Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3438 closed defect (fixed)

Clipper: focal_set is None

Reported by: rohou.alexis@… 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)

in reply to:  1 ; comment:1 by rohoua@…, 5 years ago 

This was fixed by upgrading to latest Clipper from the toolshed, as
suggested by Tristan.

On Wed, Jun 24, 2020 at 5:58 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:2 by Eric Pettersen, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper: focal_set is None

comment:3 by Eric Pettersen, 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 Tristan Croll, 5 years ago

In the home stretch on the new release front (barring any unforeseen surprises)!

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