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Opened 5 years ago
Closed 3 years ago
#3616 closed defect (fixed)
cartoon() 'atoms' parameter type changed
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.93 (2020-03-23) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.93 (2020-03-23) © 2016-2020 Regents of the University of California. All rights reserved. > open F:\1_80S\40S\40S_mainfigure.cxs format session Log from Tue May 19 11:07:14 2020UCSF ChimeraX version: 0.93 (2020-03-23) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open F:/1_80S/40S/40s_job189_14052020_edited-coot-1.pdb Chain information for 40s_job189_14052020_edited-coot-1.pdb #1 --- Chain | Description A F | No description available B | No description available C | No description available D | No description available E | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M P | No description available N | No description available O | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 h | No description available i | No description available > set bgColor white > show cartoons > hide atoms > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected Expected a keyword Expected a keyword > cartoon sel > select ~sel 38618 atoms, 39237 bonds, 1 model selected > hide sel target a > cartoon hide sel > open F:/1_80S/40S/Composite40S.mrc Opened Composite40S.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.028, step 2, values float32 > open F:/1_80S/40S/Averagemap_coot_0.mrc Opened Averagemap_coot_0.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.0143, step 2, values float32 > open F:/1_80S/40S/Composite40S.mrc Opened Composite40S.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.028, step 2, values float32 > select clear > show target ab > hide #!2 models > show cartoons > hide atoms > show #!2 models > color zone #2 near #1 distance 10 > volume zone #2 nearAtoms #3 range 2 no atoms specified for zone > surface dust #2 > volume #2 step 1 > hide #!2 models Drag select of 6707 residues Drag select of 6718 residues Missing required "range" argument > select sel @< 5 76591 atoms, 81560 bonds, 1 pseudobond, 2 models selected > volume zone #1 nearAtoms #1 range 2 > show #!2 models > volume zone #2 nearAtoms #1 range 2 > color zone #2 near #1 distance 10 > color zone #3 near #1 distance 10 > transparency #3 50 > transparency #3 80 > select clear > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > select ~sel 38618 atoms, 39237 bonds, 5 models selected > hide sel target a > hide #!3 models > hide sel cartoons > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > show #!3 models > hide #!3 models > select ::name="4ACB" 46 atoms, 48 bonds, 1 model selected > style sel sphere Changed 46 atom styles > color sel pink > style sel sphere Changed 46 atom styles > show sel target ab > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > nucleotides sel ladder > nucleotides sel stubs > cartoon style sel modeHelix tube sides 20 > nucleotides sel slab > nucleotides sel stubs > show #!2 models > hide #!2 models > display #1 cartoon style nuclix xset oval width 1.6 thick1.6 Expected ',' or a keyword > display #1 cartoon style nuclieic xset oval width 1.6 thick1.6 Expected ',' or a keyword Expected ',' or a keyword Expected ',' or a keyword Expected ',' or a keyword Expected ',' or a keyword Expected a keyword > cartoon style nucleic width 1.6 thickness 1.6 > cartoon style nucleic width 1.6 thickness 0.5 > cartoon style nucleic width 0.5 thickness 0.5 > cartoon style nucleic width 0.5 thickness 0.3 > cartoon style nucleic width 1.5 thickness 0.3 > cartoon style nucleic width 0.3 thickness 0.3 > cartoon style nucleic width 0.3 thickness 0.5 > select clear > show #!3 models > volume #!3 style image > volume #!3 style surface > transparency #3.1 0 > transparency #3.1 50 > transparency #3.1 0 > transparency #3.1 50 > transparency #3.1 10 > transparency #3.1 80 > cartoon style nucleic width 1.5 thickness 0.3 > cartoon style nucleic width 1 thickness 0.3 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > open F:/1_80S/40S/Composite40S.mrc Opened Composite40S.mrc, grid size 432,432,432, pixel 1.07, shown at level 0.028, step 2, values float32 > volume zone #4 nearAtoms #1/i range 2 > close #5 > display all > volume zone #4 nearAtoms #1/i range 2 > hide #!1 models > volume #5 level 0.02025 > volume zone #4 nearAtoms #1 range 2 > volume #4 step 1 > show #!1 models > show cartoons > hide atoms > transparency #5.1 50 > select /i 37978 atoms, 42323 bonds, 1 pseudobond, 2 models selected > display select Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select ~sel 38618 atoms, 39237 bonds, 10 models selected > hide sel target a > cartoon hide sel > select clear > volume #5 step 1 > graphics silhouettes true > lighting flat > graphics silhouettes false > lighting soft > lighting simple > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting soft > graphics silhouettes false > show #!4 models > hide #!4 models > show #!3 models > hide #!5 models > show #!5 models > hide #!5 models > transparency #3 10 > transparency #3 95 > transparency #3 90 > transparency #1 0 > select ::name="OMCB" 63 atoms, 66 bonds, 1 model selected > hide #!3 models > show sel atoms > color sel dark green > select ::name="OMGB" 120 atoms, 130 bonds, 1 model selected > show sel atoms > color sel dark cyan > select ::name="OMUB" 42 atoms, 44 bonds, 1 model selected > show sel atoms Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel pink > select ::name="A2MB" 184 atoms, 200 bonds, 1 model selected > color sel red > show sel atoms > select ::name="4ACB" 46 atoms, 48 bonds, 1 model selected > show sel atoms > color sel gray > select ::name="PS3B" 28 atoms, 29 bonds, 1 model selected > show sel atoms > color sel light sea green Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel orange red > select ::name="G7MB" 24 atoms, 26 bonds, 1 model selected > show sel atoms Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel black > select ::name="PSUB" 260 atoms, 273 bonds, 1 model selected > show sel atoms > color sel yellow > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!3 models > save session F:/1_80S/40S/40S_mainfigure.cxs > save image F:/1_80S/40S/40S_front.bmp width 787 height 773 > save image F:/1_80S/40S/Images/subunitjoining.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/headfront.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/bodyfront.bmp width 787 height 773 > supersample 3 > toolshed show "Side View" > select ::name="G7MB" 24 atoms, 26 bonds, 1 model selected > select ::name="MA6B" 48 atoms, 53 bonds, 1 model selected > show sel atoms > color sel goldenrod > volume #3 change image level -1.167e-05,0 level 0.03982,0.8 level 0.3983,1 > save image F:/1_80S/40S/Images/bodyfront_2.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/bodyfront_2.bmp width 787 height 773 > supersample 3 > save image F:/1_80S/40S/Images/bodyfront_2.bmp width 787 height 773 > supersample 3 > save session F:/1_80S/40S/40S_mainfigure.cxs > save image F:/1_80S/40S/Images/subunitjoining.bmp width 787 height 773 > supersample 3 > save session F:/1_80S/40S/40S_mainfigure.cxs Summary of feedback from opening F:\1_80S\40S\40S_mainfigure.cxs --- notes | Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time opened ChimeraX session Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Users\rupa.ale\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py", line 1222, in _set_default_cartoon_cb set_to_default_cartoon(self.session, model = self.structure) File "C:\Users\rupa.ale\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\util.py", line 55, in set_to_default_cartoon cartoon.cartoon(session, atoms = atoms, suppress_backbone_display=False) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\cartoon.py", line 71, in cartoon results = atoms.evaluate(session) AttributeError: 'Atoms' object has no attribute 'evaluate' Error processing trigger "frame drawn": AttributeError: 'Atoms' object has no attribute 'evaluate' File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\std_commands\cartoon.py", line 71, in cartoon results = atoms.evaluate(session) See log for complete Python traceback. OpenGL version: 3.3.13492 Core Profile Forward-Compatible Context 22.19.677.257 OpenGL renderer: AMD Radeon(TM) R5 Graphics OpenGL vendor: ATI Technologies Inc. Manufacturer: LENOVO Model: 20377 OS: Microsoft Windows 10 Education (Build 17134) Memory: 7,443,828,736 MaxProcessMemory: 137,438,953,344 CPU: 4 AMD A8-6410 APU with AMD Radeon R5 Graphics "
Change History (3)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → cartoon() 'atoms' parameter type changed |
comment:2 by , 5 years ago
This should not be a problem in current ChimeraX and ISOLDE. I suggest closing the ticket.
It appears the ISOLDE being used with ChimeraX 0.93 is passing an Atoms instance to the cartoon command Python code. That is what newer ChimeraX (1.0) requires. But the ChimeraX 0.93 cartoon routine wanted an AtomSpec, and it was only changed to Atoms after 0.93.
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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It looks like Tom changed the type expected by the cartoon() function for 'atoms' from atom spec to Atoms collection on March 30.