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Opened 3 months ago
Closed 3 months ago
#18380 closed defect (duplicate)
'MRCGrid' object has no attribute 'dicom_data'
| 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-14.7.7-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
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/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/ChimeraXFigures/RefineJ301-C1/cryosparc_P37_J301_009_volume_map_sharp.mrc
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.836, shown at level 0.0711, step 2, values float32
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/ChimeraXFigures/RefineJ301-C1/followed-
> by-local-refine-with-small-focus-
> mask-J674/cryosparc_P37_J674_004_volume_map_sharp.mrc
Opened cryosparc_P37_J674_004_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.836, shown at level 0.0636, step 2, values float32
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/ChimeraXFigures/RefineJ301-C1/followed-
> by-local-refine-with-small-focus-mask-J674/cryosparc_P37_J678_map_locres.mrc
Opened cryosparc_P37_J678_map_locres.mrc as #3, grid size 300,300,300, pixel
0.836, shown at level 4.02, step 2, values float32
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/ChimeraXFigures/RefineJ301-C1/cryosparc_P37_J677_map_locres.mrc
Opened cryosparc_P37_J677_map_locres.mrc as #4, grid size 300,300,300, pixel
0.836, shown at level 7, step 2, values float32
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/ChimeraXFigures/RefineJ301-C1/J301_009_volume_map_half_A_deepEMhancer-
> sharpened_highres.mrc
Opened J301_009_volume_map_half_A_deepEMhancer-sharpened_highres.mrc as #5,
grid size 300,300,300, pixel 0.836, shown at level 0.0267, step 2, values
float32
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/ChimeraXFigures/RefineJ301-C1/J301_009_volume_map_half_A_deepEMhancer-
> sharpened_tight.mrc
Opened J301_009_volume_map_half_A_deepEMhancer-sharpened_tight.mrc as #6, grid
size 300,300,300, pixel 0.836, shown at level 0.0291, step 2, values float32
> open /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/placed-TASK1.pdb
placed-TASK1.pdb title:
Crystal structure of the human two pore domain potassium ion channel task-1
(K2P3.1) In A closed conformation [more info...]
Chain information for placed-TASK1.pdb #7
---
Chain | Description | UniProt
A B | potassium channel subfamily K member 3 | KCNK3_HUMAN 1-259
Non-standard residues in placed-TASK1.pdb #7
---
DMU — decyl-β-D-maltopyranoside (decylmaltoside)
K — potassium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
Y01 — cholesterol hemisuccinate
> volume #1-6 step 1 level 0.2
> hide #!3 models
> hide #!4 models
> open /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/TASK1_6rv3.pdb
Chain information for TASK1_6rv3.pdb #8
---
Chain | Description
A | No description available
B | No description available
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> close #7
> select add #8
4267 atoms, 4368 bonds, 2 pseudobonds, 529 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models #8,1,0,0,36.61,0,1,0,43.883,0,0,1,18.282
> view matrix models #8,1,0,0,48.889,0,1,0,58.204,0,0,1,28.564
> view matrix models #8,1,0,0,42.658,0,1,0,56.446,0,0,1,37.475
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.13807,-0.80261,-0.58031,22.869,0.97284,0.21982,-0.072561,30.184,0.1858,-0.55453,0.81116,20.771
> view matrix models
> #8,0.13807,-0.80261,-0.58031,120.92,0.97284,0.21982,-0.072561,124.26,0.1858,-0.55453,0.81116,67.262
> view matrix models
> #8,0.13807,-0.80261,-0.58031,115.25,0.97284,0.21982,-0.072561,133.29,0.1858,-0.55453,0.81116,68.265
> view matrix models
> #8,0.60778,-0.6478,-0.4593,120.11,0.79184,0.45072,0.41212,127.46,-0.059954,-0.61417,0.78689,65.43
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 4 maps.
> fitmap #8 inMap #1
Fit molecule TASK1_6rv3.pdb (#8) to map
cryosparc_P37_J301_009_volume_map_sharp.mrc (#1) using 4267 atoms
average map value = 0.06377, steps = 68
shifted from previous position = 2.21
rotated from previous position = 4.77 degrees
atoms outside contour = 3436, contour level = 0.2
Position of TASK1_6rv3.pdb (#8) relative to
cryosparc_P37_J301_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.54313421 -0.69821620 -0.46636827 118.80363676
0.83511431 0.39158268 0.38632511 127.86137354
-0.08711671 -0.59929720 0.79577229 64.74603891
Axis -0.52938556 -0.20369902 0.82356398
Axis point -27.17429687 160.93041967 0.00000000
Rotation angle (degrees) 68.57736390
Shift along axis -35.61566071
> view matrix models
> #8,0.02368,-0.77188,-0.63533,118.58,0.99686,-0.029816,0.073379,120.4,-0.075583,-0.63507,0.76875,64.117
> view matrix models
> #8,0.02368,-0.77188,-0.63533,116.25,0.99686,-0.029816,0.073379,125.06,-0.075583,-0.63507,0.76875,65.487
> fitmap #8 inMap #1
Fit molecule TASK1_6rv3.pdb (#8) to map
cryosparc_P37_J301_009_volume_map_sharp.mrc (#1) using 4267 atoms
average map value = 0.3566, steps = 96
shifted from previous position = 5
rotated from previous position = 9.75 degrees
atoms outside contour = 1359, contour level = 0.2
Position of TASK1_6rv3.pdb (#8) relative to
cryosparc_P37_J301_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.12533631 -0.67308562 -0.72886663 119.80649047
0.99044941 0.04234642 0.13121262 125.90446596
-0.05745243 -0.73835123 0.67196479 67.92548227
Axis -0.43618614 -0.33679133 0.83445387
Axis point 15.11240468 133.74454344 0.00000000
Rotation angle (degrees) 94.59869596
Shift along axis -37.98078139
> save /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/6RV3-300px-grid.pdb
> select subtract #8
Nothing selected
> hide #!6 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> view
[Repeated 1 time(s)]
> ui tool show "Side View"
> hide #!1 models
> color #2 #ffffb254 models
> color #2 #ffffb274 models
> select add #8
4267 atoms, 4368 bonds, 2 pseudobonds, 529 residues, 2 models selected
> show sel atoms
> hide #!8 models
> show #!8 models
> select subtract #8
Nothing selected
> color #2 #009193ff models
> color #2 #009193f1 models
> color #2 #009193e6 models
> color #2 #009193c1 models
> color #8 #ff85ffff
> color byhetero
> color #8 #ffd479ff
> color byhetero
> color #2 #009193b3 models
> hide #!8 models
> color #2 #009193ff models
> lighting shadows true
> lighting full
> lighting shadows false
> show #!8 models
> color #2 #00919398 models
> color #2 #00919361 models
> color #2 #009193cc models
> open /Users/Celine/Seafile/TASK-1/RealSpaceRefine_1/TASK1_Cter-
> to-267x2_small-sugars_real_space_refined_001.pdb
Chain information for TASK1_Cter-to-267x2_small-
sugars_real_space_refined_001.pdb #7
---
Chain | Description
A B | No description available
> show atoms
> hide #!8 models
> color #2 #009193e1 models
> color #2 #009193ea models
> color #2 #009193f0 models
> color #2 #009193f2 models
> color #2 #009193ff models
> color #2 #ff7e79ff models
> color #7 byhetero
> color #2 #009193ff models
> color #7 #ff7e79ff
> color #7 byhetero
> hide #7 models
> lighting shadows true
> hide #!2 models
> show #!2 models
> color #2 #009193cc models
> show #7 models
> color #2 #009193b3 models
> color #2 #00919380 models
> hide #7 models
> color #2 #009193ff models
> color #2 #00919380 models
> show #7 models
> hide #7 models
> color #2 #009193ff models
> color #2 #00919380 models
> show #7 models
> ui tool show "Surface Color"
> color sample #1.1 map #4 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> show #!1 models
> hide #!2 models
> hide #7 models
> color sample #1.1 map #4 palette 3.6,#ff0000:3.2,#ffffff:2.38,#0000ff
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> color sample #1.1 map #4 palette 3.6,#ff0000:3.2,#ffffff:2.8,#0000ff
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> color sample #1.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> color sample #1.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> color single #1.1
> color sample #1.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> open /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/masks/J294_map15.mrc
Opened J294_map15.mrc as #9, grid size 150,150,150, pixel 1.67, shown at level
0.0365, step 1, values float32
> hide #!9 models
> show #!6 models
> show #!5 models
> color single #1.1
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!6 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> show #!9 models
> hide #!9 models
> show #!9 models
> vop mask#5 surfaces #9
> volume mask#5 surfaces #9
Expected a density maps specifier or a keyword
> vop mask #5 surfaces #9
Opened J301_009_volume_map_half_A_deepEMhancer-sharpened_highres.mrc masked as
#10, grid size 77,88,141, pixel 0.836, shown at step 1, values float32
> vop mask #6 surfaces #9
Opened J301_009_volume_map_half_A_deepEMhancer-sharpened_tight.mrc masked as
#11, grid size 77,88,141, pixel 0.836, shown at step 1, values float32
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!5 models
> show #!6 models
> close #5-6
> show #!10 models
> show #!11 models
> color sample #10.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.32, maximum 7.847
> hide #!11 models
> show #!11 models
> color sample #10.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.32, maximum 7.847
> hide #!10 models
> color sample #11.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.291, maximum 6.568
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> close #11
> save /Users/Celine/Desktop/image1.png supersample 3
> hide #!10 models
> show #!1 models
> vop mask #1 surfaces #9
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc masked as #5, grid size
77,88,141, pixel 0.836, shown at step 1, values float32
> color sample #1.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> color sample #1.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> color sample #1.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.449, maximum 11.54
> show #!1 models
> hide #!5 models
> show #!9 models
> hide #!9 models
> show #!9 models
> vop mask #1 surfaces #9
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc masked as #6, grid size
77,88,141, pixel 0.836, shown at step 1, values float32
> hide #!9 models
> hide #!6 models
> show #!1 models
> show #!6 models
> hide #!1 models
> show #!5 models
> close #5
> color sample #6.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.344, maximum 6.651
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #7 models
> hide #!8 models
> hide #7 models
> show #!8 models
> molmap #8/A-D 10
Opened TASK1_6rv3.pdb map 10 as #5, grid size 38,41,40, pixel 3.33, shown at
level 0.0632, step 1, values float32
> molmap #8/A-D 5
Opened TASK1_6rv3.pdb map 5 as #5, grid size 58,64,62, pixel 1.67, shown at
level 0.101, step 1, values float32
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> molmap #8/A-D 7
Opened TASK1_6rv3.pdb map 7 as #5, grid size 46,51,49, pixel 2.33, shown at
level 0.0872, step 1, values float32
> rename #5 "TASK1_6rv3.pdb molmap 7"
> vop mask #1 surfaces #7
No surfaces specified
> vop mask #1 surfaces #5
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc masked as #11, grid size
74,80,110, pixel 0.836, shown at step 1, values float32
> hide #!6 models
> hide #!5 models
> color sample #11.1 map #4 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 2.838, mean 3.262, maximum 6.52
> hide #!8 models
> show #!5 models
> hide #!5 models
> volume #11 level 0.1542
> volume #11 level 0.2
> volume #11 level 0.04363
> volume #11 level 0.2
> show #!1 models
> hide #!11 models
> color single #1.1
> show #!11 models
> hide #!1 models
> show #!1 models
> hide #!11 models
> show #!11 models
> show #!6 models
> hide #!11 models
> hide #!1 models
> show #!11 models
> hide #!6 models
> show #!6 models
> close #11
> close #5
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> lighting shadows false
> lighting shadows true
> save /Users/Celine/Desktop/image1.png supersample 3
> hide #!6 models
> show #!2 models
> color #2 #009193ff models
> color sample #2.1 map #3 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> save /Users/Celine/Desktop/image1.png supersample 3
> color sample #2.1 map #3 palette 2.8,#0000ff:2.9,#ffffff:3,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> color sample #2.1 map #3 palette 2.9,#0000ff:3.1,#ffffff:3.3,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> color sample #2.1 map #3 palette 2.9,#0000ff:3,#ffffff:3.2,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> color sample #2.1 map #3 palette 3,#0000ff:3.1,#ffffff:3.2,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> color sample #2.1 map #3 palette 2.9,#0000ff:3,#ffffff:3.1,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> color sample #2.1 map #3 palette 2.8,#0000ff:3,#ffffff:3.2,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> color sample #2.1 map #3 palette 2.8,#0000ff:3.2,#ffffff:3.6,#ff0000
Map values for surface "surface": minimum 0, mean 3.377, maximum 7.507
Map values for surface "cap near": minimum 2.94, mean 3.257, maximum 4.703
Map values for surface "cap far": minimum 3.127, mean 3.652, maximum 7.484
> open
> /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/hsTASK1_001GDN_doxapram_res34_J535.mrc
Opened hsTASK1_001GDN_doxapram_res34_J535.mrc as #5, grid size 256,256,256,
pixel 0.836, shown at level 0.081, step 1, values float32
> volume #5 level 0.2
> hide #!5 models
> hide #!2 models
> show #!1 models
> show #7 models
> rename #7 TASK1_Cter-to-267x2_small-sugars_J301.pdb
> color #1 #b2b2b29e models
> hide #!1 models
> show #!1 models
> color #1 #b2b2b2ff models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!5 models
> open /Users/Celine/Seafile/TASK-1/RealSpaceRefine_2/TASK1_Cter-
> to-267x2_small-sugars_real_space_refined_002.pdb
Chain information for TASK1_Cter-to-267x2_small-
sugars_real_space_refined_002.pdb #11
---
Chain | Description
A B | No description available
> select add #5
3 models selected
> select add #11
4310 atoms, 4406 bonds, 536 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,1,0,0,15.867,0,1,0,19.157,0,0,1,4.6396,#11,1,0,0,15.867,0,1,0,19.157,0,0,1,4.6396
> view matrix models
> #5,1,0,0,17.367,0,1,0,18.38,0,0,1,18.956,#11,1,0,0,17.367,0,1,0,18.38,0,0,1,18.956
> fitmap #5 inMap #1
Fit map hsTASK1_001GDN_doxapram_res34_J535.mrc in map
cryosparc_P37_J301_009_volume_map_sharp.mrc using 39143 points
correlation = 0.9433, correlation about mean = 0.7568, overlap = 6214
steps = 52, shift = 1.25, angle = 0.189 degrees
Position of hsTASK1_001GDN_doxapram_res34_J535.mrc (#5) relative to
cryosparc_P37_J301_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999512 0.00305405 -0.00066360 18.13365115
-0.00305476 0.99999476 -0.00107227 18.78657103
0.00066032 0.00107429 0.99999920 18.06621981
Axis 0.32479611 -0.20032202 -0.92432601
Axis point 5207.13379593 -7479.05121853 0.00000000
Rotation angle (degrees) 0.18933223
Shift along axis -14.57270149
> select subtract #5
4310 atoms, 4406 bonds, 536 residues, 1 model selected
> select subtract #11
Nothing selected
> hide #11 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> fitmap #11 inMap #5
Fit molecule TASK1_Cter-to-267x2_small-sugars_real_space_refined_002.pdb (#11)
to map hsTASK1_001GDN_doxapram_res34_J535.mrc (#5) using 4310 atoms
average map value = 0.3173, steps = 56
shifted from previous position = 1.26
rotated from previous position = 0.204 degrees
atoms outside contour = 1492, contour level = 0.2
Position of TASK1_Cter-to-267x2_small-sugars_real_space_refined_002.pdb (#11)
relative to hsTASK1_001GDN_doxapram_res34_J535.mrc (#5) coordinates:
Matrix rotation and translation
0.99999992 0.00035564 0.00017665 -0.05003705
-0.00035567 0.99999992 0.00018538 0.03386156
-0.00017658 -0.00018545 0.99999997 0.02174263
Axis -0.42308316 0.40299914 -0.81153702
Axis point 75.72217889 120.28681916 -0.00000000
Rotation angle (degrees) 0.02510956
Shift along axis 0.01717107
> show #11 models
> hide #!5 models
> hide #!1 models
> save /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/250806-Analysis.cxs
> hide #7 models
> show #7 models
> hide #11 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> color #5 #ffb2b2a5 models
> color #5 #ffb2b2a6 models
> color #1 #b2b2b288 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> color #5 #ffb2b2ee models
> color #5 #ffb2b2ff models
> hide #!5 models
> color #1 #b2b2b2be models
> color #1 #b2b2b2bd models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> molmap #8/A-D 5
Opened TASK1_6rv3.pdb map 5 as #12, grid size 58,64,62, pixel 1.67, shown at
level 0.101, step 1, values float32
> vop mask #1 surfaces #12
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc masked as #13, grid size
75,80,109, pixel 0.836, shown at step 1, values float32
> hide #!5 models
> hide #!12 models
> color #13 #009193ff models
> color #13 #009193cc models
> hide #!13 models
> show #!1 models
> color #1 #009193ff models
> select add #13
2 models selected
> select subtract #13
Nothing selected
> select add #7
4310 atoms, 4406 bonds, 536 residues, 1 model selected
> select clear
> hide #!1 models
> ui mousemode right select
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> color #7 #009193ff
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> color #7 #ff7e79ff
> color #7 #009193ff
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide #7 models
> show #7 models
> select add #7
4310 atoms, 4406 bonds, 536 residues, 1 model selected
> hide sel atoms
> select subtract #7
Nothing selected
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> color sel byhetero
> style sel stick
Changed 7 atom styles
> color sel byhetero
> color sel salmon
> color sel byhetero
> show #!1 models
> color #1 #00919380 models
> color #1 #009193ff models
> color sel salmon
> color zone #1 near sel & #7 distance 5.02
> hide #!7 models
> hide #!1 models
> show #!1 models
> color #1 #009051ff models
> color #1 #009193ff models
> show #!7 models
> color zone #1 near #7 distance 1
> color zone #1 near #7 distance 2.5
> hide #!7 models
> show #!12 models
> hide #!12 models
> show #11 models
> color #11/A salmon
> color #11/A E4A6B6
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #11/A #E4A6B6
> color #11/B #82cab1
> color #11/B teal
> color zone #1 near #11 distance 2.5
> hide #11 models
> show #!7 models
> hide #!1 models
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> show #!1 models
> color zone #1 near #7 distance 2
> color #7/B #82cab1
> color #5/B teal
> color #5/A #E4A6B6
> hide #!1 models
> color #7/A #E4A6B6
> color #7/B teal
> color sel red
> color #7/A teal
> color #7/B #E4A6B6
> color sel red
> show #!1 models
> color zone #1 near #7 distance 2
> color #13 #ff9300ff models
> show #!13 models
> show #!12 models
> molmap #8/A-D 10
Opened TASK1_6rv3.pdb map 10 as #12, grid size 38,41,40, pixel 3.33, shown at
level 0.0632, step 1, values float32
> molmap #8/A-D 15
Opened TASK1_6rv3.pdb map 15 as #12, grid size 32,34,33, pixel 5, shown at
level 0.0437, step 1, values float32
> molmap #8/A-D 20
Opened TASK1_6rv3.pdb map 20 as #12, grid size 28,30,29, pixel 6.67, shown at
level 0.031, step 1, values float32
> vop mask #1 surfaces 12
> volume mask #1 surfaces 12
Invalid "surfaces" argument: invalid surfaces specifier
> hide #!13 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!1 models
> show #!1 models
> close #13
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> color zone #6 near #7 distance 2
> hide #!7 models
> save /Users/Celine/Desktop/image1.png supersample 3
> save /Users/Celine/Desktop/image2.png supersample 3
> show #!5 models
> hide #!6 models
> color zone #5 near #7 distance 2
> color #5 silver models
> color zone #5 near #7 distance 2
> save /Users/Celine/Desktop/image3.png supersample 3
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/B:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!7 models
> select #7/A:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/B:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> color zone #6 near #7 distance 2
> color zone #5 near #7 distance 2
> hide #!7 models
> show #!6 models
> hide #!5 models
> save /Users/Celine/Desktop/image4.png supersample 3
> hide #!6 models
> show #!5 models
> save /Users/Celine/Desktop/image5.png supersample 3
> hide #!5 models
> show #!5 models
> save /Users/Celine/Desktop/image1.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/Celine/Desktop/image2.png supersample 3
> molmap #8/A-D 4
Opened TASK1_6rv3.pdb map 4 as #12, grid size 67,75,72, pixel 1.33, shown at
level 0.101, step 1, values float32
> show #!1 models
> select add #7
4310 atoms, 4406 bonds, 536 residues, 1 model selected
> hide #!1 models
> vop mask #1 surfaces #12
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc masked as #13, grid size
75,79,110, pixel 0.836, shown at step 1, values float32
> hide #!12 models
> hide #!6 models
> select subtract #7
1 model selected
> show #!8 models
> hide #!8 models
> show #!8 models
> close #13
> close #12
> molmap #7/A-D 4
Opened TASK1_Cter-to-267x2_small-sugars_J301.pdb map 4 as #12, grid size
60,70,93, pixel 1.33, shown at level 0.0968, step 1, values float32
> hide #!8 models
> show #!1 models
> molmap #7/A-D 3
Opened TASK1_Cter-to-267x2_small-sugars_J301.pdb map 3 as #12, grid size
73,87,118, pixel 1, shown at level 0.113, step 1, values float32
> molmap #7/A-D 4
Opened TASK1_Cter-to-267x2_small-sugars_J301.pdb map 4 as #12, grid size
60,70,93, pixel 1.33, shown at level 0.0968, step 1, values float32
> vop mask #1 surfaces #12
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc masked as #13, grid size
72,88,125, pixel 0.836, shown at step 1, values float32
> hide #!12 models
> show #!12 models
> close #13
> show #!1 models
> volume substract #1, #12
Expected a density maps specifier or a keyword
> molmap #7/A-D 2
Opened TASK1_Cter-to-267x2_small-sugars_J301.pdb map 2 as #12, grid size
101,121,167, pixel 0.667, shown at level 0.189, step 1, values float32
> hide #!12 models
> show #!12 models
> vop mask #1 surfaces #12
Opened cryosparc_P37_J301_009_volume_map_sharp.mrc masked as #13, grid size
70,86,123, pixel 0.836, shown at step 1, values float32
> hide #!12 models
> color #13 #941751ff models
> show #!1 models
> substract #1, #13
Unknown command: substract #1, #13
> volume substract #1, #13
Expected a density maps specifier or a keyword
> rename #13 cryosparc_P37_J301_009_volume_map_sharp_masked.mrc
> volume substract #1, #13
Expected a density maps specifier or a keyword
> volume substract #1,#13
Expected a density maps specifier or a keyword
> models
Unknown command: models
> help models
No help found for 'models'
> hide #13.1.2 models
> hide #13.1.1 models
> hide #!13.1 models
> hide #!13 models
> show #!13 models
> show #13.1 models
> hide #!13 models
> show #!7 models
> hide #!1 models
> show #!1 models
> save /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/test.mrc models #13
> close #13
> open /Users/Celine/Seafile/TASK-1/ExpDataFiles/cryoEM/test.mrc
Opened test.mrc as #13, grid size 70,86,123, pixel 0.836,0.836,0.836, shown at
level 0.555, step 1, values float32
> volume substract #1, #13
Expected a density maps specifier or a keyword
> volume substract #1,#13
Expected a density maps specifier or a keyword
> volume substract #13,#1
Expected a density maps specifier or a keyword
> volume substract
Expected a density maps specifier or a keyword
> help volume substract
> volume substract
Expected a density maps specifier or a keyword
> volume substract
Expected a density maps specifier or a keyword
> volume subtract #1,#13
Missing or invalid "volumes" argument: only initial part "#1" of atom
specifier valid
> volume subtract #1, #13
Missing or invalid "volumes" argument: only initial part "#1" of atom
specifier valid
> volume subtract #1,#13
Missing or invalid "volumes" argument: only initial part "#1" of atom
specifier valid
> volume subtract #1,#13 output #14
Missing or invalid "volumes" argument: only initial part "#1" of atom
specifier valid
> molmap #7/A-D 2 onGrid #1
Opened TASK1_Cter-to-267x2_small-sugars_J301.pdb map 2 as #12, grid size
300,300,300, pixel 0.836, shown at level 0.188, step 1, values float32
> volume subtract #1, #13
Missing or invalid "volumes" argument: only initial part "#1" of atom
specifier valid
> hide #!13 models
> hide #!12 models
> show #!12 models
> volume subtract #1, #12
Missing or invalid "volumes" argument: only initial part "#1" of atom
specifier valid
> hide #!1 models
> show #!1 models
> hide #!12 models
> show #!12 models
> hide #!7 models
> info #12
4 models
#12, TASK1_Cter-to-267x2_small-sugars_J301.pdb map 2, shown size 300,300,300,
step 1, voxel size 0.836, level 0.1883, value range 0 - 10.852, value type
float32, 0 symmetry operators
#12.1, surface, shown, 170152 triangles
#12.1.1, cap near, shown, 1781 triangles
#12.1.2, cap far, shown, 1650 triangles
> info #1
4 models
#1, cryosparc_P37_J301_009_volume_map_sharp.mrc, shown size 300,300,300, step
1, voxel size 0.836, level 0.2, value range -0.82268 - 1.2938, value type
float32, 0 symmetry operators
#1.1, surface, shown, 152728 triangles
#1.1.1, cap near, shown, 2035 triangles
#1.1.2, cap far, shown, 1051 triangles
> volume subtract #1, #12
Missing or invalid "volumes" argument: only initial part "#1" of atom
specifier valid
> ui tool show "Map Eraser"
> hide #!12 models
> select add #14
1 model selected
> hide #14 models
> ui tool show Segmentations
> ui view fourup
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AV000K0D/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.140.96
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.7 (23H723)
Kernel Version: Darwin 23.6.0
Time since boot: 7 days, 4 hours, 16 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PHL BDM3270:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.1
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
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: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.3.1
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.0
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'MRCGrid' object has no attribute 'dicom_data' |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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