#3438 closed defect (fixed)
Clipper: focal_set is None
Reported by: | Owned by: | Tristan Croll | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-04-03) Description This occurs when opening a .cxs file that includes ISOLDE settings, restraints etc. I'll drop Tristan an email too, in case he doesn't get to see these reports. Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/200616_TRPA1_0521_chimeraX_ISOLDE.cxs Error processing trigger "new frame": TypeError: object of type 'NoneType' has no len() File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/maps/mask_handler.py", line 160, in _update_mask update_origin = (len(self.coords) == 1) See log for complete Python traceback. Log from Wed Jun 17 12:21:37 2020 Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/200615_intermediate_results/volume_42_1_sharp_12_3p16_m90_0_20_fom_150.mrc Opened volume_42_1_sharp_12_3p16_m90_0_20_fom_150.mrc, grid size 150,150,150, pixel 1, shown at level 0.384, step 1, values float32 > volume #1 level 0.2678 > volume #1 level 0.1402 > volume #1 level 0.2022 > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/200615_intermediate_results/volume_20_1_mask_150.mrc Opened volume_20_1_mask_150.mrc, grid size 150,150,150, pixel 1, shown at level 1, step 1, values float32 > volume #2 style mesh > volume #2 level 0.7935 > volume #2 style surface > volume #2 style mesh > volume #2 level 0.5943 > open > /Users/rohoua/work/Genentech/TRPA1/180713_trpa1_noIP6/180820_results/volume_11_1_sharp10_m90_m90_40_fom.mrc Opened volume_11_1_sharp10_m90_m90_40_fom.mrc, grid size 256,256,256, pixel 1.3, shown at level 0.111, step 1, values float32 > select #3 2 models selected > volume #3 level 0.2114 > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > fitmap #3 inMap #1 Fit map volume_11_1_sharp10_m90_m90_40_fom.mrc in map volume_42_1_sharp_12_3p16_m90_0_20_fom_150.mrc using 17697 points correlation = 0.7246, correlation about mean = 0.1912, overlap = 1363 steps = 104, shift = 2.98, angle = 3.45 degrees Position of volume_11_1_sharp10_m90_m90_40_fom.mrc (#3) relative to volume_42_1_sharp_12_3p16_m90_0_20_fom_150.mrc (#1) coordinates: Matrix rotation and translation 0.87415844 0.48564084 -0.00000731 -151.24118657 -0.48564084 0.87415844 0.00001301 10.35028418 0.00001271 -0.00000782 1.00000000 -90.50686621 Axis -0.00002144 -0.00002061 -1.00000000 Axis point -55.64439978 297.00316866 0.00000000 Rotation angle (degrees) 29.05446695 Shift along axis 90.50989546 > ~select Nothing selected > volume #1,3 toggle > volume #3 level 0.1546 > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > volume #1,3 toggle > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_1/denmod_map.ccp4 Opened denmod_map.ccp4, grid size 150,150,150, pixel 1, shown at level 0.848, step 1, values float32 > volume #4 level 0.8303 > volume #4 level 0.3092 > volume #4 level 0.3874 > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/180820_results/generate3d_volume_11_11_1_map1_100.mrc Opened generate3d_volume_11_11_1_map1_100.mrc, grid size 100,100,100, pixel 1.3, shown at level 6.64, step 1, values float32 > hide #!4 models > volume #5 level 3.041 > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/180820_results/generate3d_volume_11_11_1_map2_128.mrc Opened generate3d_volume_11_11_1_map2_128.mrc, grid size 128,128,128, pixel 1.3, shown at level 5.36, step 1, values float32 > volume #5 level 5.096 > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_2/denmod_map.ccp4 Opened denmod_map.ccp4, grid size 97,97,114, pixel 1.3, shown at level 0.975, step 1, values float32 > volume #5 level 0.5145 > volume #5 level 0.5887 > volume #5 level 0.5145 > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_2/initial_map.ccp4 Opened initial_map.ccp4, grid size 97,97,114, pixel 1.3, shown at level 11.4, step 1, values float32 > volume #6 level 7.561 > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #6 level 8.473 > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > volume #5,6 toggle > close > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/ResolveCryoEM_3/denmod_map.mrc > name map File not found: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/ResolveCryoEM_3/denmod_map.mrc > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.mrc > name map File not found: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.mrc > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > open > /Users/rohoua/Documents/Publications/2020_TRPA1_agonist_3551/200518_deposition/dep_200609/6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb Chain information for 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb #2 --- Chain | Description A B C D | No description available > select #2 36026 atoms, 36422 bonds, 32 pseudobonds, 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > volume #1 level 0.4197 > fitmap #2 inMap #1 Fit molecule 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb (#2) to map denmod_map.ccp4 (#1) using 36026 atoms average map value = 0.03711, steps = 80 shifted from previous position = 4.75 rotated from previous position = 2.77 degrees atoms outside contour = 30856, contour level = 0.41968 Position of 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb (#2) relative to denmod_map.ccp4 (#1) coordinates: Matrix rotation and translation 0.87964263 -0.47455859 -0.03198433 23.05977282 0.47348315 0.88007014 -0.03592010 -136.25344599 0.04519465 0.01645281 0.99884270 -95.20572497 Axis 0.05497783 -0.08101769 0.99519524 Axis point 297.49122690 -17.30667646 0.00000000 Rotation angle (degrees) 28.44464059 Shift along axis -82.44156964 > fitmap #2 inMap #1 Fit molecule 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb (#2) to map denmod_map.ccp4 (#1) using 36026 atoms average map value = 0.03708, steps = 92 shifted from previous position = 3.46 rotated from previous position = 0.0143 degrees atoms outside contour = 30846, contour level = 0.41968 Position of 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb (#2) relative to denmod_map.ccp4 (#1) coordinates: Matrix rotation and translation 0.87963549 -0.47458576 -0.03177674 23.03991468 0.47350753 0.88005137 -0.03605826 -136.25244627 0.04507790 0.01667160 0.99884435 -95.22868498 Axis 0.05534993 -0.08067342 0.99520258 Axis point 297.43432710 -17.26557700 0.00000000 Rotation angle (degrees) 28.44609929 Shift along axis -82.50462435 > fitmap #2 inMap #1 Fit molecule 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb (#2) to map denmod_map.ccp4 (#1) using 36026 atoms average map value = 0.2501, steps = 72 shifted from previous position = 2.93 rotated from previous position = 2.72 degrees atoms outside contour = 24810, contour level = 0.41968 Position of 6pqq_S448-T1078_ali_lig_trim2_isolde4_moe2-coot-10_noremark.pdb (#2) relative to denmod_map.ccp4 (#1) coordinates: Matrix rotation and translation 0.87505919 -0.48400370 0.00343951 16.86500699 0.48401592 0.87503716 -0.00620973 -138.09349305 -0.00000416 0.00709866 0.99997480 -85.42761820 Axis 0.01374668 0.00355708 0.99989918 Axis point 275.91387940 -33.94623443 0.00000000 Rotation angle (degrees) 28.95081354 Shift along axis -85.67837765 > volume #1 level 0.2975 > delete /L,M,N,O > save /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1.pdb models #2 > open > /Users/rohoua/work/Genentech/TRPA1/180713_trpa1_noIP6/trpa1_0521_180820-coot-6-biomt- > nocryst1-moe2-coot-0.pdb Chain information for trpa1_0521_180820-coot-6-biomt-nocryst1-moe2-coot-0.pdb #3 --- Chain | Description A | No description available > delete #3/A > select #3 46 atoms, 50 bonds, 1 model selected > help save > save /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1.pdb models #2 > relModel #1 > save /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/L.pdb models #3 relModel > #1 > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > fitmap #3 inMap #1 Fit molecule trpa1_0521_180820-coot-6-biomt-nocryst1-moe2-coot-0.pdb (#3) to map denmod_map.ccp4 (#1) using 46 atoms average map value = 0.5761, steps = 72 shifted from previous position = 2.12 rotated from previous position = 4.73 degrees atoms outside contour = 17, contour level = 0.29746 Position of trpa1_0521_180820-coot-6-biomt-nocryst1-moe2-coot-0.pdb (#3) relative to denmod_map.ccp4 (#1) coordinates: Matrix rotation and translation -0.06521076 0.99182015 -0.10972853 -55.13023557 -0.99613820 -0.07118119 -0.05139975 265.79143086 -0.05878991 0.10595296 0.99263171 -91.47188726 Axis 0.07888040 -0.02553536 -0.99655699 Axis point 93.85902026 162.75327283 0.00000000 Rotation angle (degrees) 94.12198220 Shift along axis 80.02117402 > save /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/M.pdb models #3 relModel > #1 > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > fitmap #3 inMap #1 Fit molecule trpa1_0521_180820-coot-6-biomt-nocryst1-moe2-coot-0.pdb (#3) to map denmod_map.ccp4 (#1) using 46 atoms average map value = 0.5757, steps = 68 shifted from previous position = 0.57 rotated from previous position = 22.8 degrees atoms outside contour = 17, contour level = 0.29746 Position of trpa1_0521_180820-coot-6-biomt-nocryst1-moe2-coot-0.pdb (#3) relative to denmod_map.ccp4 (#1) coordinates: Matrix rotation and translation -0.99598077 -0.07203585 -0.05322720 266.20950019 0.06574342 -0.99155835 0.11175800 216.19867890 -0.06082846 0.10780949 0.99230893 -91.38699268 Axis -0.02860307 0.05506351 0.99807308 Axis point 127.97009006 115.18519011 0.00000000 Rotation angle (degrees) 176.04214728 Shift along axis -86.92064867 > save /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/N.pdb models #3 relModel > #1 > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > fitmap #3 inMap #1 Fit molecule trpa1_0521_180820-coot-6-biomt-nocryst1-moe2-coot-0.pdb (#3) to map denmod_map.ccp4 (#1) using 46 atoms average map value = 0.5738, steps = 64 shifted from previous position = 1.54 rotated from previous position = 37.7 degrees atoms outside contour = 18, contour level = 0.29746 Position of trpa1_0521_180820-coot-6-biomt-nocryst1-moe2-coot-0.pdb (#3) relative to denmod_map.ccp4 (#1) coordinates: Matrix rotation and translation 0.06653218 -0.99154961 0.11136808 216.15789604 0.99586737 0.07290475 0.05415786 -104.96084425 -0.06181947 0.10730459 0.99230241 -91.14407164 Axis 0.02663120 0.08678224 0.99587129 Axis point 161.20852554 68.76252222 0.00000000 Rotation angle (degrees) 86.22321139 Shift along axis -94.11995721 > save /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/O.pdb models #3 relModel > #1 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521.pdb Chain information for TRPA1_0521.pdb #4 --- Chain | Description A B C D | No description available > hide #!2 models > hide #!3 models > close > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1.pdb name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 0 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 no atoms specified for zone > close > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1.pdb name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 0 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 no atoms specified for zone > close > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1.pdb name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 0 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 no atoms specified for zone > hide #!2 models > select :LXY Nothing selected > select /L Nothing selected > show /L > close > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521.pdb name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 184 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 > volume #10 step 1 level 0.126 color rgb(255,255,153) > transparency #10 70 target s > color :LXY byhetero > volume gaussian #2 sDev 1.8 modelId 100 > volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20 > close #100 > volume #20 step 1 level 0.051 color #9999CC region 1,1,172,324,324,212 > transparency #20 90 target s executed TRPA1_0521_setup.cxc > volume #10 level 0.2181 > volume #10 level 0.4944 > view /M > volume #10 level 0.4 > view > volume #20 level -0.002426 > close > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521.pdb name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 184 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 > volume #10 step 1 level 0.5 color rgb(255,255,153) > transparency #10 70 target s > color :LXY byhetero > volume gaussian #2 sDev 1.8 modelId 100 > volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20 > close #100 > volume #20 step 1 level 0.051 color #9999CC > transparency #20 90 target s executed TRPA1_0521_setup.cxc > volume #20 level 0.02295 > volume #2 level 0.3652 > volume #20 step 1 level 0.02 color #9999CC region 1,1,100,99,99,114 > volume #20 step 1 level 0.02 color #9999CC region 1,1,90,99,99,114 > volume #20 step 1 level 0.02 color #9999CC region 1,1,70,99,99,114 > volume #20 step 1 level 0.02 color #9999CC region 1,1,60,99,99,114 > volume #20 step 1 level 0.02 color #9999CC region 1,1,65,99,99,114 > transparency #20 90 target s > close > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521.pdb name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 184 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 > volume #10 step 1 level 0.5 color rgb(255,255,153) > transparency #10 70 target s > color :LXY byhetero > volume gaussian #2 sDev 1.8 modelId 100 > volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20 > close #100 > volume #20 step 1 level 0.02 color #9999CC region 1,1,65,99,99,114 > transparency #20 90 target s executed TRPA1_0521_setup.cxc > close > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521-coot-1.pdb > name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 184 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 > volume #10 step 1 level 0.5 color rgb(255,255,153) > transparency #10 70 target s > color :LXY byhetero > volume gaussian #2 sDev 1.8 modelId 100 > volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20 > close #100 > volume #20 step 1 level 0.02 color #9999CC region 1,1,65,99,99,114 > transparency #20 90 target s executed TRPA1_0521_setup.cxc > toolshed show Shell > toolshed show ISOLDE > set selectionWidth 4 Chain information for model --- Chain | Description 1.2/A 1.2/B 1.2/C 1.2/D | No description available Done loading forcefield > close Deleting atomic symmetry model... > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521_setup.cxc > cd /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 Current working directory is: /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521 > windowsize 1600 1600 > open /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521-coot-1.pdb > name model Chain information for model #1 --- Chain | Description A B C D | No description available > open > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/phenix/ResolveCryoEM_3/denmod_map.ccp4 > name map Opened denmod_map.ccp4, grid size 99,99,114, pixel 1.26, shown at level 1.06, step 1, values float32 > set bgColor white > set silhouettes true > lighting full > lighting shadows false > name ank #1:start-618 > name linker #1:619-701 > name preS1 #1:702-715 > name helixS1 #1:715-739 > name helixS2 #1:768-783 > name helixS3 #1:804-822 > name helixS4 #1:830-853 > name S4S5Linker #1:854-875 > name helixS5 #1:876-891 > name poreH1 #1:901-911 > name poreH2 #1:919-928 > name helixS6 #1:933-967 > name TRPlike #1:972-990 > name betaSheet #1:991-1031 > name coiledCoil #1:1032-end > name membraneDomain #1:715-967 > color #1,3/A rgb(212,130,97) > color #1,3/D rgb(137,187,206) > color #1,3/C rgb(248,238,166) > color #1,3/B rgb(147,186,128) > color :LXY gold > style :LXY ball Changed 184 atom styles > color zone #2 near #1 distance 6.0 > surface dust #2 > ~show (#1 & ~ :LXY) > volume #2 step 1 level 0.3 color #9999CC > display #2 > volume #2 symmetry C4 > volume zone #2 nearAtoms #1:LXY range 1.5 newMap true modelId 10 > volume #10 step 1 level 0.5 color rgb(255,255,153) > transparency #10 70 target s > color :LXY byhetero > volume gaussian #2 sDev 1.8 modelId 100 > volume zone #100 nearAtoms #1 range 4.0 invert true newMap true modelId 20 > close #100 > volume #20 step 1 level 0.02 color #9999CC region 1,1,65,99,99,114 > transparency #20 90 target s executed TRPA1_0521_setup.cxc > toolshed show ISOLDE > set selectionWidth 4 Chain information for model --- Chain | Description 1.2/A 1.2/B 1.2/C 1.2/D | No description available Done loading forcefield No template found for residue A621 (CYS) Adding hydrogens Summary of feedback from adding hydrogens to model #1.2 --- warnings | Not adding hydrogens to /A ASP 468 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A ILE 469 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A SER 470 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 471 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 473 CB because it is missing heavy-atom bond partners 67 messages similar to the above omitted notes | No usable SEQRES records for model (#1.2) chain A; guessing termini instead No usable SEQRES records for model (#1.2) chain B; guessing termini instead No usable SEQRES records for model (#1.2) chain C; guessing termini instead No usable SEQRES records for model (#1.2) chain D; guessing termini instead Chain-initial residues that are actual N termini: /A SER 448, /B SER 448, /C SER 448, /D SER 448 Chain-initial residues that are not actual N termini: /A LEU 683, /A ASN 766, /A ILE 803, /A SER 1039, /B LEU 683, /B ASN 766, /B ILE 803, /B SER 1039, /C LEU 683, /C ASN 766, /C ILE 803, /C SER 1039, /D LEU 683, /D ASN 766, /D ILE 803, /D SER 1039 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A THR 1078, /A CYS 665, /A ASN 753, /A GLU 788, /A PRO 1007, /B THR 1078, /B CYS 665, /B ASN 753, /B GLU 788, /B PRO 1007, /C THR 1078, /C CYS 665, /C ASN 753, /C GLU 788, /C PRO 1007, /D THR 1078, /D CYS 665, /D ASN 753, /D GLU 788, /D PRO 1007 1975 hydrogen bonds Adding 'H' to /B ASN 766 Adding 'H' to /D ASN 766 /A THR 1078 is not terminus, removing H atom from 'C' /A CYS 665 is not terminus, removing H atom from 'C' /A ASN 753 is not terminus, removing H atom from 'C' /A GLU 788 is not terminus, removing H atom from 'C' /A PRO 1007 is not terminus, removing H atom from 'C' 15 messages similar to the above omitted 20 hydrogens added > select clear > isolde set timeStepsPerGuiUpdate 10 > select clear > select clear > view /L > hbonds 2098 hydrogen bonds found > save > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521-coot-1_isolde01.pdb > models #1.1 No structures to save > save > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521-coot-1_isolde01.pdb > models #1.2 > help volume > volume #1.1.1.1 subdivideSurface true subdivisionLevels 2 > volume #1.1.1.1 subdivideSurface false subdivisionLevels 2 > volume #1.1.1.1 subdivideSurface true subdivisionLevels 1 > volume #1.1.1.1 subdivideSurface true subdivisionLevels 1 squareMesh true > volume #1.1.1.1 subdivideSurface true subdivisionLevels 2 squareMesh true QWidget::repaint: Recursive repaint detected > set bgColor black > select clear Invalid "squareMesh" argument: Expected true or false (or 1 or 0) > ~hbonds > volume #1.1.1.1 level 0.3494 > select clear > volume #1.1.1.1 level 0.2374 > select clear > volume #1.1.1.1 level 0.4215 > volume #1.1.1.1 level 0.5896 > select clear > help hbonds > hbonds 2095 hydrogen bonds found > select clear > ~hbonds > hbonds 2094 hydrogen bonds found > ~hbonds > volume #1.1.1.1 level 0.4055 > hbonds 2096 hydrogen bonds found > volume #1.1.1.1 level 0.6808 > volume #1.1.1.1 level 0.3683 > volume #1.1.1.1 level 0.2195 > ~hbonds > volume #1.1.1.1 level 0.6138 > select clear > select clear > hbonds 2100 hydrogen bonds found Traceback (most recent call last): File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update self._update_graphics() File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords v[i] = a.pb_scene_coord File "cymol.pyx", line 242, in chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__ File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py", line 122, in __mul__ raise TypeError('Cannot multiply Place times "%s"' % str(p)) TypeError: Cannot multiply Place times "None" Error processing trigger "changes": TypeError: Cannot multiply Place times "None" File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py", line 122, in __mul__ raise TypeError('Cannot multiply Place times "%s"' % str(p)) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update self._update_graphics() File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords v[i] = a.pb_scene_coord File "cymol.pyx", line 242, in chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__ File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py", line 122, in __mul__ raise TypeError('Cannot multiply Place times "%s"' % str(p)) TypeError: Cannot multiply Place times "None" Error processing trigger "changes": TypeError: Cannot multiply Place times "None" File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/geometry/place.py", line 122, in __mul__ raise TypeError('Cannot multiply Place times "%s"' % str(p)) See log for complete Python traceback. > ~hbonds > save > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521-coot-1_isolde02.pdb > models #1.2 > select clear Unable to flip peptide bond after 50 rounds. Giving up. > select clear > volume #1.1.1.1 level 0.3589 > view /L > save > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/TRPA1_0521-coot-1_isolde03.pdb > models #1.2 > save2 > /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/200616_TRPA1_0521_chimeraX_ISOLDE.cxs Error processing trigger "end restore session": AttributeError: 'SymmetryManager' object has no attribute '_unit_cell' File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 867, in unit_cell return self._unit_cell See log for complete Python traceback. Summary of feedback from opening /Users/rohoua/work/Genentech/TRPA1/TRPA1_0521/200616_TRPA1_0521_chimeraX_ISOLDE.cxs --- warning | restore_snapshot for "RotamerRestraintMgr" returned None notes | Traceback (most recent call last): File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/delayed_reaction.py", line 52, in callback self.ff(*self.ff_args) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/maps/map_handler_base.py", line 165, in _use_fast_thread_result self._set_surface(va, na, ta, hidden_edges) File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 2125, in _set_surface self.set_geometry(va, na, ta) File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 653, in set_geometry art() File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/maps/mask_handler.py", line 275, in __call__ self.set_surface_mask() File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/maps/mask_handler.py", line 295, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/maps/mask_handler.py", line 170, in get_vertex_mask self._update_mask() File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/maps/mask_handler.py", line 160, in _update_mask update_origin = (len(self.coords) == 1) TypeError: object of type 'NoneType' has no len() Traceback (most recent call last): File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1134, in _end_restore_session_cb self.add_model(self.structure) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 594, in add_model self.spotlight_mode = spotlight_mode File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 243, in __setattr__ super(Drawing, self).__setattr__(key, value) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 820, in spotlight_mode if self.atomic_symmetry_model is not None: File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 842, in atomic_symmetry_model return AtomicSymmetryModel(self, self.spotlight_radius, live=self.spotlight_mode, debug=self._debug) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1197, in __init__ self.live_scrolling = live File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 243, in __setattr__ super(Drawing, self).__setattr__(key, value) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1393, in live_scrolling self._update_box() File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1455, in _update_box symops = self._current_symops = self.unit_cell.all_symops_in_box(box_corner_xyz, grid_dim, True, self._sym_search_frequency) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1220, in unit_cell return self.manager.unit_cell File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 867, in unit_cell return self._unit_cell AttributeError: 'SymmetryManager' object has no attribute '_unit_cell' opened ChimeraX session Traceback (most recent call last): File "/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1611, in _model_changed_cb self._update_sym_coords() File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1617, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) TypeError: 'NoneType' object is not subscriptable Error processing trigger "atoms changed": TypeError: 'NoneType' object is not subscriptable File "/Users/rohoua/Library/Application Support/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py", line 1617, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.19 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650 OpenGL vendor: Intel Inc.
Change History (4)
comment:2 by , 5 years ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Clipper: focal_set is None |
comment:3 by , 5 years ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
Hi Alexis,
Glad Tristan could help you. You might also consider upgrading to the 1.0 release whenever Tristan puts out a compatible ISOLDE, since some of the errors I see in the log are fixed in 1.0.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
comment:4 by , 5 years ago
In the home stretch on the new release front (barring any unforeseen surprises)!
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