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Opened 8 weeks ago
Closed 6 weeks ago
#18781 closed defect (duplicate)
Orthoplanes: 'NoneType' object has no attribute 'image_colors'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/yoshioka/Downloads/01_Suntag/surface.cxs
Log from Tue Jun 10 18:59:10 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/yoshioka/Downloads/28_Prestin/map.cxs format session
Opened 7LGU.map as #1, grid size 256,256,256, pixel 0.651, shown at level
0.21, step 1, values float32
Opened 7V73.map as #4, grid size 180,180,180, pixel 1.11, shown at level
0.0246, step 1, values float32
Log from Wed May 14 12:40:53 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/yoshioka/Downloads/28_Prestin/map.cxs
Error opening map "/Users/yoshioka/Downloads/28_Prestin/map_2": File map_2,
format ccp4
[Errno 2] No such file or directory:
'/Users/yoshioka/Downloads/28_Prestin/map_2'
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Wed May 14 12:35:38 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/yoshioka/Downloads/01_Suntag/order/for_Fig.cxs format session
Log from Wed May 14 11:37:59 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/yoshioka/Downloads/01_Suntag/order/E18_re_2_model0980.pdb
> /Users/yoshioka/Downloads/01_Suntag/order/GGGGS_MD_3_model0346.pdb
Chain information for E18_re_2_model0980.pdb #1
---
Chain | Description
? | No description available
Chain information for GGGGS_MD_3_model0346.pdb #2
---
Chain | Description
? | No description available
Computing secondary structure
[Repeated 1 time(s)]
> ui mousemode right select
Drag select of 151 residues
> graphics silhouettes true
> select clear
> lighting full
> lighting soft
> set bgColor white
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker E18_re_2_model0980.pdb, chain (blank) (#1) with
GGGGS_MD_3_model0346.pdb, chain (blank) (#2), sequence alignment score =
1116.5
RMSD between 191 pruned atom pairs is 1.011 angstroms; (across all 242 pairs:
4.165)
> view clip false
> color #1 #00f900ff
> color #2 #00f900ff
> hide #1 models
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
> ui tool show "Show Sequence Viewer"
> sequence chain #1/?
Alignment identifier is 1/
> sequence chain #2/?
Alignment identifier is 2/
> select #1/*:112
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/*:112-129
233 atoms, 232 bonds, 18 residues, 1 model selected
> select #2/*:112-113
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/*:112-131
156 atoms, 155 bonds, 20 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> delete H
> show #1 models
> select #1/*:112-113
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/*:112-129
120 atoms, 119 bonds, 18 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> hide #1 models
> mlp #2
Map values for surface "GGGGS_MD_3_model0346.pdb_ SES surface": minimum -29.6,
mean -6.928, maximum 21.24
To also show corresponding color key, enter the above mlp command and add key
true
> show #1 models
> hide #!2 models
> mlp #1
Map values for surface "E18_re_2_model0980.pdb_ SES surface": minimum -31.72,
mean -6.234, maximum 22.88
To also show corresponding color key, enter the above mlp command and add key
true
> show #!2 models
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HSD (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/5y/jpf9_yqs65b72h19zgy5ldlh0000gn/T/tmpj95us3ln/ante.in.mol2 -fi
mol2 -o
/var/folders/5y/jpf9_yqs65b72h19zgy5ldlh0000gn/T/tmpj95us3ln/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(HSD) ``
(HSD) `Welcome to antechamber 20.0: molecular input file processor.`
(HSD) ``
(HSD) `Info: Finished reading file
(/var/folders/5y/jpf9_yqs65b72h19zgy5ldlh0000gn/T/tmpj95us3ln/ante.in.mol2);
atoms read (29), bonds read (29).`
(HSD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HSD) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HSD) ``
(HSD) ``
(HSD) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HSD) `Info: Total number of electrons: 112; net charge: 0`
(HSD) ``
(HSD) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HSD) ``
(HSD) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(HSD) ``
(HSD) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HSD) ``
Charges for residue HSD determined
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HSD (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/5y/jpf9_yqs65b72h19zgy5ldlh0000gn/T/tmpg3wo8vfn/ante.in.mol2 -fi
mol2 -o
/var/folders/5y/jpf9_yqs65b72h19zgy5ldlh0000gn/T/tmpg3wo8vfn/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(HSD) ``
(HSD) `Welcome to antechamber 20.0: molecular input file processor.`
(HSD) ``
(HSD) `Info: Finished reading file
(/var/folders/5y/jpf9_yqs65b72h19zgy5ldlh0000gn/T/tmpg3wo8vfn/ante.in.mol2);
atoms read (29), bonds read (29).`
(HSD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HSD) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HSD) ``
(HSD) ``
(HSD) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HSD) `Info: Total number of electrons: 112; net charge: 0`
(HSD) ``
(HSD) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HSD) ``
(HSD) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(HSD) ``
(HSD) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HSD) ``
Charges for residue HSD determined
Coulombic values for E18_re_2_model0980.pdb_ SES surface #1.1: minimum,
-11.63, mean -0.30, maximum 15.17
Coulombic values for GGGGS_MD_3_model0346.pdb_ SES surface #2.1: minimum,
-12.34, mean -0.22, maximum 10.58
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 surfaces
> show #!2 models
> hide surfaces
> style sphere
Changed 3618 atom styles
> style stick
Changed 3618 atom styles
> style ball
Changed 3618 atom styles
> style stick
Changed 3618 atom styles
> hbonds reveal true
669 hydrogen bonds found
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> close #3
> hide #!1 atoms
> select #1/*:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/*:112-129
120 atoms, 119 bonds, 18 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 19 atoms, 11 residues, 16 bonds
Drag select of 2 residues
Drag select of 5 atoms, 14 residues, 3 bonds
> show sel atoms
> color sel byhetero
> select clear
Drag select of 54 atoms, 17 residues, 44 bonds
> hbonds sel reveal true
33 hydrogen bonds found
> select clear
> show #!2 models
> hide #!1 models
> select #2/*:112
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/*:112-131
88 atoms, 87 bonds, 20 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 1 residues
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> hide #!2 atoms
> select #2/*:112-113
8 atoms, 7 bonds, 2 residues, 1 model selected
> select #2/*:112-131
88 atoms, 87 bonds, 20 residues, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]Drag select of 10 residues
> show sel atoms
> color sel byhetero
> select clear
> show #!1 models
> hide #!2 models
> color #3 #fffb00ff models
> show #!2 models
> hide #!1 models
> show #!1 models
> select #1/*:112-113
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/*:112-129
120 atoms, 119 bonds, 1 pseudobond, 18 residues, 2 models selected
> color (#!1 & sel) cyan
> color sel byhetero
> select clear
> hide #!2 models
> select #1/*:24
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/*:24-37
97 atoms, 97 bonds, 14 residues, 1 model selected
> select #1/*:24-37,53-59
147 atoms, 147 bonds, 21 residues, 1 model selected
> select #1/*:24-37,53-59,92-100
231 atoms, 236 bonds, 30 residues, 1 model selected
> select #1/*:24-37,53-59,92-100,160-164
270 atoms, 275 bonds, 35 residues, 1 model selected
> select #1/*:24-37,53-59,92-100,160-164,179-194
394 atoms, 401 bonds, 51 residues, 1 model selected
> select #1/*:24-37,53-59,92-100,160-164,179-194,227-231
437 atoms, 445 bonds, 56 residues, 1 model selected
> color (#!1 & sel) red
> select clear
> select #1/*:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/*:27-31
30 atoms, 29 bonds, 5 residues, 1 model selected
> undo
[Repeated 4 time(s)]
> select clear
> select #1/*:27
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/*:27-35
63 atoms, 63 bonds, 9 residues, 1 model selected
> select #1/*:27-35,53-55
82 atoms, 81 bonds, 12 residues, 1 model selected
> select #1/*:27-35,53-55,92-100
166 atoms, 170 bonds, 21 residues, 1 model selected
> select #1/*:27-35,53-55,92-100,155-162
226 atoms, 231 bonds, 29 residues, 1 model selected
> select #1/*:27-35,53-55,92-100,155-162,180-186
279 atoms, 285 bonds, 36 residues, 1 model selected
> select #1/*:27-35,53-55,92-100,155-162,180-186,225-231
336 atoms, 343 bonds, 43 residues, 1 model selected
> color (#!1 & sel) red
> select clear
> select #1/*:227
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/*:227-231
43 atoms, 44 bonds, 5 residues, 1 model selected
> select clear
> select #2/*:27
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/*:27-35
63 atoms, 63 bonds, 9 residues, 1 model selected
> select #2/*:27-35,53-55
82 atoms, 81 bonds, 12 residues, 1 model selected
> show #!2 models
> hide #!1 models
> select #2/*:27-35,53-55,92-100
166 atoms, 170 bonds, 21 residues, 1 model selected
> select #2/*:27-35,53-55,92-100,157-164
226 atoms, 231 bonds, 29 residues, 1 model selected
> select #2/*:27-35,53-55,92-100,157-164,182-188
279 atoms, 285 bonds, 36 residues, 1 model selected
> select #2/*:27-35,53-55,92-100,157-164,182-188,227-233
336 atoms, 343 bonds, 43 residues, 1 model selected
> color (#!2 & sel) red
> select clear
> save /Users/yoshioka/Downloads/01_Suntag/order/for_Fig.cxs
——— End of log from Wed May 14 11:37:59 2025 ———
opened ChimeraX session
> close
> open /Users/yoshioka/Downloads/emd_31757.map
Opened emd_31757.map as #1, grid size 180,180,180, pixel 1.11, shown at level
0.0246, step 1, values float32
> volume #1 level 0.03841
> volume #1 level 0.01957
> open /Users/yoshioka/Downloads/18_pdb_Files/Prestin.pdb
Prestin.pdb title:
Structure of human prestin In the presence of nacl [more info...]
Chain information for Prestin.pdb #2
---
Chain | Description | UniProt
A B | solute carrier family 26 member 5 | S26A5_HUMAN 1-744
Non-standard residues in Prestin.pdb #2
---
C14 — tetradecane
CL — chloride ion
CLR — cholesterol
D10 — decane
D12 — dodecane
HEX — hexane
HP6 — heptane
OCT — N-octane
> hide #!1 models
> select add #2
11597 atoms, 11620 bonds, 2 pseudobonds, 1581 residues, 3 models selected
> show #!1 models
> volume #1 level 0.04348
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.7204,-0.6342,-0.28075,220.18,-0.1234,0.51555,-0.84793,122.77,0.6825,-0.5762,-0.44966,114.48
> view matrix models
> #2,-0.53698,-0.6988,-0.47258,226.6,-0.055975,0.58847,-0.80658,107.57,0.84174,-0.40666,-0.35511,79.055
> view matrix models
> #2,-0.63388,-0.43123,0.64206,117.54,-0.65216,-0.1483,-0.74344,213.21,0.41581,-0.88997,-0.18722,140.5
> view matrix models
> #2,-0.33405,-0.937,0.10218,180.63,-0.40992,0.046802,-0.91092,191.04,0.84875,-0.34618,-0.39973,77.226
> view matrix models
> #2,-0.17626,-0.79866,0.5754,115.69,-0.76639,-0.25549,-0.58938,218.58,0.61772,-0.54486,-0.56705,127.25
> view matrix models
> #2,0.067659,-0.95929,0.27419,134.39,-0.41199,-0.27716,-0.86801,214.57,0.90867,-0.054237,-0.41398,49.125
> view matrix models
> #2,-0.64721,-0.55943,-0.51783,228.04,-0.55628,0.81106,-0.18094,77.502,0.52121,0.17095,-0.83613,98.506
> view matrix models
> #2,-0.36439,-0.89872,-0.24399,209.44,-0.92235,0.38444,-0.03855,131.41,0.12844,0.21099,-0.96901,139.19
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.36439,-0.89872,-0.24399,226.86,-0.92235,0.38444,-0.03855,147.09,0.12844,0.21099,-0.96901,138.67
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.3425,-0.87281,-0.3477,231.71,-0.89305,0.41739,-0.16808,152.93,0.29183,0.25294,-0.92242,117.6
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.3425,-0.87281,-0.3477,228.84,-0.89305,0.41739,-0.16808,153.31,0.29183,0.25294,-0.92242,117.53
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule Prestin.pdb (#2) to map emd_31757.map (#1) using 11597 atoms
average map value = 0.008619, steps = 104
shifted from previous position = 2.38
rotated from previous position = 4.93 degrees
atoms outside contour = 10351, contour level = 0.043483
Position of Prestin.pdb (#2) relative to emd_31757.map (#1) coordinates:
Matrix rotation and translation
-0.41412290 -0.83832574 -0.35455914 233.55293351
-0.85315365 0.49325628 -0.16978542 144.61433200
0.31722401 0.23218140 -0.91948938 118.88533459
Axis 0.51336725 -0.85796005 -0.01893730
Axis point 145.93041361 0.00000000 85.98967542
Rotation angle (degrees) 156.95211838
Shift along axis -6.42625908
> volume #1 level 0.02536
> volume #1 level 0.02609
> fitmap #2 inMap #1
Fit molecule Prestin.pdb (#2) to map emd_31757.map (#1) using 11597 atoms
average map value = 0.008619, steps = 72
shifted from previous position = 0.0101
rotated from previous position = 0.0087 degrees
atoms outside contour = 9562, contour level = 0.026089
Position of Prestin.pdb (#2) relative to emd_31757.map (#1) coordinates:
Matrix rotation and translation
-0.41415155 -0.83827086 -0.35465542 233.55457521
-0.85309392 0.49333631 -0.16985300 144.61579047
0.31734721 0.23220950 -0.91943977 118.87396884
Axis 0.51333385 -0.85798029 -0.01892537
Axis point 145.92488275 0.00000000 85.99437554
Rotation angle (degrees) 156.94472905
Shift along axis -6.43576246
> view matrix models
> #2,-0.41415,-0.83827,-0.35466,229.46,-0.85309,0.49334,-0.16985,145.95,0.31735,0.23221,-0.91944,119.46
> fitmap #2 inMap #1
Fit molecule Prestin.pdb (#2) to map emd_31757.map (#1) using 11597 atoms
average map value = 0.009811, steps = 220
shifted from previous position = 4.3
rotated from previous position = 12.9 degrees
atoms outside contour = 9369, contour level = 0.026089
Position of Prestin.pdb (#2) relative to emd_31757.map (#1) coordinates:
Matrix rotation and translation
-0.48895772 -0.85913566 -0.15101741 217.33627378
-0.85496531 0.50634986 -0.11244616 138.34045599
0.17307415 0.07413323 -0.98211486 152.80643824
Axis 0.49889570 -0.86659029 0.01115113
Axis point 140.16702433 -0.00000000 89.38658400
Rotation angle (degrees) 169.22268544
Shift along axis -9.75239925
> view matrix models
> #2,-0.48896,-0.85914,-0.15102,219.22,-0.85497,0.50635,-0.11245,139.64,0.17307,0.074133,-0.98211,152.39
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.41913,-0.90172,-0.10593,213.12,-0.89034,0.43106,-0.14658,151.75,0.17784,0.032875,-0.98351,155.55
> fitmap #2 inMap #1
Fit molecule Prestin.pdb (#2) to map emd_31757.map (#1) using 11597 atoms
average map value = 0.009311, steps = 100
shifted from previous position = 1.53
rotated from previous position = 3.37 degrees
atoms outside contour = 9481, contour level = 0.026089
Position of Prestin.pdb (#2) relative to emd_31757.map (#1) coordinates:
Matrix rotation and translation
-0.42570061 -0.90354302 -0.04887735 209.12547077
-0.89356985 0.42828119 -0.13456650 152.59906540
0.14251987 -0.01360972 -0.98969837 163.54612921
Axis 0.53371013 -0.84452176 0.04400566
Axis point 147.26280927 0.00000000 92.96729422
Rotation angle (degrees) 173.49344260
Shift along axis -10.06389214
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.4257,-0.90354,-0.048877,213.82,-0.89357,0.42828,-0.13457,150.47,0.14252,-0.01361,-0.9897,164.4
> fitmap #2 inMap #1
Fit molecule Prestin.pdb (#2) to map emd_31757.map (#1) using 11597 atoms
average map value = 0.0154, steps = 116
shifted from previous position = 1.52
rotated from previous position = 8.79 degrees
atoms outside contour = 8551, contour level = 0.026089
Position of Prestin.pdb (#2) relative to emd_31757.map (#1) coordinates:
Matrix rotation and translation
-0.52607837 -0.84913420 -0.04703889 217.97054201
-0.84909145 0.52755165 -0.02707336 128.87690872
0.04780436 0.02569761 -0.99852610 168.39532305
Axis 0.48620798 -0.87384303 0.00039388
Axis point 142.22254002 0.00000000 87.66298754
Rotation angle (degrees) 176.88915040
Shift along axis -6.57284482
> view matrix models
> #2,-0.52608,-0.84913,-0.047039,221.13,-0.84909,0.52755,-0.027073,129.73,0.047804,0.025698,-0.99853,168.15
> fitmap #2 inMap #1
Fit molecule Prestin.pdb (#2) to map emd_31757.map (#1) using 11597 atoms
average map value = 0.0154, steps = 80
shifted from previous position = 3.28
rotated from previous position = 0.0185 degrees
atoms outside contour = 8558, contour level = 0.026089
Position of Prestin.pdb (#2) relative to emd_31757.map (#1) coordinates:
Matrix rotation and translation
-0.52618832 -0.84907438 -0.04688878 217.96710507
-0.84901554 0.52766083 -0.02732498 128.87844228
0.04794231 0.02543122 -0.99852631 168.42310374
Axis 0.48615159 -0.87387433 0.00054217
Axis point 142.21588294 -0.00000000 87.68702262
Rotation angle (degrees) 176.88966099
Shift along axis -6.56719392
> volume #1 level 0.04566
> hide #!1 models
> show #!1 models
> volume #1 level 0.02826
> volume #1 level 0.02681
> volume #1 level 0.01739
> volume #1 level 0.02464
> hide #!1 models
> color bfactor sel
11597 atoms, 1581 residues, atom bfactor range 32.7 to 124
> show #!1 models
> volume #1 level 0.01739
> volume #1 level 0.02826
> fitmap #2 inMap #1
Fit molecule Prestin.pdb (#2) to map emd_31757.map (#1) using 11597 atoms
average map value = 0.0154, steps = 48
shifted from previous position = 0.021
rotated from previous position = 0.0175 degrees
atoms outside contour = 8730, contour level = 0.028263
Position of Prestin.pdb (#2) relative to emd_31757.map (#1) coordinates:
Matrix rotation and translation
-0.52610759 -0.84911341 -0.04708724 217.97276010
-0.84906982 0.52758428 -0.02711579 128.88161218
0.04786687 0.02571453 -0.99852267 168.38879890
Axis 0.48619160 -0.87385214 0.00040118
Axis point 142.22046824 -0.00000000 87.66429742
Rotation angle (degrees) 176.88554316
Shift along axis -6.57939539
> volume #1 level 0.01884
> volume #1 level 0.02174
> hide #!1 models
> hide #!2 models
> show #!2 models
> close #2
> show #!1 models
> open /Users/yoshioka/Downloads/7v73.cif
Summary of feedback from opening /Users/yoshioka/Downloads/7v73.cif
---
notes | Fetching CCD CL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif
Fetching CCD CLR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/CLR/CLR.cif
Fetching CCD LBN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/LBN/LBN.cif
7v73.cif title:
Thermostabilized human prestin in complex with chloride [more info...]
Chain information for 7v73.cif #2
---
Chain | Description
A | Prestin
Non-standard residues in 7v73.cif #2
---
CL — chloride ion
CLR — cholesterol
LBN — 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
((2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl
2-(trimethylammonio)ethyl phosphate)
7v73.cif mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
> hide #!1 models
> show #!1 models
> volume #1 level 0.0587
> open /Users/yoshioka/Downloads/18_pdb_Files/Prestin.pdb
Prestin.pdb title:
Structure of human prestin In the presence of nacl [more info...]
Chain information for Prestin.pdb #3
---
Chain | Description | UniProt
A B | solute carrier family 26 member 5 | S26A5_HUMAN 1-744
Non-standard residues in Prestin.pdb #3
---
C14 — tetradecane
CL — chloride ion
CLR — cholesterol
D10 — decane
D12 — dodecane
HEX — hexane
HP6 — heptane
OCT — N-octane
> ui tool show Matchmaker
> matchmaker #!3 to #2
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7v73.cif, chain A (#2) with Prestin.pdb, chain A (#3), sequence
alignment score = 2561.1
RMSD between 140 pruned atom pairs is 1.376 angstroms; (across all 597 pairs:
3.974)
> hide #!3 models
> volume #1 level 0.02971
> volume #1 level 0.02464
> volume #1 level 0.06015
> show #!3 models
> hide #!1 models
> hide #!2 models
> open /Users/yoshioka/Downloads/emd_23329.map
Opened emd_23329.map as #4, grid size 256,256,256, pixel 0.651, shown at level
0.171, step 1, values float32
> show #!1 models
> hide #!1 models
> close #1
> close
> open /Users/yoshioka/Downloads/7v73.cif
> /Users/yoshioka/Downloads/emd_23329.map
7v73.cif title:
Thermostabilized human prestin in complex with chloride [more info...]
Chain information for 7v73.cif #1
---
Chain | Description
A | Prestin
Non-standard residues in 7v73.cif #1
---
CL — chloride ion
CLR — cholesterol
LBN — 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
((2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl
2-(trimethylammonio)ethyl phosphate)
7v73.cif mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
Opened emd_23329.map as #2, grid size 256,256,256, pixel 0.651, shown at level
0.171, step 1, values float32
> close #1
> open /Users/yoshioka/Downloads/18_pdb_Files/Prestin.pdb
Prestin.pdb title:
Structure of human prestin In the presence of nacl [more info...]
Chain information for Prestin.pdb #1
---
Chain | Description | UniProt
A B | solute carrier family 26 member 5 | S26A5_HUMAN 1-744
Non-standard residues in Prestin.pdb #1
---
C14 — tetradecane
CL — chloride ion
CLR — cholesterol
D10 — decane
D12 — dodecane
HEX — hexane
HP6 — heptane
OCT — N-octane
> volume #2 level 0.07379
> volume #2 level 0.3315
> volume #2 level 0.07379
> open /Users/yoshioka/Downloads/7v73.cif
> /Users/yoshioka/Downloads/emd_31757.map
7v73.cif title:
Thermostabilized human prestin in complex with chloride [more info...]
Chain information for 7v73.cif #3
---
Chain | Description
A | Prestin
Non-standard residues in 7v73.cif #3
---
CL — chloride ion
CLR — cholesterol
LBN — 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
((2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl
2-(trimethylammonio)ethyl phosphate)
7v73.cif mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
Opened emd_31757.map as #4, grid size 180,180,180, pixel 1.11, shown at level
0.0246, step 1, values float32
> hide #!1 models
> hide #!2 models
> volume #4 level 0.05073
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> volume #2 level 0.1162
> volume #2 level 0.07682
> hide #!1 models
> hide #!2 models
> open
> /Users/yoshioka/Downloads/05_AlphaFold2_results/OXTR/TR_OXTR_1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
TR_OXTR_1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #5
---
Chain | Description
A | No description available
Computing secondary structure
> close #5
> show #!1 models
> show #!2 models
> view clip false
> volume #2 level 0.1041
> hide #!2 models
> open
> /Users/yoshioka/Downloads/05_AlphaFold2_results/OXTR/TR_OXTR_1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
TR_OXTR_1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #5
---
Chain | Description
A | No description available
Computing secondary structure
> view #5 clip false
> select add #5
2663 atoms, 2749 bonds, 344 residues, 1 model selected
> view matrix models #5,1,0,0,90.527,0,1,0,68.319,0,0,1,69.907
> view matrix models #5,1,0,0,40.213,0,1,0,149.71,0,0,1,58.408
> view #1 clip false
> view matrix models #5,1,0,0,62.858,0,1,0,141.13,0,0,1,68.937
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.022805,0.82659,0.56234,56.898,-0.76739,-0.37499,0.52009,148.65,0.64077,-0.41967,0.64287,72.08
> view matrix models
> #5,-0.07558,0.94728,0.31138,53.706,-0.72286,0.16305,-0.67148,135.5,-0.68685,-0.27583,0.67242,63.401
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.07558,0.94728,0.31138,34.225,-0.72286,0.16305,-0.67148,142.71,-0.68685,-0.27583,0.67242,97.787
> view matrix models
> #5,-0.07558,0.94728,0.31138,34.196,-0.72286,0.16305,-0.67148,142.72,-0.68685,-0.27583,0.67242,97.816
> ui mousemode right select
> select clear
> show #!2 models
> hide #5 models
> color bfactor #!1
11597 atoms, 1581 residues, atom bfactor range 32.7 to 124
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
> color bfactor #!3
4872 atoms, 608 residues, atom bfactor range 71.2 to 570
> hide #!4 models
> show #!4 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> volume #2 level 0.07076
> volume #2 level 0.08592
> volume #2 level 0.3952
> volume #2 level 0.1708
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!1 models
Drag select of 7 residues, 4 emd_31757.map
> select clear
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> volume #2 level 0.07986
> volume #2 level 0.1102
> close #5
> save /Users/yoshioka/Downloads/28_Prestin/map.cxs
——— End of log from Wed May 14 12:35:38 2025 ———
opened ChimeraX session
> close
> open /Users/yoshioka/Downloads/28_Prestin/7LGU.map
> /Users/yoshioka/Downloads/28_Prestin/7LGU.pdb
> /Users/yoshioka/Downloads/28_Prestin/7v7c.map
> /Users/yoshioka/Downloads/28_Prestin/7v73.cif
Opened 7LGU.map as #1, grid size 180,180,180, pixel 1.11, shown at level
0.0246, step 1, values float32
7LGU.pdb title:
Structure of human prestin In the presence of nacl [more info...]
Chain information for 7LGU.pdb #2
---
Chain | Description | UniProt
A B | solute carrier family 26 member 5 | S26A5_HUMAN 1-744
Non-standard residues in 7LGU.pdb #2
---
C14 — tetradecane
CL — chloride ion
CLR — cholesterol
D10 — decane
D12 — dodecane
HEX — hexane
HP6 — heptane
OCT — N-octane
Opened 7v7c.map as #3, grid size 256,256,256, pixel 0.651, shown at level
0.171, step 1, values float32
7v73.cif title:
Thermostabilized human prestin in complex with chloride [more info...]
Chain information for 7v73.cif #4
---
Chain | Description
A | Prestin
Non-standard residues in 7v73.cif #4
---
CL — chloride ion
CLR — cholesterol
LBN — 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
((2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl
2-(trimethylammonio)ethyl phosphate)
7v73.cif mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #1 level 0.06377
> close #1
> close
> open /Users/yoshioka/Downloads/28_Prestin/7LGU.map
> /Users/yoshioka/Downloads/28_Prestin/7LGU.pdb
> /Users/yoshioka/Downloads/28_Prestin/7v73.cif
> /Users/yoshioka/Downloads/28_Prestin/7V73.map
Opened 7LGU.map as #1, grid size 256,256,256, pixel 0.651, shown at level
0.171, step 1, values float32
7LGU.pdb title:
Structure of human prestin In the presence of nacl [more info...]
Chain information for 7LGU.pdb #2
---
Chain | Description | UniProt
A B | solute carrier family 26 member 5 | S26A5_HUMAN 1-744
Non-standard residues in 7LGU.pdb #2
---
C14 — tetradecane
CL — chloride ion
CLR — cholesterol
D10 — decane
D12 — dodecane
HEX — hexane
HP6 — heptane
OCT — N-octane
7v73.cif title:
Thermostabilized human prestin in complex with chloride [more info...]
Chain information for 7v73.cif #3
---
Chain | Description
A | Prestin
Non-standard residues in 7v73.cif #3
---
CL — chloride ion
CLR — cholesterol
LBN — 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
((2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl
2-(trimethylammonio)ethyl phosphate)
7v73.cif mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
Opened 7V73.map as #4, grid size 180,180,180, pixel 1.11, shown at level
0.0246, step 1, values float32
> hide #!3 models
> hide #!4 models
> volume #1 step 2
> volume #4 step 2
> volume #1 level 0.2099
> volume #1 step 1
> volume #4 step 1
> save /Users/yoshioka/Downloads/28_Prestin/map.cxs
——— End of log from Wed May 14 12:40:53 2025 ———
opened ChimeraX session
> volume #1 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #1 style mesh
> volume #1 style surface
> volume #1 style image
> volume #1 style surface
> volume #1 region 0,0,0,255,255,255
> ui tool show "Map Eraser"
> ui tool show "Map Coordinates"
> volume erase #1 center 82.964,82.964,82.964 radius 28.708 outside true
Opened 7LGU.map copy as #6, grid size 256,256,256, pixel 0.651, shown at step
1, values float32
> volume erase #6 center 82.964,82.964,82.964 radius 28.652
> close
> open
> /Users/yoshioka/Downloads/22_OPN4/Boltz-1_hOPN4_AA92593/test_9b12f_model_0.cif
Summary of feedback from opening
/Users/yoshioka/Downloads/22_OPN4/Boltz-1_hOPN4_AA92593/test_9b12f_model_0.cif
---
warning | Atom C30 is not in the residue template for LIG /B:1
test_9b12f_model_0.cif title:
. [more info...]
Chain information for test_9b12f_model_0.cif #1
---
Chain | Description
A | .
Non-standard residues in test_9b12f_model_0.cif #1
---
LIG — (LIG)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Computing secondary structure
> close
> open
> /Users/yoshioka/Downloads/01_Suntag/fold_flag_a2a_5xgcn4_w218_complex/fold_flag_a2a_5xgcn4_w218_complex_model_0.cif
Chain information for fold_flag_a2a_5xgcn4_w218_complex_model_0.cif #1
---
Chain | Description
A | .
B C D E F | .
> hide atoms
> show cartoons
Computing secondary structure
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> lighting full
> lighting soft
> color bychain
Alignment identifier is 1/A
Alignment identifier is 1
> select /B-F:1
40 atoms, 35 bonds, 5 residues, 1 model selected
> select /B-F:1-111
4200 atoms, 4295 bonds, 555 residues, 1 model selected
> color sel #00f900ff
> select /B-F:112-113
50 atoms, 45 bonds, 10 residues, 1 model selected
> select /B-F:112-129
530 atoms, 530 bonds, 90 residues, 1 model selected
> color sel #ff2600ff
> select /B-F:130
45 atoms, 40 bonds, 5 residues, 1 model selected
> select /B-F:130-242
4325 atoms, 4415 bonds, 565 residues, 1 model selected
> color sel #00fdffff
> select /A:1-2
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A
3182 atoms, 3251 bonds, 398 residues, 1 model selected
> color sel #00f900ff
> ui mousemode right select
> select clear
> select /B-F:1-2
80 atoms, 75 bonds, 10 residues, 1 model selected
> select /B-F:1-111
4200 atoms, 4295 bonds, 555 residues, 1 model selected
> color sel yellow
> select clear
> select /B-F:241-242
65 atoms, 60 bonds, 10 residues, 1 model selected
> select /B-F:241-242
65 atoms, 60 bonds, 10 residues, 1 model selected
> select clear
> select /A:1-2
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A:1-7
61 atoms, 61 bonds, 7 residues, 1 model selected
> select clear
> save /Users/yoshioka/Desktop/5xGCN4.png width 1986 height 1263 supersample 3
> transparentBackground true
> lighting full
> lighting soft
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting simple
> lighting full
> lighting shadows false
> lighting simple
> lighting full
> lighting soft
> lighting simple
> save /Users/yoshioka/Desktop/5xGCN4_simple.png width 1986 height 1263
> supersample 3 transparentBackground true
> close
> close #
Expected a models specifier or a keyword
> open
> /Users/yoshioka/Downloads/16_卒研用データ/Linker_Order/order_pdbs/W218_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
W218_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> color #1 #00f900ff
Alignment identifier is 1/A
> select /A:27
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:27-35
63 atoms, 63 bonds, 9 residues, 1 model selected
> select /A:27-35,53-55
82 atoms, 81 bonds, 12 residues, 1 model selected
> select /A:27-35,53-55,92-100
166 atoms, 170 bonds, 21 residues, 1 model selected
> select /A:27-35,53-55,92-100,155-162
226 atoms, 231 bonds, 29 residues, 1 model selected
> select /A:27-35,53-55,92-100,155-162,180-186
279 atoms, 285 bonds, 36 residues, 1 model selected
> color #1 #ff2600ff
> undo
> color sel red
> select /A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:225-231
57 atoms, 58 bonds, 7 residues, 1 model selected
> color sel purple
> select clear
> select /A:42,225-231
66 atoms, 66 bonds, 8 residues, 1 model selected
> select /A:42,45,225-231
75 atoms, 74 bonds, 9 residues, 1 model selected
> select /A:111-112
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:111-114
28 atoms, 27 bonds, 4 residues, 1 model selected
> select /A:206
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:206-207
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:42,45
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:42,45,48
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /A:42,45,48,73-74
41 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:42,45,48,73-74
41 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:42,45,48,73-74
41 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:42,45,48,73-74
41 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:42,45,48,73-75
48 atoms, 44 bonds, 6 residues, 1 model selected
> select /A:42,45,48,73-76
56 atoms, 52 bonds, 7 residues, 1 model selected
> select /A:42,45,48,73-76
56 atoms, 52 bonds, 7 residues, 1 model selected
> select /A:42,45,48,73-76
56 atoms, 52 bonds, 7 residues, 1 model selected
> select /A:42,45,48,73-76
56 atoms, 52 bonds, 7 residues, 1 model selected
> select /A:42,45,48,73-76
56 atoms, 52 bonds, 7 residues, 1 model selected
> select /A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:42,45
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:42,45,48
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /A:42,45,48,73
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A:42,45,48,73,106
45 atoms, 40 bonds, 5 residues, 1 model selected
> select /A:42,45,48,73,106,110
54 atoms, 48 bonds, 6 residues, 1 model selected
> select /A:42,45,48,73,106,110,119
63 atoms, 56 bonds, 7 residues, 1 model selected
> select /A:42,45,48,73,106,110,119,128
72 atoms, 64 bonds, 8 residues, 1 model selected
> select /A:42,45,48,73,106,110,119,128,132
81 atoms, 72 bonds, 9 residues, 1 model selected
> select /A:42,45,48,73,106,110,119,128,132,148
90 atoms, 80 bonds, 10 residues, 1 model selected
> select /A:42,45,48,73,106,110,119,128,132,148,193
99 atoms, 88 bonds, 11 residues, 1 model selected
> select /A:42,45,48,73,106,110,119,128,132,148,193,204
108 atoms, 96 bonds, 12 residues, 1 model selected
> select /A:42,45,48,73,106,110,119,128,132,148,193,200,204
117 atoms, 104 bonds, 13 residues, 1 model selected
> select /A:42,45,48,73,106,110,119,128,132,148,193,200,204,213
126 atoms, 112 bonds, 14 residues, 1 model selected
> color sel yellow
> show sel atoms
> color sel byhetero
> select clear
> 6
Unknown command: 6
> save /Users/yoshioka/Desktop/1_3.png width 1986 height 1263 supersample 3
> transparentBackground true
> save /Users/yoshioka/Downloads/01_Suntag/surface.cxs
——— End of log from Tue Jun 10 18:59:10 2025 ———
> view name session-start
opened ChimeraX session
> close
> open
> /Users/yoshioka/Downloads/22_OPN4/boltz_results_5_Hatori_AA92593/predictions/hOPN4_AA92593_affinity/hOPN4_AA92593_affinity_model_0.cif
Summary of feedback from opening
/Users/yoshioka/Downloads/22_OPN4/boltz_results_5_Hatori_AA92593/predictions/hOPN4_AA92593_affinity/hOPN4_AA92593_affinity_model_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
hOPN4_AA92593_affinity_model_0.cif title:
. [more info...]
Chain information for hOPN4_AA92593_affinity_model_0.cif #1
---
Chain | Description
A | .
Non-standard residues in hOPN4_AA92593_affinity_model_0.cif #1
---
LIG1 — (LIG1)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Computing secondary structure
> lighting full
> lighting soft
Alignment identifier is 1/A
> select /A:308-309
20 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:308-311
32 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:308
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:308
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
Drag select of 3 residues
> select clear
> close
> open /Users/yoshioka/Downloads/04_A2AR/Cryo-EM/J325_008_volume_map.mrc
Opened J325_008_volume_map.mrc as #1, grid size 360,360,360, pixel 0.75, shown
at level 0.0364, step 2, values float32
> volume #1 step 1
> volume #1 level 0.05727
> close
> open
> /Users/yoshioka/Downloads/41_scenm/解析例/01_4HHB_deoxyhaemoglobin/4hhb.pdb
4hhb.pdb title:
The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution
[more info...]
Chain information for 4hhb.pdb #1
---
Chain | Description | UniProt
A C | hemoglobin subunit α | HBA_HUMAN 1-141
B D | hemoglobin subunit β | HBB_HUMAN 1-146
Non-standard residues in 4hhb.pdb #1
---
HEM — protoporphyrin IX containing Fe (HEME)
PO4 — phosphate ion
> hide atoms
> show atoms
> hide atoms
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
4384 atoms, 4500 bonds, 574 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> lighting full
> lighting soft
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> lighting soft
Desktop color scheme is light
Desktop color scheme is dark
> close
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
> open /Users/yoshioka/Downloads/41_scenm/解析例/00_1csp/1csp_scwrl4.pdb
> /Users/yoshioka/Downloads/41_scenm/解析例/00_1csp/1csp.pdb
Chain information for 1csp_scwrl4.pdb #1
---
Chain | Description
A | No description available
1csp.pdb title:
Crystal structure of the bacillus subtilis major cold shock protein, CSPB: A
universal nucleic-acid binding domain [more info...]
Chain information for 1csp.pdb #2
---
Chain | Description | UniProt
A | cold shock protein B(CSPB) | CSPB_BACSU 1-67
Computing secondary structure
> show atoms
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1csp_scwrl4.pdb, chain A (#1) with 1csp.pdb, chain A (#2), sequence
alignment score = 344.3
RMSD between 67 pruned atom pairs is 0.000 angstroms; (across all 67 pairs:
0.000)
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> close
> open
> /Users/yoshioka/Downloads/boltz_results_FGFR2_validation/predictions/FGFR2_validation/FGFR2_validation_model_0.cif
FGFR2_validation_model_0.cif title:
. [more info...]
Chain information for FGFR2_validation_model_0.cif #1
---
Chain | Description
A | .
B | .
Color FGFR2_validation_model_0.cif by residue attribute pLDDT_score
Computing secondary structure
> lighting full
> lighting soft
> lighting flat
> color bychain
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
1734 atoms, 1781 bonds, 220 residues, 1 model selected
> select clear
> select /A
1734 atoms, 1781 bonds, 220 residues, 1 model selected
> color sel #00f900ff
> select /B
514 atoms, 518 bonds, 61 residues, 1 model selected
> color sel cyan
> select clear
> save /Users/yoshioka/Downloads/FGFR2_Binder.png width 1930 height 1237
> supersample 3
> open
> /Users/yoshioka/Downloads/boltz_results_FGFR2_validation/boltz_results_FGFR2_validation/predictions/FGFR2_validation/FGFR2_validation_model_0.cif
FGFR2_validation_model_0.cif title:
. [more info...]
Chain information for FGFR2_validation_model_0.cif #2
---
Chain | Description
A | .
B | .
Color FGFR2_validation_model_0.cif by residue attribute pLDDT_score
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FGFR2_validation_model_0.cif, chain A (#1) with
FGFR2_validation_model_0.cif, chain A (#2), sequence alignment score = 1154.7
RMSD between 110 pruned atom pairs is 0.415 angstroms; (across all 220 pairs:
20.089)
> hide #1 models
> select #2/A
1734 atoms, 1781 bonds, 220 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> select #2/B
514 atoms, 518 bonds, 61 residues, 1 model selected
> color sel #00fdffff
> select clear
> show #1 models
> hide #1 models
> set bgColor black
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> set bgColor white
> save /Users/yoshioka/Downloads/10_25.png width 1930 height 1237 supersample
> 3
> show #2 models
> hide #1 models
> set bgColor black
> save /Users/yoshioka/Downloads/3_1.png width 1930 height 1237 supersample 3
> set bgColor white
> lighting full
> lighting soft
> color bfactor #2
2248 atoms, 281 residues, atom bfactor range 57.3 to 98.9
> show #1 models
> color bfactor
4496 atoms, 562 residues, atom bfactor range 51.1 to 98.9
> close
> open /Users/yoshioka/Downloads/3vg9_validation_2fo-fc_map_coef.cif
Summary of feedback from opening
/Users/yoshioka/Downloads/3vg9_validation_2fo-fc_map_coef.cif
---
warning | No mmCIF models found.
> open /Users/yoshioka/Downloads/3vg9.ccp4
Opened 3vg9.ccp4 as #1, grid size 100,80,96, pixel 1.21,1.13,1.18, shown at
level 0.423, step 1, values float32
> volume #1 level 0.2159
> volume #1 level 0.1614
> close
> open /Users/yoshioka/Downloads/r3vg9sf.ent
Summary of feedback from opening /Users/yoshioka/Downloads/r3vg9sf.ent
---
warnings | Ignored bad PDB record found on line 1
data_r3vg9sf
Ignored bad PDB record found on line 2
#
Ignored bad PDB record found on line 3
_audit.revision_id 1_0
Ignored bad PDB record found on line 4
_audit.creation_date 2012-02-01
Ignored bad PDB record found on line 5
_audit.update_record 'Initial release'
45320 messages similar to the above omitted
> open /Users/yoshioka/Downloads/3vg9_diff.ccp4
Opened 3vg9_diff.ccp4 as #1, grid size 100,80,96, pixel 1.21,1.13,1.18, shown
at level 0.122, step 1, values float32
> volume #1 level 0.05845
> volume #1 level 0.08639
> close
> open /Users/yoshioka/Downloads/3vg9.ccp4
Opened 3vg9.ccp4 as #1, grid size 100,80,96, pixel 1.21,1.13,1.18, shown at
level 0.423, step 1, values float32
> close
> open
> /Users/yoshioka/Downloads/22_OPN4/boltz_results_5_Hatori_AA92593/predictions/hOPN4_AA92593_affinity/hOPN4_AA92593_affinity_model_0.cif
> format mmcif
Summary of feedback from opening
/Users/yoshioka/Downloads/22_OPN4/boltz_results_5_Hatori_AA92593/predictions/hOPN4_AA92593_affinity/hOPN4_AA92593_affinity_model_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
hOPN4_AA92593_affinity_model_0.cif title:
. [more info...]
Chain information for hOPN4_AA92593_affinity_model_0.cif #1
---
Chain | Description
A | .
Non-standard residues in hOPN4_AA92593_affinity_model_0.cif #1
---
LIG1 — (LIG1)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Computing secondary structure
> close
> open
> /Users/yoshioka/Downloads/12_BINDS/250828_cryoEM_workshop/alphafold_model.pdb
> format pdb
Chain information for alphafold_model.pdb #1
---
Chain | Description
A | No description available
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting flat
> color #1 #00f900ff
> close
> open /Volumes/share/4_ラボメンバー過去の発表資料/宮下靖臣/0_分解能力コンテスト/3/3.mrc format mrc
Opened 3.mrc as #1, grid size 256,256,256, pixel 1.22, shown at level 0.325,
step 1, values float32
> graphics silhouettes false
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> volume #1 level 0.7213
> ui tool show Boltz
> open /Users/yoshioka/Downloads/29_Boltz_2/pdb/3rze_H1R.pdb
> /Users/yoshioka/Downloads/29_Boltz_2/pdb/4u14_mAChR.pdb
> /Users/yoshioka/Downloads/29_Boltz_2/pdb/9j5v_LPA1.cif
> /Users/yoshioka/Downloads/29_Boltz_2/pdb/caffeine.pdb
Summary of feedback from opening
/Users/yoshioka/Downloads/29_Boltz_2/pdb/9j5v_LPA1.cif
---
note | Fetching CCD A1L3Q from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/A1L3Q/A1L3Q.cif
3rze_H1R.pdb title:
Structure of the human histamine H1 receptor In complex with doxepin [more
info...]
Chain information for 3rze_H1R.pdb #2
---
Chain | Description | UniProt
A | histamine H1 receptor, lysozyme chimera | HRH1_HUMAN 20-221 405-487, LYS_BPT4 1002-1161
Non-standard residues in 3rze_H1R.pdb #2
---
5EH — (3E)-3-(dibenzo[B,E]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine
D7V — (3Z)-3-(dibenzo[B,E]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)
PO4 — phosphate ion
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
4u14_mAChR.pdb title:
Structure of the M3 muscarinic acetylcholine receptor bound to the antagonist
tiotropium crystallized with disulfide-stabilized T4 lysozyme (DST4L) [more
info...]
Chain information for 4u14_mAChR.pdb #3
---
Chain | Description | UniProt
A | muscarinic acetylcholine receptor M3,endolysin,muscarinic acetylcholine receptor M3 | ACM3_RAT 57-259 482-563, ENLYS_BPT4 1001-1161
Non-standard residues in 4u14_mAChR.pdb #3
---
0HK —
(1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane
(tiotropium)
9j5v_LPA1.cif title:
Human Lysophosphatidic Acid Receptor 1-Gi complex bound to CpY [more info...]
Chain information for 9j5v_LPA1.cif #4
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_BOVIN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-68
R | Lysophosphatidic acid receptor 1,Lysophosphatidic acid receptor 1,Lysophosphatidic acid receptor 1,LgBiT | LPAR1_HUMAN 2-364
S | scFv16 |
Non-standard residues in 9j5v_LPA1.cif #4
---
A1L3Q — CpY
((2~{R})-2-(diethylamino)-2-(2-ethyl-3-methyl-1-benzofuran-7-yl)ethanol)
caffeine.pdb title:
Thermostabilised adenosine A2A receptor In complex with caffeine [more
info...]
Chain information for caffeine.pdb #5
---
Chain | Description | UniProt
A | adenosine receptor A2A | AA2AR_HUMAN 1-317
Non-standard residues in caffeine.pdb #5
---
CFF — caffeine (3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione)
> close #1
> tile
4 models tiled
> lighting full
> style stick
Changed 18039 atom styles
> hide atoms
> show cartoons
> lighting full
> lighting soft
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1okc.ccp4
> /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC.cif
Summary of feedback from opening
/Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC.cif
---
notes | Fetching CCD CXT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/CXT/CXT.cif
Fetching CCD LDM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/LDM/LDM.cif
Fetching CCD PC1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/PC1/PC1.cif
Opened 1okc.ccp4 as #1, grid size 80,80,48, pixel 1.07,1.04,1.04, shown at
level 0.798, step 1, values float32
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #2
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #2
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> volume #1 level 0.5435
> select clear
> ui tool show Segmentations
Created segmentation sphere cursor with ID #3
Created segmentation sphere cursor with ID #4
Created segmentation sphere cursor with ID #5
> ui view fourup
> ui tool show Segmentations
Created segmentation sphere cursor with ID #3
Created segmentation sphere cursor with ID #4
Created segmentation sphere cursor with ID #5
> ui view fourup
> ui view default
Created segmentation sphere cursor with ID #3
No segmentations to remove.
> ui tool show "Segment Map"
Segmenting 1okc.ccp4, density threshold 0.543475
Only showing 60 of 78 regions.
Showing 60 of 78 region surfaces
2001 watershed regions, grouped to 78 regions
Showing 1okc.seg - 78 regions, 60 surfaces
Ungrouped to 77 regions, but did not show all surfaces, see Options
Ungrouped to 158 regions, but did not show all surfaces, see Options
Smoothing and grouping, standard deviation 3 voxels
Only showing 60 of 126 regions.
Showing 60 of 126 region surfaces
Got 126 regions after smoothing 3 voxels.
> close #3
> ui tool show "Volume Viewer"
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> close #1.1
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC.cif
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #1
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #1
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1okc.ccp4
Opened 1okc.ccp4 as #2, grid size 80,80,48, pixel 1.07,1.04,1.04, shown at
level 0.798, step 1, values float32
> hide #!2 models
> lighting full
> lighting soft
> lighting flat
> rainbow
> hide atoms
> select helix
1984 atoms, 2022 bonds, 257 residues, 1 model selected
> color sel red
> select clear
> select helix
1984 atoms, 2022 bonds, 257 residues, 1 model selected
> rainbow sel
> color sel bychain
> color sel bypolymer
> rainbow sel
> select clear
> rainbow
> show surfaces
> lighting full
> lighting soft
> show atoms
> transparency #1 50
> lighting simple
> lighting flat
> lighting full
> lighting soft
> color byhetero
> color bychain
> lighting simple
> color byhetero
> color bychain
> hide surfaces
> rainbow
> show #!2 models
> volume #2 level 0.4338
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC.cif
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #1
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #1
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ASP 2
/A ARG 170
/A LYS 205
/A VAL 207
/A LYS 267
/A ILE 293
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1OKC.cif_A SES surface #1.1: minimum, -11.35, mean 2.83,
maximum 18.00
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting flat
> lighting full
> lighting simple
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1okc.ccp4
> /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC.cif
Opened 1okc.ccp4 as #1, grid size 80,80,48, pixel 1.07,1.04,1.04, shown at
level 0.798, step 1, values float32
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #2
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #2
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1okc.ccp4 format ccp4
Opened 1okc.ccp4 as #1, grid size 80,80,48, pixel 1.07,1.04,1.04, shown at
level 0.798, step 1, values float32
> volume #1 level 0.7585
> volume #1 level 0.5786
> open /Users/yoshioka/Downloads/2rh1_validation_2fo-fc_map_coef.cif
Summary of feedback from opening
/Users/yoshioka/Downloads/2rh1_validation_2fo-fc_map_coef.cif
---
warning | No mmCIF models found.
> open /Users/yoshioka/Downloads/2rh1_validation_2fo-fc_map_coef.cif
Summary of feedback from opening
/Users/yoshioka/Downloads/2rh1_validation_2fo-fc_map_coef.cif
---
warning | No mmCIF models found.
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1okc.ccp4
Opened 1okc.ccp4 as #2, grid size 80,80,48, pixel 1.07,1.04,1.04, shown at
level 0.798, step 1, values float32
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC.cif
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #3
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #3
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> close #2
> volume #1 level 0.3197
> volume #1 style mesh
> close
> open /Users/yoshioka/Downloads/1BL8.cif
Summary of feedback from opening /Users/yoshioka/Downloads/1BL8.cif
---
note | Fetching CCD K from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif
1BL8.cif title:
Potassium channel (KCSA) from streptomyces lividans [more info...]
Chain information for 1BL8.cif #1
---
Chain | Description | UniProt
A B C D | PROTEIN (POTASSIUM CHANNEL PROTEIN) | KCSA_STRLI 23-119
Non-standard residues in 1BL8.cif #1
---
K — potassium ion
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ARG 27
/A ILE 60
/A ARG 64
/A GLU 71
/A ARG 117
/A GLN 119
/B ARG 27
/B ILE 60
/B ARG 64
/B GLU 71
/B ARG 117
/B GLN 119
/C ARG 27
/C ILE 60
/C ARG 64
/C GLU 71
/C ARG 117
/C GLN 119
/D ARG 27
/D ILE 60
/D ARG 64
/D GLU 71
/D ARG 117
/D GLN 119
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1BL8.cif_A SES surface #1.2: minimum, -13.66, mean -0.84,
maximum 8.95
Coulombic values for 1BL8.cif_B SES surface #1.3: minimum, -13.63, mean -0.84,
maximum 8.70
Coulombic values for 1BL8.cif_C SES surface #1.4: minimum, -13.37, mean -0.86,
maximum 9.09
Coulombic values for 1BL8.cif_D SES surface #1.5: minimum, -13.63, mean -0.86,
maximum 8.75
To also show corresponding color key, enter the above coulombic command and
add key true
> color #1 white
> coulombic
Coulombic values for 1BL8.cif_A SES surface #1.2: minimum, -13.66, mean -0.84,
maximum 8.95
Coulombic values for 1BL8.cif_B SES surface #1.3: minimum, -13.63, mean -0.84,
maximum 8.70
Coulombic values for 1BL8.cif_C SES surface #1.4: minimum, -13.37, mean -0.86,
maximum 9.09
Coulombic values for 1BL8.cif_D SES surface #1.5: minimum, -13.63, mean -0.86,
maximum 8.75
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> transparency 50
> color #1 #00f900ff
> coulombic
Coulombic values for 1BL8.cif_A SES surface #1.2: minimum, -13.66, mean -0.84,
maximum 8.95
Coulombic values for 1BL8.cif_B SES surface #1.3: minimum, -13.63, mean -0.84,
maximum 8.70
Coulombic values for 1BL8.cif_C SES surface #1.4: minimum, -13.37, mean -0.86,
maximum 9.09
Coulombic values for 1BL8.cif_D SES surface #1.5: minimum, -13.63, mean -0.86,
maximum 8.75
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting full
> lighting soft
> transparency 40
> select /A
708 atoms, 724 bonds, 7 pseudobonds, 100 residues, 2 models selected
> select clear
> hide surfaces
> hide cartoons
> hide atoms
> show cartoons
> select /A
708 atoms, 724 bonds, 7 pseudobonds, 100 residues, 2 models selected
> coulombic sel
Coulombic values for 1BL8.cif_A SES surface #1.2: minimum, -13.66, mean -0.84,
maximum 8.95
To also show corresponding color key, enter the above coulombic command and
add key true
> select /B
706 atoms, 724 bonds, 98 residues, 1 model selected
> coulombic sel
Coulombic values for 1BL8.cif_B SES surface #1.3: minimum, -13.63, mean -0.84,
maximum 8.70
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select /C
705 atoms, 724 bonds, 97 residues, 1 model selected
> hide sel cartoons
> select /D
705 atoms, 724 bonds, 97 residues, 1 model selected
> hide sel cartoons
> select clear
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting soft
> transparency 40
> select /B
706 atoms, 724 bonds, 98 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> select clear
> select /C
705 atoms, 724 bonds, 97 residues, 1 model selected
> show sel cartoons
> coulombic sel
Coulombic values for 1BL8.cif_C SES surface #1.4: minimum, -13.37, mean -0.86,
maximum 9.09
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> transparency 10
> lighting flat
> lighting full
> lighting soft
> lighting simple
> show atoms
> hide atoms
> select ::name="HOH"::name="K"
4 atoms, 2 pseudobonds, 4 residues, 2 models selected
> show sel atoms
> select clear
> transparency 50
Drag select of 1BL8.cif_A SES surface, 12616 of 96322 triangles, 1BL8.cif_C
SES surface, 22746 of 95966 triangles, 4 atoms, 32 residues, 12 pseudobonds
> show sel atoms
> color sel byhetero
> undo
> select clear
> close
> close #
Expected a models specifier or a keyword
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC.cif
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #1
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #1
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ASP 2
/A ARG 170
/A LYS 205
/A VAL 207
/A LYS 267
/A ILE 293
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1OKC.cif_A SES surface #1.1: minimum, -11.35, mean 2.83,
maximum 18.00
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting full
> lighting soft
> lighting flat
> lighting simple
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC_TMDET.cif
Summary of feedback from opening
/Users/yoshioka/Downloads/19_講義資料等/生化学特論/1OKC_TMDET.cif
---
notes | PDBx/mmCIF styling lost on line 3746. Rereading mmCIF file from the beginning.
Fetching CCD AG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/AG/AG.cif
1OKC_TMDET.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC_TMDET.cif #1
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC_TMDET.cif #1
---
AG — (AG)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> lighting full
> lighting soft
> lighting full
> lighting soft
> rainbow
> hide atoms
> select ::name="PC1"
117 atoms, 113 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select ::name="AG"
204 atoms, 1 residue, 1 model selected
> show sel atoms
> select clear
> lighting flat
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/r1okcsf.ent
Summary of feedback from opening
/Users/yoshioka/Downloads/19_講義資料等/生化学特論/r1okcsf.ent
---
warnings | Ignored bad PDB record found on line 1
data_r1okcsf
Ignored bad PDB record found on line 2
#
Ignored bad PDB record found on line 3
loop_
Ignored bad PDB record found on line 4
_audit.revision_id
Ignored bad PDB record found on line 5
_audit.creation_date
18640 messages similar to the above omitted
> lighting full
[Repeated 1 time(s)]
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> lighting full
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting simple
> lighting full
> lighting soft
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/1_a.png width 1930 height
> 1237 supersample 3 transparentBackground true
> lighting flat
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/1_a_2.png width 1930
> height 1237 supersample 3 transparentBackground true
> lighting full
> lighting soft
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/1_a.png width 1930 height
> 1237 supersample 3
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/1_a.png width 1930 height
> 1237 supersample 3 transparentBackground true
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/pdb/1OKC.cif
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #1
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #1
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> color byhetero
> rainbow
> lighting full
> lighting soft
> select ::name="CDL"::name="CXT"::name="HOH"::name="LDM"::name="PC1"
432 atoms, 344 bonds, 93 residues, 1 model selected
> hide sel atoms
> select clear
> color byhetero
> hide atoms
> select clear
> select ::name="CDL"
142 atoms, 139 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> color byhetero
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/1_b.png width 1930 height
> 1237 supersample 3 transparentBackground true
> lighting full
> lighting soft
> hide atoms
> undo
> hide atoms
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/1_c.png width 1930 height
> 1237 supersample 3 transparentBackground true
Alignment identifier is 1/A
> select helix
1984 atoms, 2022 bonds, 257 residues, 1 model selected
> select clear
> select /A:4
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:4-38
256 atoms, 258 bonds, 35 residues, 1 model selected
> select clear
> hide cartoons
> select /A:4
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:4-38
256 atoms, 258 bonds, 35 residues, 1 model selected
> select /A:4-5
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:4-92
698 atoms, 712 bonds, 89 residues, 1 model selected
> show sel cartoons
> select clear
> select /A:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:4-99
764 atoms, 780 bonds, 96 residues, 1 model selected
> show sel cartoons
> select /A:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:93-99
66 atoms, 67 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select clear
> lighting full
> lighting soft
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/2_a_1.png width 1930
> height 1237 supersample 3 transparentBackground true
> hide cartoons
> select /A:109
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:109-195
656 atoms, 671 bonds, 87 residues, 1 model selected
> show sel cartoons
> select clear
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/2_a_2.png width 1930
> height 1237 supersample 3 transparentBackground true
> select /A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:206-291
665 atoms, 680 bonds, 86 residues, 1 model selected
> show sel cartoons
> select ~sel
2021 atoms, 1968 bonds, 299 residues, 1 model selected
> hide sel cartoons
> select clear
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/2_a_3.png width 1930
> height 1237 supersample 3 transparentBackground true
> show cartoons
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ASP 2
/A ARG 170
/A LYS 205
/A VAL 207
/A LYS 267
/A ILE 293
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1OKC.cif_A SES surface #1.1: minimum, -11.35, mean 2.83,
maximum 18.00
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> hide #1.1 models
> show #1.1 models
> lighting full
> lighting soft
> lighting simple
> lighting flat
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting flat
> lighting full
> lighting soft
> lighting simple
> transparency 20
> lighting full
> lighting soft
> lighting flat
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> transparency 10
> undo
> show #1.1 models
> surface style mesh
> surface style dot
> surface style solid
> transparency 50
> transparency 10
> transparency 30
> hide #1.1 models
> show #1.1 models
> transparency 10
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/2_b.png width 1930 height
> 1237 supersample 3 transparentBackground true
> save /Users/yoshioka/Downloads/19_講義資料等/生化学特論/Fig/2_c.png width 1930 height
> 1237 supersample 3 transparentBackground true
> close
> open /Users/yoshioka/Downloads/19_講義資料等/生化学特論/pdb/1okc.ccp4
> /Users/yoshioka/Downloads/19_講義資料等/生化学特論/pdb/1OKC.cif
Opened 1okc.ccp4 as #1, grid size 80,80,48, pixel 1.07,1.04,1.04, shown at
level 0.798, step 1, values float32
1OKC.cif title:
structure of mitochondrial ADP/ATP carrier in complex with
carboxyatractyloside [more info...]
Chain information for 1OKC.cif #2
---
Chain | Description | UniProt
A | ADP, ATP CARRIER PROTEIN HEART ISOFORM T1 | ADT1_BOVIN 1-297
Non-standard residues in 1OKC.cif #2
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CXT — Carboxyatractyloside
LDM — 3-laurylamido-N,N'-dimethylpropylaminoxyde
([3-(dodecanoylamino)propyl](hydroxy)dimethylammonium)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> volume #1 level 0.5391
> volume #1 level 0.3767
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> volume #1 style mesh
> volume #1 style surface
> volume #1 level 0.3636
> volume #1 color #b2b2b299
> lighting soft
> lighting full
> lighting simple
> select ::name="CXT"
51 atoms, 55 bonds, 1 residue, 1 model selected
> volume #1 level 0.346
> volume zone near sel 1.5
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone near sel 1.5 newmap true
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone near sel 1.5 newmap true
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone #1 nearAtoms sel 1.5 newmap true
Expected a keyword
> volume zone #1 nearAtoms sel range 1.5 Newmap true
Expected a keyword
> volume zone #1 nearAtoms sel range 1.5 newMap true
Opened 1okc.ccp4 zone as #3, grid size 80,80,48, pixel 1.07,1.04,1.04, shown
at step 1, values float32
> hide #!1 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1925, in
_color_chosen
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 ATI-7.0.23
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 8-Core Intel Core i7
Processor Speed: 3.8 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: 8 GB
System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0)
OS Loader Version: 583~2210
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 27日 1時間 29分
Graphics/Displays:
AMD Radeon Pro 5500 XT:
Chipset Model: AMD Radeon Pro 5500 XT
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0041
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XT-012
Option ROM Version: 113-D322A1XT-012
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 8 weeks ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Orthoplanes: 'NoneType' object has no attribute 'image_colors' |
comment:2 by , 6 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Same resolution as #18854.