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Opened 6 years ago
Closed 6 years ago
#2117 closed defect (can't reproduce)
map stopped updating
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.15.0-51-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-06-25) Description My map stopped updating. I can change levels, step, etc), but the map itself does not reflect these changes. I tried making the changes with the volume viewer and with the comman line, but neither worked. I tried closing session and reloading everything, and that didn't help. Restaring chimerax did that trick Log: UCSF ChimeraX version: 0.91 (2019-06-25) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open maps_and_models/State1_composite.cif name State1 Summary of feedback from opening maps_and_models/State1_composite.cif --- warnings | skipping chem_comp category: Missing column 'type' near line 297 Unknown polymer entity '?' near line 342 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. skipping chem_comp category: Missing column 'type' near line 72840 skipping chem_comp category: Missing column 'type' near line 72867 Chain information for State1 #1 --- Chain | Description A1 A2 A3 | No description available B1 | No description available B2 | No description available B3 | No description available C | No description available D | No description available E1 E2 E3 | No description available F | No description available G1 | No description available G2 | No description available G3 | No description available K1 | No description available K2 | No description available K3 | No description available a | No description available ac | No description available b | No description available c1 c2 c3 c4 c5 c6 c7 c8 c9 | No description available d | No description available e | No description available f | No description available pr | No description available > open maps_and_models/J1509_state1_Vo.mrc Opened J1509_state1_Vo.mrc, grid size 340,340,340, pixel 1.06, shown at level 0.16, step 2, values float32 > set bgColor white > set silhouettes true > camera ortho > surface cap true > lighting soft shadows true intensity 0.1 > close #1.1 > split #1 chains Chain information for State1 A1 #1.1 --- Chain | Description A1 | No description available Chain information for State1 A2 #1.2 --- Chain | Description A2 | No description available Chain information for State1 A3 #1.3 --- Chain | Description A3 | No description available Chain information for State1 B1 #1.4 --- Chain | Description B1 | No description available Chain information for State1 B2 #1.5 --- Chain | Description B2 | No description available Chain information for State1 B3 #1.6 --- Chain | Description B3 | No description available Chain information for State1 C #1.7 --- Chain | Description C | No description available Chain information for State1 D #1.8 --- Chain | Description D | No description available Chain information for State1 E1 #1.9 --- Chain | Description E1 | No description available Chain information for State1 E2 #1.10 --- Chain | Description E2 | No description available Chain information for State1 E3 #1.11 --- Chain | Description E3 | No description available Chain information for State1 F #1.12 --- Chain | Description F | No description available Chain information for State1 G1 #1.13 --- Chain | Description G1 | No description available Chain information for State1 G2 #1.14 --- Chain | Description G2 | No description available Chain information for State1 G3 #1.15 --- Chain | Description G3 | No description available Chain information for State1 K1 #1.16 --- Chain | Description K1 | No description available Chain information for State1 K2 #1.17 --- Chain | Description K2 | No description available Chain information for State1 K3 #1.18 --- Chain | Description K3 | No description available Chain information for State1 a #1.19 --- Chain | Description a | No description available Chain information for State1 ac #1.20 --- Chain | Description ac | No description available Chain information for State1 b #1.21 --- Chain | Description b | No description available Chain information for State1 c1 #1.22 --- Chain | Description c1 | No description available Chain information for State1 c2 #1.23 --- Chain | Description c2 | No description available Chain information for State1 c3 #1.24 --- Chain | Description c3 | No description available Chain information for State1 c4 #1.25 --- Chain | Description c4 | No description available Chain information for State1 c5 #1.26 --- Chain | Description c5 | No description available Chain information for State1 c6 #1.27 --- Chain | Description c6 | No description available Chain information for State1 c7 #1.28 --- Chain | Description c7 | No description available Chain information for State1 c8 #1.29 --- Chain | Description c8 | No description available Chain information for State1 c9 #1.30 --- Chain | Description c9 | No description available Chain information for State1 d #1.31 --- Chain | Description d | No description available Chain information for State1 e #1.32 --- Chain | Description e | No description available Chain information for State1 f #1.33 --- Chain | Description f | No description available Chain information for State1 pr #1.34 --- Chain | Description pr | No description available Split State1 (#1) into 34 models > dssp > select #1.1-3 13993 atoms, 14279 bonds, 3 models selected > name frozen subunitA sel > select #1.4-6 10847 atoms, 11060 bonds, 3 models selected > name frozen subunitB sel > select #1.7 2927 atoms, 2981 bonds, 1 model selected > name frozen subunitC sel > select #1.8 1726 atoms, 1744 bonds, 1 model selected > name frozen subunitD sel > select #1.9-11 5040 atoms, 5079 bonds, 3 models selected > name frozen subunitE sel > select #1.12 876 atoms, 890 bonds, 1 model selected > name frozen subunitF sel > select #1.13-15 2392 atoms, 2401 bonds, 3 models selected > name frozen subunitG sel > select #1.16-18 5441 atoms, 5542 bonds, 3 models selected > name frozen SidK sel > select #1.19 5615 atoms, 5754 bonds, 1 model selected > name frozen V0a sel > select #1.21 1503 atoms, 1537 bonds, 1 model selected > name frozen V0b sel > select #1.22-30 9612 atoms, 9747 bonds, 9 models selected > name frozen V0cring sel > select #1.31 2833 atoms, 2899 bonds, 1 model selected > name frozen V0d sel > select #1.32 628 atoms, 653 bonds, 1 model selected > name frozen V0e sel > select #1.33 675 atoms, 691 bonds, 1 model selected > name frozen V0RNAseK sel > select #1.20 337 atoms, 347 bonds, 1 model selected > name frozen V0Ac45 sel > select #1.34 443 atoms, 456 bonds, 1 model selected > name frozen V0PRR sel > hide SidK target c > hide subunitG target c > hide subunitF target c > hide subunitE target c > hide subunitC target c > hide subunitA target c > hide subunitB target c > hide subunitD target c > hide subunitF target c > color subunitA #F2EA42 target cabp > color subunitB #D01F26 target cabp > color subunitC #996633 target cabp > color subunitD #3A53A3 target cabp > color subunitE #804F9F target cabp > color subunitF #B9529E target cabp > color subunitG #fce94f target cabp > color SidK #D2D2D2 target cabp > color V0a #8ae234 target cabp > color V0b #9d42bf target cabp > color V0cring #e182d9 target cabp > color V0d #8ab7ff target cabp > color V0e #3465a4 target cabp > color V0RNAseK #cc0000 target cabp > color V0Ac45 #EEEEEC target cabp > color V0PRR #edd400 target cabp > select clear > hide atoms > show cartoons > surface dust #2 size 6 > volume #2 step 1 level 0.5 color #EEEEEC surfaceSmoothing true subdivideSurface true smoothingIterations 4 > cartoon style V0cring modeHelix tube OpenGL version: 3.3.0 NVIDIA 418.56 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → map stopped updating |
comment:2 by , 6 years ago
comment:3 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Likely a previous error stopped graphics rendering.
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Did you submit this bug report about map display not updating after you restarted ChimeraX and it was working again? Or did you submit it in ChimeraX while map display was broken? If you submitted the bug after quitting and restarting then the log of the commands given in this report is of no use in debugging the problem since the problem was not in this session.
If you only reported after restarting I suspect that there was an error in your previous session. When an error occurs drawing the graphics it disables the graphics redraw so that you don't get a continuous stream of errors. The error message says this has been done and that you will need to use command "graphics restart" to make the graphics draw again. My guess that is what happened. If that is the situation then the graphics would not update at all (not molecules, not maps).