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Opened 5 years ago
Closed 5 years ago
#3124 closed defect (fixed)
open2/save2 still used by dialogs
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-5.3.0-46-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.94 (2020-04-30) Description When trying to open a session file through the gui, it doesn't work and the message 'Unknown command: open2 /path/to/session.cxs' is given. Using just 'open /path/to/session.cxs' in the command line works. Log: UCSF ChimeraX version: 0.94.dev202004301855 (2020-04-30) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/caillan/rqcH-project/figures/chimerax- > sessions/200430_H69-comparison_5.cxs Log from Thu Apr 30 22:46:43 2020UCSF ChimeraX version: 0.94.dev202004280056 (2020-04-28) © 2016-2020 Regents of the University of California. All rights reserved. > open2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200430_H69-comparison_3.cxs Log from Thu Apr 30 18:35:55 2020UCSF ChimeraX version: 0.94.dev202004280056 (2020-04-28) © 2016-2020 Regents of the University of California. All rights reserved. > open2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200429_H69-comparison_2.cxs Log from Thu Apr 30 14:51:35 2020UCSF ChimeraX version: 0.94.dev202004280056 (2020-04-28) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/caillan/rqcH-project/figures/chimerax- > sessions/200429_H69-comparison_1.cxs format session Log from Wed Apr 29 19:49:22 2020 Startup Errors --- error | Bundle 'ChimeraX-Registration' custom initialization failed warning | Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/toolshed/info.py", line 432, in initialize api._api_caller.initialize(api, session, self) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 1652, in initialize return cls._get_func(api, "initialize")(session, bi) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/registration/__init__.py", line 41, in initialize nag(session) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/registration/nag.py", line 28, in nag if not check_registration(logger=session.logger): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/registration/nag.py", line 49, in check_registration return _check_expiration(param, logger) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/registration/nag.py", line 131, in _check_expiration expires = datetime.strptime(param["Expires"], TimeFormat) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/_strptime.py", line 577, in _strptime_datetime tt, fraction, gmtoff_fraction = _strptime(data_string, format) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/_strptime.py", line 359, in _strptime (data_string, format)) ValueError: time data 'Tue Apr 13 07:53:02 2021' does not match format '%a %b %d %H:%M:%S %Y' UCSF ChimeraX version: 0.94.dev202004280056 (2020-04-28) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open2 /home/caillan/rqcH-project/maps/locally-filtered/rqcH- > pulldown/LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc /home/caillan/rqcH- > project/maps/locally-filtered/rqcH-pulldown/LocFilt_EPA- > cl1_state-a-1_ws08_job042.mrc /home/caillan/rqcH-project/maps/locally- > filtered/rqcH-pulldown/LocFilt_EPA-cl6_E-tRNA_job107.mrc /home/caillan/rqcH- > project/maps/locally-filtered/rqcH-pulldown/LocFilt_EPA-cl4_NFACT-sub- > cl1_job255.mrc Opened LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0179, step 2, values float32 Opened LocFilt_EPA-cl1_state-a-1_ws08_job042.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0137, step 2, values float32 Opened LocFilt_EPA-cl6_E-tRNA_job107.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0131, step 2, values float32 Opened LocFilt_EPA-cl4_NFACT-sub-cl1_job255.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0122, step 2, values float32 > set bgColor white > fitmap #1 inMap #2 Fit map LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc in map LocFilt_EPA- cl1_state-a-1_ws08_job042.mrc using 92603 points correlation = 0.9928, correlation about mean = 0.8867, overlap = 48.05 steps = 88, shift = 0.747, angle = 3.64 degrees Position of LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc (#1) relative to LocFilt_EPA-cl1_state-a-1_ws08_job042.mrc (#2) coordinates: Matrix rotation and translation 0.99902582 0.04211214 0.01319019 -9.40718037 -0.04146702 0.99808671 -0.04586287 14.97699509 -0.01509634 0.04527124 0.99886066 -5.75176049 Axis 0.71843756 0.22299119 -0.65887965 Axis point 0.00000000 129.68876365 319.34624399 Rotation angle (degrees) 3.63643796 Shift along axis 0.37098423 > fitmap #3 inMap #2 Fit map LocFilt_EPA-cl6_E-tRNA_job107.mrc in map LocFilt_EPA- cl1_state-a-1_ws08_job042.mrc using 92558 points correlation = 0.9839, correlation about mean = 0.7924, overlap = 32.12 steps = 80, shift = 0.224, angle = 3.56 degrees Position of LocFilt_EPA-cl6_E-tRNA_job107.mrc (#3) relative to LocFilt_EPA- cl1_state-a-1_ws08_job042.mrc (#2) coordinates: Matrix rotation and translation 0.99817648 -0.04948449 0.03456890 2.81264974 0.04897986 0.99868264 0.01529582 -10.73982101 -0.03528027 -0.01357474 0.99928526 8.40563374 Axis -0.23258788 0.56272102 0.79325149 Axis point 220.23297511 48.58266047 0.00000000 Rotation angle (degrees) 3.55827866 Shift along axis -0.02992979 > fitmap #4 inMap #2 Fit map LocFilt_EPA-cl4_NFACT-sub-cl1_job255.mrc in map LocFilt_EPA- cl1_state-a-1_ws08_job042.mrc using 92559 points correlation = 0.9453, correlation about mean = 0.5095, overlap = 25.37 steps = 68, shift = 0.113, angle = 0.889 degrees Position of LocFilt_EPA-cl4_NFACT-sub-cl1_job255.mrc (#4) relative to LocFilt_EPA-cl1_state-a-1_ws08_job042.mrc (#2) coordinates: Matrix rotation and translation 0.99988117 0.00021391 -0.01541426 2.61415103 -0.00018570 0.99999831 0.00183158 -0.26161214 0.01541463 -0.00182850 0.99987952 -2.36543899 Axis -0.11788461 -0.99294389 -0.01287046 Axis point 154.78437179 0.00000000 168.26245177 Rotation angle (degrees) 0.88949435 Shift along axis -0.01795771 > volume #2 level 0.01038 > hide #!3 models > hide #!4 models > hide #!1 models > show #!1 models > volume #1 level 0.01063 > volume #3 level 0.008931 > volume #4 level 0.006442 > open2 /home/caillan/rqcH-project/modelling/EPA- > cl1_modelling/200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-hand-edited-header- > stripped.pdb Chain information for 200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-hand-edited- header-stripped.pdb #5 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available A | No description available B | No description available E | No description available F | No description available G | No description available H | No description available I | No description available K | No description available L | No description available N | No description available O | No description available P | 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 a | No description available b | No description available c | No description available d | No description available f | No description available g | No description available h | No description available i | No description available j | No description available > hide atoms > show cartoons > hide #!2 models > hide #!4 models > open2 /home/caillan/rqcH-project/modelling/aligned-pdbs/200418_1vy4-pre- > attack-cl1-aligned.pdb Chain information for 200418_1vy4-pre-attack-cl1-aligned.pdb #6 --- Chain | Description A | No description available B | No description available B | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 31793, resource id: 56623167, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31794, resource id: 56623167, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31796, resource id: 56623170, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31797, resource id: 56623170, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31799, resource id: 56623173, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31800, resource id: 56623173, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31802, resource id: 56623176, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31803, resource id: 56623176, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31805, resource id: 56623179, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31806, resource id: 56623179, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31814, resource id: 56623182, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31815, resource id: 56623182, major code: 25 (SendEvent), minor code: 0 > hide atoms > hide cartoons > show cartoons > hide #!5 models > show #!1 models > volume #1 level 0.009274 > volume #1 level 0.01153 > show #!5 models > hide #!6 models > hide #!2 models > save2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200429_H69-comparison_1.cxs opened ChimeraX session > open2 /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/pre- > trans-eco-4v7d-no-ssu.pdb /home/caillan/rqcH-project/modelling/aligned- > pdbs/H69-comparison/non-rot-tth-APE-tRNAs-4v5d-no-ssu.pdb > /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/rot- > hsa-6y57-no-SSU.pdb Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned- pdbs/H69-comparison/pre-trans-eco-4v7d-no-ssu.pdb --- warnings | Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 1889 messages similar to the above omitted Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned- pdbs/H69-comparison/rot-hsa-6y57-no-SSU.pdb --- warnings | Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 40302 messages similar to the above omitted Chain information for pre-trans-eco-4v7d-no-ssu.pdb #7 --- Chain | Description A | No description available A | No description available B | No description available B | No description available Chain information for non-rot-tth-APE-tRNAs-4v5d-no-ssu.pdb #8 --- Chain | Description C | No description available D | No description available D | No description available Chain information for rot-hsa-6y57-no-SSU.pdb #9 --- Chain | Description A | No description available B | No description available D | No description available L | No description available L | No description available S | No description available > select #9/L:4596@OP1 1 atom, 1 model selected > hide sel atoms > hide sel atoms > hide sel atoms > select clear > hide #!7 models > hide #!8 models > hide #!9 models > show #!9 models > show #!8 models > hide #!8 models > hide #!5,9 atoms > show #!5,9 cartoons > hide #!9 models > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!6 models > show #!4 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!6 models > hide #!5 models > save2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200429_H69-comparison_2.cxs opened ChimeraX session > open2 /home/caillan/rqcH-project/modelling/aligned- > pdbs/H69-comparison/200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-partial.pdb > /home/caillan/rqcH-project/modelling/aligned- > pdbs/H69-comparison/200326_cl4-50S-AP-tRNA-RqcH-H69-partial.pdb > /home/caillan/rqcH-project/modelling/aligned- > pdbs/H69-comparison/200326_cl4-50S-AP-tRNA-RqcH-H69-full.pdb > /home/caillan/rqcH-project/modelling/aligned- > pdbs/H69-comparison/200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-full.pdb Chain information for 200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-partial.pdb #10 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available A | No description available B | No description available E | No description available F | No description available G | No description available H | No description available I | No description available K | No description available L | No description available N | No description available O | No description available P | 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 a | No description available b | No description available c | No description available d | No description available f | No description available g | No description available h | No description available i | No description available j | No description available Chain information for 200326_cl4-50S-AP-tRNA-RqcH-H69-partial.pdb #11 --- Chain | Description 0 | No description available 2 | No description available A | No description available B | No description available E | No description available F | No description available G | No description available H | No description available I | No description available K | No description available L | No description available N | No description available O | No description available P | 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 a | No description available b | No description available c | No description available d | No description available f | No description available g | No description available h | No description available i | No description available j | No description available Chain information for 200326_cl4-50S-AP-tRNA-RqcH-H69-full.pdb #12 --- Chain | Description 0 | No description available 2 | No description available A | No description available B | No description available E | No description available F | No description available G | No description available H | No description available I | No description available K | No description available L | No description available N | No description available O | No description available P | 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 a | No description available b | No description available c | No description available d | No description available f | No description available g | No description available h | No description available i | No description available j | No description available Chain information for 200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-full.pdb #13 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available A | No description available B | No description available E | No description available F | No description available G | No description available H | No description available I | No description available K | No description available L | No description available N | No description available O | No description available P | 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 a | No description available b | No description available c | No description available d | No description available f | No description available g | No description available h | No description available i | No description available j | No description available > hide #!6,10-13 atoms > show #!6,10-13 cartoons > select clear > hide #!12 models > hide #!11 models > hide #!10 models > hide #!13 models > show #!13 models > rename #13 cl1-H69-full > show #!10 models > hide #!13 models > rename #10 cl1-H69-partial > hide #!10 models > show #!11 models > rename #14 cl4-H69-partial > show #!12 models > hide #!11 models > rename #11 cl4-H69-partial > rename #12 cl4-H69-pull > rename #12 cl4-H69-full > hide #!12 models > show #!10 models > show #!11 models > hide #!6 models > hide #!4 models > show #!13 models > show #!12 models > hide #!11 models > hide #!10 models > hide #!13 models > show #!11 models > hide #!12 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.008937 > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > save2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200430_H69-comparison_3.cxs opened ChimeraX session > hide #!11 models > show #!8 models > show #!10 models > hide #!8,10 atoms > close #5-9 > open2 /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/post- > trans-tth-4v5n-no-ssu.pdb /home/caillan/rqcH-project/modelling/aligned- > pdbs/H69-comparison/pre-trans-tth-4v5m-no-ssu.pdb /home/caillan/rqcH- > project/modelling/aligned-pdbs/H69-comparison/post-acc-tth-4v6f-no-ssu.pdb > /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/pre-acc- > tth-4v5g-no-ssu.pdb /home/caillan/rqcH-project/modelling/aligned- > pdbs/H69-comparison/non-rot-eco-4v9d-no-ssu.pdb /home/caillan/rqcH- > project/modelling/aligned-pdbs/H69-comparison/rot-eco-4v9d-no-ssu.pdb Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned- pdbs/H69-comparison/post-trans-tth-4v5n-no-ssu.pdb --- warnings | Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 848 messages similar to the above omitted Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned- pdbs/H69-comparison/pre-trans-tth-4v5m-no-ssu.pdb --- warnings | Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 848 messages similar to the above omitted Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned- pdbs/H69-comparison/pre-acc-tth-4v5g-no-ssu.pdb --- warnings | Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 Duplicate atom serial number found: 99999 3293 messages similar to the above omitted Chain information for post-trans-tth-4v5n-no-ssu.pdb #5 --- Chain | Description A | No description available A | No description available B | No description available B | No description available Chain information for pre-trans-tth-4v5m-no-ssu.pdb #6 --- Chain | Description A | No description available A | No description available B | No description available B | No description available Chain information for post-acc-tth-4v6f-no-ssu.pdb #7 --- Chain | Description A | No description available A | No description available B | No description available Chain information for pre-acc-tth-4v5g-no-ssu.pdb #8 --- Chain | Description A | No description available A | No description available B | No description available B | No description available Chain information for non-rot-eco-4v9d-no-ssu.pdb #9 --- Chain | Description B | No description available D | No description available D | No description available Chain information for rot-eco-4v9d-no-ssu.pdb #14 --- Chain | Description A | No description available A | No description available C | No description available C | No description available > hide #!5-10,14 atoms > hide #!2 models > hide #!1 models Drag select of 64 residues > select up 322534 atoms, 361228 bonds, 5 models selected > color sel skyblue > select clear Drag select of 84 residues > select up 387236 atoms, 433689 bonds, 6 models selected > color sel lightgrey > select clear > save2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200430_H69-comparison_4.cxs > hide #!14 models > hide #!10 models > color #5 tan > color #6 plum > color #7 lightgreen > color #8 salmon > color #9 deeppink > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > show #!2 models > show #!10 models > color #10 grey > color #10/A/B lightgrey > color #10/0 darkviolet > color #10/1 gold > color #10/2 skyblue > select clear > hide #!2 models > name #10/A:1935-1955 cl1-H69-part "cl1-H69-part": invalid atom specifier > name cl1-H69-part #10/A:1935-1955 > show cl1-H69-part atoms > nucleotides #!10 atoms > style nucleic & #!10 stick Changed 64453 atom styles > show #!2 models > save2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200430_H69-comparison_4.cxs > volume #2 step 1 > hide #!2 models > select #10/1:11 11 atoms, 10 bonds, 1 model selected > select clear > show #!1 models > show #!2 models > hide #!1 models > show #!4 models > hide #!4 models > show #!11 models > hide #!11 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > color #10/A grey > volume #2 color #bfadad > volume #2 color #b09f9f > volume #2 color #b0a6a6 > volume #2 color #b9aeae > volume #2 color #b9b9b9 > volume #2 color #c7c7c7 > volume #2 color #c6c6c6 > volume #2 color #c5c5c5 > volume #2 color #c4c4c4 > volume #2 color #c3c3c3 > volume #2 color #c2c2c2 > volume #2 color #c2c1c1 > volume #2 color #bab9b9 > volume #2 color #b5b3b3 > volume #2 color #b3b1b1 > volume #2 color #b3b2b2 > volume #2 color #b4b3b3 > volume #2 color #b4b4b4 > volume #2 color #b5b5b5 > volume #2 color #b8b8b8 > volume #2 color #bababa > volume #2 color #bababafb > volume #2 color #bababac0 > volume #2 color #bababa06 > volume #2 color #bababa04 > volume #2 color #bababa07 > volume #2 color #bababa17 > volume #2 color #bababa19 > volume #2 color #bababa28 > volume #2 color #bababa2d > volume #2 color #bababa2e > volume #2 color #bababa38 > volume #2 color #bababa3d > volume #2 color #bababa3e > volume #2 color #bababa44 > volume #2 color #bababa45 > volume #2 color #bababa47 > volume #2 color #bababa4b > volume #2 color #bababa4f > volume #2 color #bababa4e > volume #2 color #bababa4d > volume #2 color #bababa4c > volume #2 color #bababa4a > volume #2 color #bababa5f > volume #2 color #bababa74 > volume #2 color #bababa79 > volume #2 color #bababa7a > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide cl1-H69-part atoms > volume #!2 style mesh > toolshed show "Side View" > toolshed show "Side View" > hide #!2 models > show #!2 models > hide #!2 models > select #10/2:28 20 atoms, 21 bonds, 1 model selected > select up 1563 atoms, 1744 bonds, 1 model selected > show sel atoms > color sel byhetero > select clear > show cl1-H69-part atoms > color cl1-H69-part byhetero > select clear > show #!2 models > hide #!2 models > show #!2 models > volume #!2 style surface > hide #!2 models > show #!2 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > pwd Current working directory is: /home/caillan > cd /home/caillan/rqcH-project/figures Current working directory is: /home/caillan/Dropbox/rqcH-project/figures > cd /home/caillan/rqcH-project/figures/H69-comp/close-panels Current working directory is: /home/caillan/Dropbox/rqcH- project/figures/H69-comp/close-panels > save 200430_cl1-part-w-density_1.png width 800 height 600 > transparentBackground true > hide #10.1 models > volume #2 color #bfbbbb > volume #2 color #c0bcbc > volume #2 color #c0bfbf > volume #2 color silver > volume #2 color #c0c0c0fd > volume #2 color #c0c0c0ca > volume #2 color #c0c0c07c > volume #2 color #c0c0c07b > volume #2 color #c0c0c04f > volume #2 color #c0c0c02c > volume #2 color #c0c0c027 > volume #2 color #c0c0c026 > volume #2 color #c0c0c025 > volume #2 color #c0c0c021 > volume #2 color #c0c0c016 > volume #2 color #c0c0c012 > volume #2 color #c0c0c00c > volume #2 color #c0c0c00b > volume #2 color #c0c0c00f > volume #2 color #c0c0c010 > volume #2 color #c0c0c011 > volume #2 color #c0c0c012 > volume #2 color #c0c0c011 > volume #2 color #c0c0c00f > volume #2 color #c0c0c010 > volume #2 color #c0c0c012 > volume #2 color #c0c0c014 > volume #2 color #c0c0c015 > save 200430_cl1-part-w-density_1.png width 800 height 600 > transparentBackground true > volume #2 color #bfbbbb > volume #2 color #c5c1c1 > volume #2 color #c5c0c0 > volume #2 color #c3bebe > volume #2 color #c1bdbd > volume #2 color #c1bfbf > volume #2 color #c3c0c0 > volume #2 color #c3c1c1 > volume #2 color #c3c3c3 > volume #2 color #c4c4c4 > volume #2 color #c5c5c5 > volume #2 color #c5c5c522 > volume #2 color #c5c5c521 > volume #2 color #c5c5c523 > volume #2 color #c5c5c53a > volume #2 color #c5c5c554 > volume #2 color #c5c5c568 > volume #2 color #c5c5c569 > volume #2 color #c5c5c568 > volume #2 color #c5c5c558 > volume #2 color #c5c5c528 > volume #2 color #c5c5c527 > volume #2 color #c5c5c526 > save 200430_cl1-part-w-density_1.png width 800 height 600 > transparentBackground true > save 200430_cl1-part-w-density_1.png width 800 height 600 > transparentBackground true > save 200430_cl1-part-w-density_1.png width 800 height 600 > transparentBackground true > volume #2 color #bfb8b8 > volume #2 color #b8b0b0 > volume #2 color #b8b1b1 > volume #2 color #b9b2b2 > volume #2 color #b9b4b4 > volume #2 color #beb9b9 > volume #2 color #bebaba > volume #2 color #bfbbbb > volume #2 color #bfbcbc > volume #2 color #c1bfbf > volume #2 color #c1c0c0 > volume #2 color #c1c1c1 > volume #2 color #c1c1c18e > volume #2 color #c1c1c18f > volume #2 color #c1c1c19a > volume #2 color #c1c1c19c > volume #2 color #c1c1c1d2 > volume #2 color #c1c1c1d3 > volume #2 color #c1c1c1d1 > volume #2 color #c1c1c1a0 > volume #2 color #c1c1c197 > volume #2 color #c1c1c190 > volume #2 color #c1c1c17b > volume #2 color #c1c1c15e > volume #2 color #c1c1c15c > volume #2 color #c1c1c159 > volume #2 color #c1c1c158 > volume #2 color #c1c1c159 > volume #2 color #c1c1c15a > volume #2 color #c1c1c15d > volume #2 color #c1c1c15e > volume #2 color #c1c1c15f > volume #2 color #c1c1c160 > volume #2 color #c1c1c164 > volume #2 color #c1c1c165 > volume #2 color #c1c1c166 > save 200430_cl1-part-w-density_1.png width 800 height 600 > transparentBackground true > view name H69-close > view lsit Expected an objects specifier or a view name or a keyword > view list Named views: H69-close > hide #2 > save 200430_cl1-part-model_1.png width 800 height 600 transparentBackground > true > save 200430_cl1-part-model_1.png width 800 height 600 transparentBackground > true > save 200430_cl1-part-model_1.png width 800 height 600 transparentBackground > true > save 200430_cl1-part-density_1.png width 800 height 600 > transparentBackground true > view name H69-close > hide #!10 atoms > show #!5 models > select #5/A:20 50 atoms, 52 bonds, 1 model selected > select clear > select #5/A:17 48 atoms, 49 bonds, 1 model selected > select up 1922 atoms, 2140 bonds, 1 model selected > color sel lightgreen > select clear > select #5/A:579 9 atoms, 8 bonds, 1 model selected > select up 134 atoms, 134 bonds, 1 model selected > select up 7149 atoms, 7471 bonds, 1 model selected > select clear > view list Named views: H69-close > view H69-close > hide #!10 models Drag select of 11 residues > hide sel cartoons > save2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200430_H69-comparison_5.cxs opened ChimeraX session > view list Named views: H69-close > view H69-close > show #!9 models > hide #!9 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > open2 /home/caillan/rqcH-project/figures/chimerax- > sessions/200430_H69-comparison_5.cxs Unknown command: open2 /home/caillan/rqcH-project/figures/chimerax- sessions/200430_H69-comparison_5.cxs OpenGL version: 4.5 (Core Profile) Mesa 19.2.8 OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) OpenGL vendor: Intel Open Source Technology Center Manufacturer: LENOVO Model: 20L6S01W00 OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz Cache Size: 6144 KB Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07) Subsystem: Lenovo UHD Graphics 620 [17aa:225d] Kernel driver in use: i915
Change History (3)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → open2/save2 still used by dialogs |
comment:2 by , 5 years ago
comment:3 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
The fix is in the build currently on the web site.
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Hi Caillan,
--Eric