id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3175 Save options widgets deleted caillancm@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-5.3.0-51-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-05-08) Description Sometimes after opening a model, the save dialgue no longer works. I cannot reproduce this bug yet. However, using the command line to save still works. Log: UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/caillan/rqcH-project/figures/chimerax- > sessions/200509_cl1-4_comparison_1-0-rc_4.cxs Log from Sat May 9 15:39:33 2020UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/caillan/rqcH-project/figures/chimerax- > sessions/200509_cl1-4_comparison_1-0-rc_2.cxs Log from Sat May 9 15:21:07 2020UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/caillan/rqcH-project/figures/chimerax-sessions/200508_A-P-tRNA- > comparison_f2_2.cxs format session Log from Sat May 9 03:08:20 2020 Startup Errors --- error | Bundle 'ChimeraX-Registration' custom initialization failed warning | Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/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/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/lib/python3.7/site- packages/chimerax/registration/__init__.py"", line 41, in initialize nag(session) File ""/usr/lib/ucsf-chimerax/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/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 49, in check_registration return _check_expiration(param, logger) File ""/usr/lib/ucsf-chimerax/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/lib/python3.7/_strptime.py"", line 577, in _strptime_datetime tt, fraction, gmtoff_fraction = _strptime(data_string, format) File ""/usr/lib/ucsf-chimerax/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: 1.0rc202005080235 (2020-05-08) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /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 #1 --- 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 > open /home/caillan/rqcH-project/modelling/EPA- > cl4_modelling/200408_cl4-model-cl1-aligned.pdb Chain information for 200408_cl4-model-cl1-aligned.pdb #2 --- 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 > hide atoms > show cartoons > set bgColor white > open /home/caillan/rqcH-project/modelling/aligned-pdbs/200424_cl4-AP- > tRNA.pdb /home/caillan/rqcH-project/modelling/aligned-pdbs/200416_6cfj-E- > tRNA-cl1-aligned.pdb /home/caillan/rqcH-project/modelling/aligned- > pdbs/200416_6cfj-P-tRNA-cl1-aligned.pdb /home/caillan/rqcH- > project/modelling/aligned-pdbs/200416_6cfj-A-tRNA-cl1-aligned.pdb Chain information for 200424_cl4-AP-tRNA.pdb #3 --- Chain | Description 2 | No description available Chain information for 200416_6cfj-E-tRNA-cl1-aligned.pdb #4 --- Chain | Description 2 | No description available Chain information for 200416_6cfj-P-tRNA-cl1-aligned.pdb #5 --- Chain | Description 2 | No description available Chain information for 200416_6cfj-A-tRNA-cl1-aligned.pdb #6 --- Chain | Description 2 | No description available > name #1 cl1-model ""cl1-model"": invalid atom specifier > rename #1 cl1-model > rename #4 cl4-model > hide #!2 models > hide #!1 models > hide #!4 models > show #!4 models > rename #4 E-tRNA > rename #4 E-tRNA-6cfj > select up Nothing selected > select down Nothing selected > rename #2 cl4-model > rename #3 AP-tRNA > rename #5 P-tRNA-6cfj > rename #6 A-tRNA-6cfj > hide #!6 models > show #!6 models > hide #5 models > show #5 models > hide #!4 models > show #!4 models > hide #3 models > show #3 models > hide #1-6 atoms > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > show #1,2/2 cartoons > show #!2 models > show #!1 models > hide #!2 cartoons > hide #!1 cartoons > show #1,2/2 cartoons > color #1/2 skyblue > color #2/2 cyan > hide #3 models > color #4-6 gainsboro > cartoon style width 2.5 thickness 1 > lighting flat > hide #4 models > color #2 palecyan Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #2 lightcyan > color #2 cyan > graphics silhouettes thickness 2 Expected true or false or a keyword > graphics silhouettes width 2 > hide #!2 models > show #!2 models > color #2 lightcyan > color #2 cyan > save /home/caillan/rqcH-project/figures/chimerax-sessions/200508_A-P-tRNA- > comparison_f2.cxs > cd /home/caillan/rqcH-project/figures/figure_23/A-P-tRNA-comparisons Current working directory is: /home/caillan/Dropbox/rqcH- project/figures/figure_23/A-P-tRNA-comparisons > save 200508_a-b_mixed_test_1.png width 600 height 1000 transparentBackground > true > save 200508_a-b_mixed_test_1.png width 600 height 1000 transparentBackground > true > save 200508_a-b_mixed_test_1.png width 600 height 1000 transparentBackground > true > save 200508_a-b_mixed_test_1.png width 600 height 950 transparentBackground > true > view name A-P-comp_600-950 > hide #!2 models > save 200508_b_AP-comp_1.png width 600 height 950 transparentBackground true > show #!2 models > hide #!1 models > color #2 lavendar Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #2 lavender > save 200508_a_AP-comp_1.png width 600 height 950 transparentBackground true > wait wait requires a frame count argument unless motion is in progress > save 200508_a_AP-comp_1.png width 600 height 950 transparentBackground true > color #2 paleturquoise > save 200508_a_AP-comp_1.png width 600 height 950 transparentBackground true > color #4-6 lightgrey > save 200508_a_AP-comp_1.png width 600 height 950 transparentBackground true > show #!1 models > hide #!2 models > save 200508_b_AP-comp_1.png width 600 height 950 transparentBackground true > show #!2 models > save 200508_ab_AP-comp_1.png width 600 height 950 transparentBackground true > graphics silhouettes width 3 > save 200508_ab_AP-comp_1.png width 600 height 950 transparentBackground true > hide #!2 models > save 200508_b_AP-comp_1.png width 600 height 950 transparentBackground true > show #!2 models > hide #!1 models > save 200508_a_AP-comp_1.png width 600 height 950 transparentBackground true > save /home/caillan/rqcH-project/figures/chimerax-sessions/200508_A-P-tRNA- > comparison_f2_2.cxs opened ChimeraX session > open /home/caillan/rqcH-project/figures/chimerax- > sessions/200506_cl1-4-6_comparison_4.cxs Unable to restore all of session; missing bundle: ChimeraX-Std-Commands > close session > open /home/caillan/Downloads/run_class001.mrc Opened run_class001.mrc, grid size 120,120,120, pixel 2.46, shown at level 0.0736, step 1, values float32 > volume #1 level 0.02209 > volume #1 level 0.05641 > volume #1 level 0.05086 > volume #1 level 0.02865 > volume #1 level 0.03875 > volume #1 level 0.04985 > volume #1 level 0.02159 > lighting soft > volume #1 level 0.03269 > close session > open /home/caillan/chimera/200506_tRNA-comparison.png Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF, I, RGB) > open /home/caillan/rqcH-project/maps/isolated-densities/lpf-7A_LocFilt_EPA- > cl1_state-a-1_50S-only.mrc /home/caillan/rqcH-project/maps/isolated- > densities/lpf-6A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc /home/caillan/rqcH- > project/maps/isolated-densities/lpf-6A_LocFilt_EPA-cl4_state-b_50S-only.mrc Opened lpf-7A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0123, step 2, values float32 Opened lpf-6A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0127, step 2, values float32 Opened lpf-6A_LocFilt_EPA-cl4_state-b_50S-only.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0119, step 2, values float32 > fitmap #1 inMap #2 Fit map lpf-7A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc in map lpf-6A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc using 92599 points correlation = 0.9914, correlation about mean = 0.7286, overlap = 22.66 steps = 40, shift = 0.00795, angle = 0.00811 degrees Position of lpf-7A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc (#1) relative to lpf-6A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc (#2) coordinates: Matrix rotation and translation 0.99999999 -0.00001074 -0.00011595 0.02309979 0.00001073 1.00000000 -0.00008053 0.01138992 0.00011595 0.00008053 0.99999999 -0.02532017 Axis 0.56877640 -0.81899207 0.07579839 Axis point 219.62024871 0.00000000 189.93059860 Rotation angle (degrees) 0.00811184 Shift along axis 0.00189114 > fitmap #3 inMap #2 Fit map lpf-6A_LocFilt_EPA-cl4_state-b_50S-only.mrc in map lpf-6A_LocFilt_EPA- cl1_state-a-1_50S-only.mrc using 92598 points correlation = 0.9921, correlation about mean = 0.7642, overlap = 21.91 steps = 64, shift = 0.124, angle = 0.895 degrees Position of lpf-6A_LocFilt_EPA-cl4_state-b_50S-only.mrc (#3) relative to lpf-6A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc (#2) coordinates: Matrix rotation and translation 0.99987923 0.00050612 -0.01553285 2.60203871 -0.00048219 0.99999869 0.00154430 -0.17255638 0.01553361 -0.00153662 0.99987817 -2.43190873 Axis -0.09863820 -0.99462019 -0.03164142 Axis point 157.87815967 0.00000000 166.23955957 Rotation angle (degrees) 0.89483890 Shift along axis -0.00808330 > hide #!1 models > hide #!2 models > hide #!3 models > open /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 #4 --- 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 > open /home/caillan/rqcH-project/modelling/EPA- > cl4_modelling/200408_cl4-model-cl1-aligned.pdb Chain information for 200408_cl4-model-cl1-aligned.pdb #5 --- 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 > hide atoms > color #4/0 darkviolet > color #4/1 gold > color #4/2 skyblue > color #4/A grey > name #4/A:1085-1162 cl1-stalk-base ""cl1-stalk-base"": invalid atom specifier > name cl1-stalk-base #4/A:1085-1162 > name cl4-stalk-base #5/A:1085-1162 > hide #4,5 cartoons > show #4,5:0 cartoons > hide #!4 models > show #!4 models > show #4:0 cartoons > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #4.1 models > show #4.1 models > show #4/0 cartoons > view matrix camera > -0.38487,0.41629,0.82376,487.89,0.90318,0.35367,0.24326,298.87,-0.19007,0.83763,-0.5121,34.792 > view name 3comparison-density-1700-1150 > show #4/1,2 cartoons > show #4/K cartoons > show cl1-stalk-base cartoons > color #4/K lightyellow > color #4/K tan > graphics silhouettes width 1 > graphics silhouettes width 2 > cartoon style width 2.5 > cartoon style width 2.5 thickness 1 > cartoon style modeHelix tube > save /home/caillan/rqcH-project/figures/chimerax- > sessions/200509_cl1-4_comparison_1-0-rc_1.cxs > hide #!4 models > show #5/0-2 cartoons > color #5/0 pink > show cl4-stalk-base cartoons > color #5/K pink > color #5/K tan > show #5/K tan Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #5/K cartoons > color cl4-stalk-base lightgrey > view list Named views: 3comparison-density-1700-1150 > view 3comparison-density-1700-1150 > cartoon style width 2.5 thickness 1.5 > cartoon style width 2.5 thickness 1 > cartoon style width 3 thickness 1 > cartoon style width 2.5 thickness 1 > color #5/2 lightturquoie Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #5/2 paleturquoie Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #5/2 paleturquoise > hide #5.1 models > hide #4.1 models > show #!1 models > show #!2 models > hide #!2 models > volume #1 level 0.009501 > volume #1 step 1 > volume #2 step 1 > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > volume #2 level 0.01143 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > volume #3 level 0.008551 > volume #3 step 1 > volume #3 level 0.008 > volume #3 level 0.008988 > volume #3 level 0.009 > save /home/caillan/rqcH-project/figures/chimerax- > sessions/200509_cl1-4_comparison_1-0-rc_2.cxs opened ChimeraX session > open /home/caillan/rqcH-project/maps/isolated-densities/lpf-7A_LocFilt_EPA- > cl4_state-b_50S-only.mrc Opened lpf-7A_LocFilt_EPA-cl4_state-b_50S-only.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0117, step 2, values float32 > fitmap #6 inMap #3 Fit map lpf-7A_LocFilt_EPA-cl4_state-b_50S-only.mrc in map lpf-6A_LocFilt_EPA- cl4_state-b_50S-only.mrc using 92589 points correlation = 0.9959, correlation about mean = 0.8389, overlap = 19.97 steps = 56, shift = 0.113, angle = 0.901 degrees Position of lpf-7A_LocFilt_EPA-cl4_state-b_50S-only.mrc (#6) relative to lpf-6A_LocFilt_EPA-cl4_state-b_50S-only.mrc (#3) coordinates: Matrix rotation and translation 0.99999999 0.00010239 -0.00010907 0.00133931 -0.00010239 0.99999999 0.00001364 0.01275417 0.00010907 -0.00001363 0.99999999 -0.00711808 Axis -0.09077000 -0.72608334 -0.68158916 Axis point 93.57004143 0.00000000 8.49908989 Rotation angle (degrees) 0.00860710 Shift along axis -0.00453055 > volume #6 level 0.09 > volume #6 level 0.009 > volume #6 color #01010001 > volume #6 step 1 > volume #6 level 0.0085 > close #2-3 > save /home/caillan/rqcH-project/figures/chimerax- > sessions/200509_cl1-4_comparison_1-0-rc_3.cxs > view list Named views: 3comparison-density-1700-1150 > view 3comparison-density-1700-1150 > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > color #5/K bisque > hide #!4 models > view 3comparison-density-1700-1150 > view 3comparison-density-1700-1150 > save /home/caillan/rqcH-project/figures/chimerax- > sessions/200509_cl1-4_comparison_1-0-rc_4.cxs opened ChimeraX session > open /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 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 > 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 #6 inMap #3 Fit map lpf-7A_LocFilt_EPA-cl4_state-b_50S-only.mrc in map LocFilt_EPA-cl6_E- tRNA_job107.mrc using 1408740 points correlation = 0.9367, correlation about mean = 0.5136, overlap = 233.8 steps = 44, shift = 0.0399, angle = 0.0799 degrees Position of lpf-7A_LocFilt_EPA-cl4_state-b_50S-only.mrc (#6) relative to LocFilt_EPA-cl6_E-tRNA_job107.mrc (#3) coordinates: Matrix rotation and translation 0.99754592 0.04880371 -0.05020290 0.69058333 -0.04938272 0.99872622 -0.01035763 10.43059508 0.04963346 0.01281137 0.99868533 -10.45232374 Axis 0.16324018 -0.70341008 -0.69178530 Axis point 210.59067298 0.00000000 3.44033678 Rotation angle (degrees) 4.06947123 Shift along axis 0.00650910 > hide #!6 models > show #!6 models > fitmap #6 inMap #1 Fit map lpf-7A_LocFilt_EPA-cl4_state-b_50S-only.mrc in map lpf-7A_LocFilt_EPA- cl1_state-a-1_50S-only.mrc using 1408740 points correlation = 0.991, correlation about mean = 0.8512, overlap = 230.1 steps = 60, shift = 0.0529, angle = 0.0991 degrees Position of lpf-7A_LocFilt_EPA-cl4_state-b_50S-only.mrc (#6) relative to lpf-7A_LocFilt_EPA-cl1_state-a-1_50S-only.mrc (#1) coordinates: Matrix rotation and translation 0.99987961 0.00099256 -0.01548485 2.52009846 -0.00096953 0.99999841 0.00149489 -0.08835160 0.01548631 -0.00147970 0.99987898 -2.42844932 Axis -0.09541416 -0.99344606 -0.06293694 Axis point 158.07413248 0.00000000 161.51802934 Rotation angle (degrees) 0.89314813 Shift along axis 0.00015863 > open /home/caillan/rqcH-project/maps/isolated-densities/lpf-7A_LocFilt_RqcH- > EPA-cl6_50S-only-copy.mrc Opened lpf-7A_LocFilt_RqcH-EPA-cl6_50S-only-copy.mrc, grid size 420,420,420, pixel 0.82, shown at level 0.0126, step 2, values float32 > fitmap #7 inMap #3 Fit map lpf-7A_LocFilt_RqcH-EPA-cl6_50S-only-copy.mrc in map LocFilt_EPA- cl6_E-tRNA_job107.mrc using 92585 points correlation = 0.9492, correlation about mean = 0.3537, overlap = 22.13 steps = 76, shift = 0.693, angle = 3.2 degrees Position of lpf-7A_LocFilt_RqcH-EPA-cl6_50S-only-copy.mrc (#7) relative to LocFilt_EPA-cl6_E-tRNA_job107.mrc (#3) coordinates: Matrix rotation and translation 0.99512436 0.09814743 -0.00972610 -14.49246910 -0.09830930 0.99499562 -0.01786037 19.88551762 0.00792448 0.01872945 0.99979318 -4.51663344 Axis 0.18239000 -0.08798321 -0.97928180 Axis point 194.29132724 157.36804463 0.00000000 Rotation angle (degrees) 5.75682251 Shift along axis 0.03018377 > volume #7 level 0.008471 > volume #7 level 0.009 > volume #7 color #01010001 > hide #!5 models > show #!5 models > hide #!5 models > hide #!6 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!3 models > close #2-3 > show #!6 models > hide #!6 models > hide #!7 models > show #!7 models > volume #7 step 1 > save /home/caillan/rqcH-project/figures/chimerax- > sessions/200509_cl1-4_comparison_1-0-rc_5.cxs > open /home/caillan/rqcH-project/modelling/rqcH-cl6-modelling/cl1-stalk-for- > comp.pdb /home/caillan/rqcH-project/modelling/rqcH- > cl6-modelling/200501_domains-fitted_1.pdb Chain information for cl1-stalk-for-comp.pdb #2 --- Chain | Description A | No description available K | No description available L | No description available Chain information for 200501_domains-fitted_1.pdb --- Chain | Description 3.1/0 | No description available 3.2/0 | No description available 3.3/0 | No description available 3.4/0 | No description available 3.5/0 | No description available > open /home/caillan/rqcH-project/modelling/aligned-pdbs/200428_cl4-AP-tRNA- > cl1-aligned.pdb Chain information for 200428_cl4-AP-tRNA-cl1-aligned.pdb #8 --- Chain | Description 2 | No description available > open /home/caillan/rqcH-project/maps/locally-filtered/rqcH- > pulldown/LocFilt_EPA-cl6_E-tRNA_job107.mrc 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 > open /home/caillan/rqcH-project/maps/locally-filtered/rqcH- > pulldown/LocFilt_EPA-cl1_state-a-1_ws08_job042.mrc 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 > fitmap #9 inMap #10 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 (#9) relative to LocFilt_EPA- cl1_state-a-1_ws08_job042.mrc (#10) 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 > hide #!3 models > show #!3 models > color #3 deeppink Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1543, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 111, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 122, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 24, in display self._customize_dialog(session, dialog) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 86, in _customize_dialog self._format_selected(session, dialog) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) See log for complete Python traceback. > cd /home/caillan/rqcH-project/figures Current working directory is: /home/caillan/Dropbox/rqcH-project/figures > save chimerax-sessions/200509_cl1-4_comparison_1-0-rc_6.cxs > fitmap #3 inMap #9 Fit molecules 200501_domains-fitted_1.pdb (#3.1), 200501_domains-fitted_1.pdb (#3.2), 200501_domains-fitted_1.pdb (#3.3), 200501_domains-fitted_1.pdb (#3.4), 200501_domains-fitted_1.pdb (#3.5) to map LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) using 3986 atoms average map value = 0.005588, steps = 92 shifted from previous position = 6.09 rotated from previous position = 3.55 degrees atoms outside contour = 3985, contour level = 0.013066 Position of 200501_domains-fitted_1.pdb (#3.1) relative to LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) coordinates: Matrix rotation and translation 0.99999884 -0.00043776 0.00145815 -0.17956066 0.00044874 0.99997153 -0.00753190 1.37620484 -0.00145481 0.00753254 0.99997057 -1.12395639 Axis 0.98017848 0.18953384 0.05768074 Axis point 0.00000000 150.07625513 181.64627706 Rotation angle (degrees) 0.44029601 Shift along axis 0.02000524 Position of 200501_domains-fitted_1.pdb (#3.2) relative to LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) coordinates: Matrix rotation and translation 0.99999884 -0.00043776 0.00145815 -0.17956066 0.00044874 0.99997153 -0.00753190 1.37620484 -0.00145481 0.00753254 0.99997057 -1.12395639 Axis 0.98017848 0.18953384 0.05768074 Axis point 0.00000000 150.07625513 181.64627706 Rotation angle (degrees) 0.44029601 Shift along axis 0.02000524 Position of 200501_domains-fitted_1.pdb (#3.3) relative to LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) coordinates: Matrix rotation and translation 0.99999884 -0.00043776 0.00145815 -0.17956066 0.00044874 0.99997153 -0.00753190 1.37620484 -0.00145481 0.00753254 0.99997057 -1.12395639 Axis 0.98017848 0.18953384 0.05768074 Axis point 0.00000000 150.07625513 181.64627706 Rotation angle (degrees) 0.44029601 Shift along axis 0.02000524 Position of 200501_domains-fitted_1.pdb (#3.4) relative to LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) coordinates: Matrix rotation and translation 0.99999884 -0.00043776 0.00145815 -0.17956066 0.00044874 0.99997153 -0.00753190 1.37620484 -0.00145481 0.00753254 0.99997057 -1.12395639 Axis 0.98017848 0.18953384 0.05768074 Axis point 0.00000000 150.07625513 181.64627706 Rotation angle (degrees) 0.44029601 Shift along axis 0.02000524 Position of 200501_domains-fitted_1.pdb (#3.5) relative to LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) coordinates: Matrix rotation and translation 0.99999884 -0.00043776 0.00145815 -0.17956066 0.00044874 0.99997153 -0.00753190 1.37620484 -0.00145481 0.00753254 0.99997057 -1.12395639 Axis 0.98017848 0.18953384 0.05768074 Axis point 0.00000000 150.07625513 181.64627706 Rotation angle (degrees) 0.44029601 Shift along axis 0.02000524 > fitmap #8 inMap #9 Fit molecule 200428_cl4-AP-tRNA-cl1-aligned.pdb (#8) to map LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) using 1603 atoms average map value = 0.008894, steps = 120 shifted from previous position = 3.29 rotated from previous position = 9.62 degrees atoms outside contour = 1456, contour level = 0.013066 Position of 200428_cl4-AP-tRNA-cl1-aligned.pdb (#8) relative to LocFilt_EPA- cl6_E-tRNA_job107.mrc (#9) coordinates: Matrix rotation and translation 0.99402751 0.01336019 0.10830888 -20.35413895 -0.00351445 0.99588206 -0.09059016 16.90227550 -0.10907317 0.08966847 0.98998112 8.01953589 Axis 0.63717957 0.76840370 -0.05964861 Axis point 55.97589943 0.00000000 188.30833040 Rotation angle (degrees) 8.13178420 Shift along axis -0.45982459 > hide #!10 models > hide #!9 models > show #!9 models > volume #9 level 0.01059 > volume #9 level 0.008849 > volume #9 level 0.006533 > fitmap #2 inMap #9 Fit molecule cl1-stalk-for-comp.pdb (#2) to map LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) using 3527 atoms average map value = 0.008718, steps = 140 shifted from previous position = 8.68 rotated from previous position = 14.2 degrees atoms outside contour = 1142, contour level = 0.0065335 Position of cl1-stalk-for-comp.pdb (#2) relative to LocFilt_EPA-cl6_E- tRNA_job107.mrc (#9) coordinates: Matrix rotation and translation 0.98357712 -0.18039977 0.00565440 51.53356898 0.18008508 0.97880459 -0.09752401 -7.50752394 0.01205875 0.09694066 0.99521711 -25.40568420 Axis 0.47471819 -0.01563400 0.87999899 Axis point 73.63932441 273.10608369 0.00000000 Rotation angle (degrees) 11.81903085 Shift along axis 2.22431913 > hide #!9 models > hide #8 models > show #8 models > hide #8#3.4-5#!2#!3.1-3 atoms > close #9-10 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1543, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 111, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 122, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 24, in display self._customize_dialog(session, dialog) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 86, in _customize_dialog self._format_selected(session, dialog) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) See log for complete Python traceback. 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 }}} " defect closed normal Input/Output duplicate all ChimeraX