36 Lj | 60S ribosomal protein L37 Lk | 60S ribosomal protein L38 Ll | 60S ribosomal protein L39 Lm | Ubiquitin-60S ribosomal protein L40 Ln | 60S ribosomal protein L41 Lo | 60S ribosomal protein L36a Lp | 60S ribosomal protein L37a Lr | 60S ribosomal protein L28 Ls | 60S acidic ribosomal protein P0 Lt | 60S ribosomal protein L12 Lz | 60S ribosomal protein L10a S2 | 18S ribosomal RNA SA | 40S ribosomal protein SA SB | 40S ribosomal protein S3a SC | 40S ribosomal protein S2 SD | 40S ribosomal protein S3 SE | 40S ribosomal protein S4, X isoform SF | 40S ribosomal protein S5 SG | 40S ribosomal protein S6 SH | 40S ribosomal protein S7 SI | 40S ribosomal protein S8 SJ | 40S ribosomal protein S9 SK | 40S ribosomal protein S10 SL | 40S ribosomal protein S11 SM | 40S ribosomal protein S12 SN | 40S ribosomal protein S13 SO | 40S ribosomal protein S14 SP | 40S ribosomal protein S15 SQ | 40S ribosomal protein S16 SR | 40S ribosomal protein S17 SS | 40S ribosomal protein S18 ST | 40S ribosomal protein S19 SU | 40S ribosomal protein S20 SV | 40S ribosomal protein S21 SW | 40S ribosomal protein S15a SX | 40S ribosomal protein S23 SY | 40S ribosomal protein S24 SZ | 40S ribosomal protein S25 Sa | 40S ribosomal protein S26 Sb | 40S ribosomal protein S27 Sc | 40S ribosomal protein S28 Sd | 40S ribosomal protein S29 Se | 40S ribosomal protein S30 Sf | Ubiquitin-40S ribosomal protein S27a Sg | Receptor of activated protein C kinase 1 Non-standard residues in 6zm7 #1 --- MG — magnesium ion ZN — zinc ion > label nucleic 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/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/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/view.py"", line 250, in _draw_scene draw_on_top(r, on_top_drawings) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1502, in draw_on_top _draw_multiple(drawings, renderer, Drawing.LAST_DRAW_PASS) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 1438, in _draw_multiple d.draw(renderer, draw_pass) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 716, in draw self.draw_self(renderer, draw_pass) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 732, in draw_self self._draw_geometry(renderer) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/drawing.py"", line 762, in _draw_geometry t.bind_texture() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 2892, in bind_texture self.fill_opengl_texture() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 2927, in fill_opengl_texture self.initialize_texture(size, format, iformat, tdtype, ncomp, data) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 2829, in initialize_texture tdtype, data) File ""src/latebind.pyx"", line 39, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src/wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1281, description = b'invalid value', baseOperation = glTexImage2D, pyArgs = ( GL_TEXTURE_2D, 0, GL_RGBA8, 2048, 39384, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ), cArgs = ( GL_TEXTURE_2D, 0, GL_RGBA8, 2048, 39384, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ), cArguments = ( GL_TEXTURE_2D, 0, GL_RGBA8, 2048, 39384, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ) ) OpenGL version: 3.3.0 NVIDIA 450.51.05 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 9.4G 43G 291M 9.7G 52G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Graphics fixed all ChimeraX