![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#4518 closed defect (fixed)
'Model' object has no attribute 'is_clip_cap'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202104140542 (2021-04-14 05:42:12 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.dev202104140542 (2021-04-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/gmontoya/Documents/Cas_phi/flexiblemaps/maps500.cxs format
> session
Opened J503_28_sharpened_map.ccp4 as #2, grid size 256,256,256, pixel 0.832,
shown at level 4.9, step 1, values float32
Opened J504.mrc as #3, grid size 256,256,256, pixel 0.832, shown at level
0.175, step 1, values float32
Opened J505.mrc as #4, grid size 256,256,256, pixel 0.832, shown at level
0.235, step 1, values float32
Opened J506.mrc as #5, grid size 256,256,256, pixel 0.832, shown at level
0.36, step 1, values float32
Log from Wed Apr 14 14:16:17 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/gmontoya/Documents/Cas_phi/Final_maps/maps2.cxs format session
Log from Thu Apr 1 10:56:17 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/gmontoya/Documents/Cas_phi/similar_proteins/mapgen.cxs format
> session
Log from Wed Mar 31 10:31:54 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/gmontoya/Documents/Cas_phi/Final_maps/fig3.cxs format session
Log from Sat Mar 27 19:22:45 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/gmontoya/Documents/Cas_phi/Final_maps/J503_28_sharpened_map.ccp4
> format ccp4
Opened J503_28_sharpened_map.ccp4, grid size 256,256,256, pixel 0.832, shown
at level 1.67, step 1, values float32
> close session
> open /Users/gmontoya/Documents/Cas_phi/Final_maps/test-coot-0.pdb format pdb
Summary of feedback from opening
/Users/gmontoya/Documents/Cas_phi/Final_maps/test-coot-0.pdb
---
warning | Ignored bad PDB record found on line 6952
Chain information for test-coot-0.pdb #1
---
Chain | Description
A | No description available
C | No description available
E | No description available
F | No description available
G | No description available
> hide atoms
> show cartoons
> select /F
919 atoms, 1027 bonds, 43 residues, 1 model selected
> color sel orange
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> color sel grey
> select /G
186 atoms, 208 bonds, 9 residues, 1 model selected
> color sel lime green
> select /B
1 atom, 1 residue, 1 model selected
> color sel yellow
> select /C
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel red
> select /A:1-51
336 atoms, 340 bonds, 44 residues, 1 model selected
> color sel ivory
> select /A:52-70
146 atoms, 150 bonds, 19 residues, 1 model selected
> color sel cyan
> select /A:71-197
771 atoms, 789 bonds, 2 pseudobonds, 108 residues, 2 models selected
> color sel wheat
> select /A:198-383
1364 atoms, 1402 bonds, 186 residues, 1 model selected
> color sel cyan
> select /A:384-444
436 atoms, 441 bonds, 61 residues, 1 model selected
> color sel plum
> select /A:445-474
251 atoms, 252 bonds, 30 residues, 1 model selected
> color sel slate blue
> select /A:475-561
632 atoms, 641 bonds, 87 residues, 1 model selected
> color sel pale green
> select /A:562-609
383 atoms, 386 bonds, 48 residues, 1 model selected
> color sel slate blue
> select /A:610-621
93 atoms, 92 bonds, 12 residues, 1 model selected
> color sel plum
> select /A:622-647
219 atoms, 223 bonds, 26 residues, 1 model selected
> color sel dark orchid
> select /A:648-729
582 atoms, 597 bonds, 82 residues, 1 model selected
> color sel plum
> hide pseudobonds
> dssp
> select /B
1 atom, 1 residue, 1 model selected
> show sel atoms
> select /F
919 atoms, 1027 bonds, 43 residues, 1 model selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 919 atom styles
> show sel atoms
> select /G
186 atoms, 208 bonds, 9 residues, 1 model selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 186 atom styles
> show sel atoms
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 486 atom styles
> show sel atoms
> select /C
41 atoms, 45 bonds, 2 residues, 1 model selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 41 atom styles
> show sel atoms
> cartoon style nucleic width 1 thickness 0.5
> lighting multiShadow 600
> set bgColor white
> graphics silhouettes width 1
> lighting model #1 depthCue true
> graphics silhouettes true
> lighting soft
> select clear
> select /A:539-540
10 atoms, 9 bonds, 2 residues, 1 model selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 2 items
> select clear
> select /A:544-546
15 atoms, 14 bonds, 3 residues, 1 model selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 3 items
> select clear
> select /G:5-7
59 atoms, 64 bonds, 3 residues, 1 model selected
> color sel orchid
> ui tool show "Color Actions"
> color sel medium orchid
> select clear
> select /G:19-21
Nothing selected
> color sel medium orchid
> select /E:19-21
64 atoms, 72 bonds, 3 residues, 1 model selected
> color sel medium orchid
> select clear
> open /Users/gmontoya/Documents/Cas_phi/Final_maps/J503_28_sharpened_map.ccp4
Opened J503_28_sharpened_map.ccp4, grid size 256,256,256, pixel 0.832, shown
at level 1.67, step 1, values float32
> volume #2 level 4.898
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> surface #2 dust
Expected a keyword
> surfacedust
Unknown command: surfacedust
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> surface dust #2
> hide #!2 models
> select /S
Nothing selected
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> hide sel cartoons
> volume zone #2 nearAtoms #1/F,E,G,C range 2 newMap false
> show #!2 models
> select /F:44
20 atoms, 21 bonds, 1 residue, 1 model selected
> volume zone #2 nearAtoms sel range 5 newMap true
> show #!2 models
> volume zone #2 nearAtoms sel range 2 newMap true
> volume #3 level 5.883
> hide #!4 models
> hide #!3 models
> show #!2 models
> select clear
> volume zone #2 nearAtoms #1/F,E,G,C,B range 2 newMap false
> close #4
> close #3
> volume #2 level 6.962
> volume #2 level 6.704
> volume #2 level 8
> volume #2 level 6.6
> volume #2 level 6.7
> volume #2 level 6.75
> volume #2 level 6.8
> surface dust #2
> surface dust #2
> volume zone #2 nearAtoms #1/F,E,G,C,B range 2 newMap false
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> show sel cartoons
> select clear
> hide #!2 models
> save /Users/gmontoya/Documents/Cas_phi/Fig1_d1.png width 2800 height 2400
> supersample 4 transparentBackground true
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> hide sel cartoons
> show #!2 models
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> volume #2 level 7
> volume #2 level 7.8
> volume #2 level 4.575
> select up
6846 atoms, 7146 bonds, 2 pseudobonds, 782 residues, 2 models selected
> select clear
> save /Users/gmontoya/Documents/Cas_phi/Fig1d2.png width 2800 height 2400
> supersample 4 transparentBackground true
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> show sel cartoons
> hide #!2 models
> select clear
> lighting model #1 depthCue true
> save /Users/gmontoya/Documents/Cas_phi/Fig1d4.png width 2800 height 2400
> supersample 4 transparentBackground true
> save /Users/gmontoya/Documents/Cas_phi/Final_maps/fig1_final.cxs
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> select clear
> view
> ui tool show "Side View"
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> color zone #1.2 near #1 distance 3
> lighting soft
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> color sel white
> select clear
> lighting multiShadow 60
> lighting multiShadow 10
> lighting multiShadow 100
> lighting multiShadow 600
> lighting multiShadow 60
> save /Users/gmontoya/Documents/Cas_phi/Fig2a.png width 2800 height 2400
> supersample 4 transparentBackground true
> hide #!2 models
> show #!2 models
> hide #1.1 models
> hide #1.2 models
> ui tool show "Side View"
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> volume zone #2 nearAtoms #1/A range 2 newMap false
> show #2.1 models
> nucleotides fill
> style nucleic stick
Changed 1632 atom styles
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> color sel grey
> select clear
> select clear
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> style sel stick
Changed 5213 atom styles
> style sel stick
Changed 5213 atom styles
> show sel atoms
> hide sel cartoons
> select clear
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> hide #!2 models
> select clear
> select /A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byelement
> select clear
> color sel byhetero
> color sel byhetero
> select /A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> color sel byhetero
> select clear
> select clear
> select /A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select /A:624
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select /A:627
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> select /A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select /A:642
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select clear
> select /A:557
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /A:559
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select /A:630
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> color sel byhetero
> select clear
> select /A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select clear
> select /A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:643@ca,cb,cg dark orchid
Expected a keyword
> select clear
> select /A:643@ca,cb,cg color dark orchid
Expected a keyword
> select /A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
> color /A:643@ca, cb dark orchid
> color /A:643@ca, cb, cg dark orchid
> select clear
> select clear
> color /A:643@ca, cb, cd, cz, cg dark orchid
> select /F
919 atoms, 1027 bonds, 43 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 919 atom styles
> color sel byhetero
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 486 atom styles
> color sel byhetero
> select /C
41 atoms, 45 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 41 atom styles
> color sel byhetero
> select clear
> select /A:538
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> save /Users/gmontoya/Documents/Cas_phi/fig3a.png width 3000 height 2574
> supersample 4 transparentBackground true
> show #!2 models
> hide #!2 models
> show #1.2 models
> hide #!1.2 models
> show #!2 models
> hide #!2 models
> hbonds
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A PRO 729 N
688 hydrogen bonds found
> ~hbonds
> ui tool show H-Bonds
> hbonds reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A PRO 729 N
688 hydrogen bonds found
> ~hbonds
> style stick
Changed 6846 atom styles
> hide atoms
> show atoms
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> hide sel atoms
> select clear
> cartoon style nucleic width 0.7 thickness 0.5
> cartoon style nucleic width 0.6 thickness 0.5
> cartoon style nucleic width 0.5 thickness 0.5
> select /F:24-40
368 atoms, 412 bonds, 17 residues, 1 model selected
> hide sel atoms
> undo
> select clear
> select /F:27-28
43 atoms, 47 bonds, 2 residues, 1 model selected
> select /F:27-29
63 atoms, 69 bonds, 3 residues, 1 model selected
> select /F:26-28
65 atoms, 72 bonds, 3 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> undo
> undo
> select clear
> select clear
> Sel /A:624,627,628,538,630,643,642,557,559
Unknown command: Sel /A:624,627,628,538,630,643,642,557,559
> select /A:624,627,628,538,630,643,642,557,559
73 atoms, 67 bonds, 9 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 73 atom styles
> color sel byhetero
> select clear
> select clear
> hbonds
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A PRO 729 N
688 hydrogen bonds found
> ~hbonds
> save /Users/gmontoya/Documents/Cas_phi/Final_maps/fig3.cxs
opened ChimeraX session
> show #!2 models
> hide #2.1 models
> volume zone #2 nearAtoms #1/F range 3 newMap false
> show #2.1 models
> volume zone #2 nearAtoms #1/F range 3 newMap false
> volume style mesh
> ui tool show "Segment Map"
> hide #2.1 models
> volume style image
> show #2.1 models
> hide #2.2 models
> hide #!2.1 models
> show #2.2 models
> select #2.2
1 model selected
> close #2.2
> show #!2.1 models
> ui tool show "Side View"
> hide #!2 models
> hide #!2.1 models
> show #!2.1 models
> surface dust #2
> surface dust #2.1
> ui tool show "Volume Viewer"
> volume #2 change image level -0.4938,0 level 1.669,0.8 level 44.55,1
> volume #2 level 10.25
> nucleotides atoms
> style nucleic stick
Changed 1632 atom styles
> volume #2 color #aaafae61
> select /A:200-383
1354 atoms, 1392 bonds, 184 residues, 1 model selected
> style sel stick
Changed 1354 atom styles
> style sel stick
Changed 1354 atom styles
> show sel atoms
> select clear
> select /A:200-383
1354 atoms, 1392 bonds, 184 residues, 1 model selected
> style sel stick
Changed 1354 atom styles
> color sel byhetero
> select clear
> select chain /F
Expected an objects specifier or a keyword
> select /F
919 atoms, 1027 bonds, 43 residues, 1 model selected
> hide sel cartoons
> select #2
4 models selected
> select clear
> hide #!2 models
> show #!2 models
> volume #2 style mesh
> volume #2 style surface
> volume #2 style image
> volume #2 style surface
> ui mousemode right label
> save /Users/gmontoya/Documents/Cas_phi/similar_proteins/map1.cxs
> save /Users/gmontoya/Documents/Cas_phi/map1.png width 2800 height 2400
> supersample 4 transparentBackground true
> hide #!2.1 models
> label delete residues
> label delete residues
> show #!2.1 models
> volume zone #2 nearAtoms #1/F,E,G,C, A range 3 newMap false
> volume #2 level 7.026
> hide #!2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> view #!1 clip false
> hide #2.2 models
> show #!2.1 models
> volume #2 level 4.317
> volume #2 level 4.317
> select /A
5213 atoms, 5323 bonds, 2 pseudobonds, 703 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 486 atom styles
> color sel byhetero
> select clear
> select /C
41 atoms, 45 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 41 atom styles
> color sel byhetero
> hide sel cartoons
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> hide sel cartoons
> select clear
> select /G
186 atoms, 208 bonds, 9 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 186 atom styles
> color sel byhetero
> select clear
> hide #!2.1 models
> hide #!2 models
> show #!2 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2 models
> show #!2 models
> show #!2.1 models
> hide #2.1.2 models
> show #2.1.2 models
> hide #2.1.2 models
> show #2.1.2 models
> volume #2 level 5.607
> hide #!2 models
> hide #!2.1 models
> hide #2.1.2 models
> show #!2 models
> show #!2.1 models
> volume #2 level 5.8
> volume #2 level 6.058
> volume #2 level 5.7
> save /Users/gmontoya/Documents/Cas_phi/similar_proteins/mapgen.cxs
opened ChimeraX session
> hide #!2 models
> select /F
919 atoms, 1027 bonds, 43 residues, 1 model selected
> show sel cartoons
> color sel orange
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> color sel grey
> select clear
> select /G
186 atoms, 208 bonds, 9 residues, 1 model selected
> color sel lime green
> select clear
> select /C
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel red
> select clear
> ui tool show "Side View"
> show #!2 models
> volume #2 level 7.7
> volume #2 level 4.7
> fitmap #1 inMap #2
Fit molecule test-coot-0.pdb (#1) to map J503_28_sharpened_map.ccp4 (#2) using
6846 atoms
average map value = 12.12, steps = 40
shifted from previous position = 0.00653
rotated from previous position = 0.0267 degrees
atoms outside contour = 941, contour level = 4.7
Position of test-coot-0.pdb (#1) relative to J503_28_sharpened_map.ccp4 (#2)
coordinates:
Matrix rotation and translation
0.99999989 -0.00031762 0.00033964 -0.00145234
0.00031763 0.99999995 -0.00002786 -0.03083611
-0.00033963 0.00002797 0.99999994 0.02679718
Axis 0.05991700 0.72906640 0.68181533
Axis point 87.52901678 0.00000000 3.54579992
Rotation angle (degrees) 0.02669101
Shift along axis -0.00429787
> color zone #2 near #1 distance 2.5
> hide #!1 models
> show #!1 models
> lighting soft
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> fitmap #1 inMap #2
Fit molecule test-coot-0.pdb (#1) to map J503_28_sharpened_map.ccp4 (#2) using
6846 atoms
average map value = 12.12, steps = 28
shifted from previous position = 0.0175
rotated from previous position = 0.0206 degrees
atoms outside contour = 942, contour level = 4.7
Position of test-coot-0.pdb (#1) relative to J503_28_sharpened_map.ccp4 (#2)
coordinates:
Matrix rotation and translation
0.99999999 -0.00006730 0.00011767 -0.01192924
0.00006732 0.99999998 -0.00016157 0.01462084
-0.00011766 0.00016158 0.99999998 0.00392883
Axis 0.76608627 0.55789695 0.31915954
Axis point 0.00000000 -23.76684614 89.55459198
Rotation angle (degrees) 0.01208425
Shift along axis 0.00027202
> color zone #2 near #1 distance 2.5
> color zone #2 near #1 distance 3
> hide #!1 models
> color zone #2 near #1 distance 1
> color zone #2 near #1 distance 4
> lighting soft
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> show #!1 models
> graphics silhouettes true
> lighting soft
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> volume #2 color #c7cccd61
> volume #2 color #c7cccd60
> volume #2 color #c7cccd5f
> volume #2 color #c7cccd5b
> volume #2 color #c7cccd56
> volume #2 color #c7cccd52
> volume #2 color #c7cccd4f
> volume #2 color #c7cccd4e
> volume #2 color #c7cccd4d
> volume #2 color #c7cccd4c
> volume #2 color #c7cccd4b
> volume #2 color #c7cccd4a
> volume #2 color #c7cccd49
> volume #2 color #c7cccd48
> volume #2 color #c7cccd47
> volume #2 color #c7cccd46
> volume #2 color #c7cccd45
> volume #2 color #c7cccd44
> volume #2 color #c7cccd43
> volume #2 color #c7cccd42
> volume #2 color #c7cccd43
> volume #2 color #c7cccd44
> volume #2 color #c0c5c544
> volume #2 color #b6bbbc44
> volume #2 color #b1b6b744
> volume #2 level 4.9
> volume #2 level 5.9
> volume #2 level 6.9
> volume #2 level 5.9
> save /Users/gmontoya/Documents/Cas_phi/general_map.png width 2800 height
> 2400 supersample 4 transparentBackground true
> save /Users/gmontoya/Documents/Cas_phi/Final_maps/generamap.cxs
> fitmap #1 inMap #2
Fit molecule test-coot-0.pdb (#1) to map J503_28_sharpened_map.ccp4 (#2) using
6846 atoms
average map value = 12.12, steps = 48
shifted from previous position = 0.011
rotated from previous position = 0.0115 degrees
atoms outside contour = 1423, contour level = 5.9
Position of test-coot-0.pdb (#1) relative to J503_28_sharpened_map.ccp4 (#2)
coordinates:
Matrix rotation and translation
0.99999996 -0.00025377 0.00014006 0.01518096
0.00025378 0.99999996 -0.00009315 -0.01763474
-0.00014004 0.00009318 0.99999999 0.01224032
Axis 0.30599869 0.45999990 0.83352558
Axis point 81.70487793 51.68619102 0.00000000
Rotation angle (degrees) 0.01744426
Shift along axis 0.00673599
> color zone #2 near #1 distance 2.5
> hide atoms
> show cartoons
> select /F
919 atoms, 1027 bonds, 43 residues, 1 model selected
> color sel orange
> select /E
486 atoms, 543 bonds, 24 residues, 1 model selected
> color sel grey
> select /G
186 atoms, 208 bonds, 9 residues, 1 model selected
> color sel lime green
> select /B
1 atom, 1 residue, 1 model selected
> color sel yellow
> select /C
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel red
> select /A:1-51
336 atoms, 340 bonds, 44 residues, 1 model selected
> color sel ivory
> select /A:52-70
146 atoms, 150 bonds, 19 residues, 1 model selected
> color sel cyan
> select /A:71-197
771 atoms, 789 bonds, 2 pseudobonds, 108 residues, 2 models selected
> color sel wheat
> select /A:198-383
1364 atoms, 1402 bonds, 186 residues, 1 model selected
> color sel cyan
> select /A:384-444
436 atoms, 441 bonds, 61 residues, 1 model selected
> color sel plum
> select /A:445-474
251 atoms, 252 bonds, 30 residues, 1 model selected
> color sel slate blue
> select /A:475-561
632 atoms, 641 bonds, 87 residues, 1 model selected
> color sel pale green
> select /A:562-609
383 atoms, 386 bonds, 48 residues, 1 model selected
> color sel slate blue
> select /A:610-621
93 atoms, 92 bonds, 12 residues, 1 model selected
> color sel plum
> select /A:622-647
219 atoms, 223 bonds, 26 residues, 1 model selected
> color sel dark orchid
> select /A:648-729
582 atoms, 597 bonds, 82 residues, 1 model selected
> color sel plum
> hide pseudobonds
> fitmap #1 inMap #2
Fit molecule test-coot-0.pdb (#1) to map J503_28_sharpened_map.ccp4 (#2) using
6846 atoms
average map value = 12.12, steps = 44
shifted from previous position = 0.00165
rotated from previous position = 0.00336 degrees
atoms outside contour = 1419, contour level = 5.9
Position of test-coot-0.pdb (#1) relative to J503_28_sharpened_map.ccp4 (#2)
coordinates:
Matrix rotation and translation
0.99999996 -0.00023677 0.00013085 0.01345687
0.00023679 0.99999996 -0.00014854 -0.00845354
-0.00013082 0.00014857 0.99999998 0.00518714
Axis 0.48134592 0.42392825 0.76719681
Axis point 48.01320808 42.85475162 -0.00000000
Rotation angle (degrees) 0.01768314
Shift along axis 0.00687327
> color zone #2 near #1 distance 2.5
> select clear
> volume #2 level 7.9
> volume #2 level 6.9
> volume #2 level 5.9
> volume #2 level 4.9
> hide #!1 models
> lighting soft
> lighting soft
> graphics silhouettes false
> fitmap #1 inMap #2
Fit molecule test-coot-0.pdb (#1) to map J503_28_sharpened_map.ccp4 (#2) using
6846 atoms
average map value = 12.12, steps = 44
shifted from previous position = 0.0152
rotated from previous position = 0.0133 degrees
atoms outside contour = 1013, contour level = 4.9
Position of test-coot-0.pdb (#1) relative to J503_28_sharpened_map.ccp4 (#2)
coordinates:
Matrix rotation and translation
0.99999989 -0.00030542 0.00034342 -0.00240385
0.00030545 0.99999995 -0.00008660 -0.02322354
-0.00034340 0.00008670 0.99999994 0.01914509
Axis 0.18527395 0.73427025 0.65308558
Axis point 65.25005610 0.00000000 4.32533813
Rotation angle (degrees) 0.02679647
Shift along axis -0.00499434
> color zone #2 near #1 distance 2.5
> surface dust #2
> surface dust #2.1
> graphics silhouettes true
> save /Users/gmontoya/Documents/Cas_phi/Gmap1.png width 2800 height 2400
> supersample 4 transparentBackground true
> show #!1 models
> hide #!1 models
> save /Users/gmontoya/Documents/Cas_phi/Final_maps/maps2.cxs
opened ChimeraX session
> open /Users/gmontoya/Documents/Cas_phi/flexiblemaps/J504.mrc
Opened J504.mrc, grid size 256,256,256, pixel 0.832, shown at level 0.121,
step 1, values float32
> open /Users/gmontoya/Documents/Cas_phi/flexiblemaps/J505.mrc
Opened J505.mrc, grid size 256,256,256, pixel 0.832, shown at level 0.129,
step 1, values float32
> open /Users/gmontoya/Documents/Cas_phi/flexiblemaps/J506.mrc
Opened J506.mrc, grid size 256,256,256, pixel 0.832, shown at level 0.118,
step 1, values float32
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> volume #3 level 0.121
> volume #3 level 0.124
> volume #3 level 0.13
> volume #3 level 0.13
> volume #3 level 0.136
> volume #3 level 0.139
> volume #3 level 0.148
> volume #3 level 0.151
> volume #3 level 0.154
> volume #3 level 0.157
> volume #3 level 0.163
> volume #3 level 0.1661
> volume #3 level 0.1721
> volume #3 level 0.1751
> hide #!3 models
> show #!4 models
> volume #4 color #b2ffb25b
> volume #4 level 0.2349
> volume #5 level 0.3631
> volume #5 level 0.3528
> volume #5 level 0.3631
> volume #5 level 0.3665
> hide #!1 models
> show #!1 models
> volume #5 level 0.2099
> volume #5 level 0.3597
> hide #!1 models
> save /Users/gmontoya/Documents/Cas_phi/flexiblemaps/maps500.cxs
——— End of log from Wed Apr 14 14:16:17 2021 ———
opened ChimeraX session
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #3 color #ffb2b2bb
> volume #3 color #ffb2b2
> show #!1 models
> hide #!1 models
> show #!4 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!1 models
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
> volume #2 color #ffffff7c
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
> volume #2 color #ffffff97
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
> volume #2 color #ffffff31
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
> volume #2 color #ffffff56
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!3 models
> hide #!4 models
> show #!2 models
> hide #!5 models
> show #!4 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!5 models
> volume #5 level 0.3281
> volume #5 level 0.3561
> hide #!2 models
> show #!2 models
> volume #5 level 0.3421
> volume #5 level 0.3561
> volume #2 level 5.697
> hide #!2 models
> hide #!5 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!5 models
> getcrd view
Missing or invalid "atoms" argument: invalid atom specifier
> getcrd matrix
Missing or invalid "atoms" argument: invalid atom specifier
> getcrd matrix view
Missing or invalid "atoms" argument: invalid atom specifier
> matrix view
Unknown command: matrix view
> view matrix
camera position:
-0.08303,-0.99521,0.051595,124.43,0.37006,-0.078863,-0.92566,-98.865,0.92529,-0.057764,0.37483,197.92
model positions:
#1,1,-0.00030542,0.00034342,-0.0024038,0.00030545,1,-8.6598e-05,-0.023224,-0.0003434,8.6703e-05,1,0.019145,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0
> save /Users/gmontoya/Documents/Cas_phi/flexible.maps.png width 2800 height
> 2400 supersample 4 transparentBackground true
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2606, in _color_chosen
self.set_threshold_parameters_from_gui(show = True, log = False)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py", line 2801, in
set_threshold_parameters_from_gui
s.rgba = color
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2015, in _set_rgba
self.set_color([int(min(255,max(0,255*r))) for r in rgba])
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2045, in set_color
self._set_clip_cap_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
AttributeError: 'Model' object has no attribute 'is_clip_cap'
AttributeError: 'Model' object has no attribute 'is_clip_cap'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 2051, in _set_clip_cap_color
if getattr(c, 'is_clip_cap'):
See log for complete Python traceback.
> volume #2 color #ffffff64
OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 1554.60.15.0.0 (iBridge: 18.16.13030.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H114)
Kernel Version: Darwin 19.6.0
Time since boot: 5:48
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
LEN P27q-10:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
Thunderbolt Display:
Display Type: LCD
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: C02LW4BYF2GC
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.1
ChimeraX-AtomicLibrary: 3.1.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202104140542
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.3
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'Model' object has no attribute 'is_clip_cap' |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Fixed in 1.2.
Error was from a volume surface having a non-clip cap submodel and the code to color the cap assumed an is_clip_cap attribute on that model. Fixed code to correctly handle when submodel does not have that attribute. Could not figure out how the user created a submodel of a volume surface but I tested by renaming a marker model to be a child of the surface.