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Opened 5 months ago
Closed 5 months ago
#17906 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: Windows-10-10.0.26120
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:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Tue Jun 3 15:19:52 2025 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 E:\analysis\pcox\Native\Full\Native-Pcox.pdb format pdb
Chain information for Native-Pcox.pdb #1
---
Chain | Description
A B C D | No description available
> set bgColor white
> 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
> color #1 cyan
> open E:/analysis/pcox/Complex/Final/refined_real_space_44a.pdb
Summary of feedback from opening
E:/analysis/pcox/Complex/Final/refined_real_space_44a.pdb
---
warnings | Cannot find LINK/SSBOND residue ZN (1103 )
Cannot find LINK/SSBOND residue ZN (1103 )
Cannot find LINK/SSBOND residue ZN (1103 )
Cannot find LINK/SSBOND residue ZN (1103 )
Cannot find LINK/SSBOND residue ZN (1103 )
3 messages similar to the above omitted
Chain information for refined_real_space_44a.pdb #2
---
Chain | Description
A B C D | No description available
> 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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> 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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> color #2 #ffaaffff
> select ::name="ACO"::name="ADP"::name="HOH"::name="ZN"
329 atoms, 328 bonds, 25 residues, 1 model selected
> color sel orange red
> color sel lime
[Repeated 1 time(s)]
> color sel blue
> color sel forest green
> select clear
[Repeated 1 time(s)]
> save "D:/AIIMS/PCOX/structure comparision nativevscomplexpcox.cxs"
> color bychain
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C #1/D
Alignment identifier is 1
> sequence chain #2/A #2/B #2/C #2/D
Alignment identifier is 2
> color #2 #ffaaffff
> color #1 cyan
> select ::name="ACO"::name="ADP"::name="HOH"::name="ZN"
329 atoms, 328 bonds, 25 residues, 1 model selected
> show sel target ab
> color sel red
> select #2/A-D:562
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A-D:562-954
11724 atoms, 11984 bonds, 1572 residues, 1 model selected
> select
> #2/A-D:12-24,34-36,40-43,57-61,64-73,90-98,110-125,178-188,249-266,295-304,309-316,399-412,422-429,432-436,443-446,448-450,453-455,459-472,485-488,502-509,511-520,545-558,572-578,584-594,617-630,648-657,682-694,711-724,740-748,760-762,771-778,789-805,807-809,819-821,827-839,847-859,867-882,889-891,894-896,901-908,941-948,952-962,964-977,985-989,1042-1044
12517 atoms, 12581 bonds, 1612 residues, 1 model selected
> select #2/A-D:432
28 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A-D:432-1045
18599 atoms, 18995 bonds, 2456 residues, 1 model selected
> select #2/A-D:682
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A-D:682-1045
10932 atoms, 11164 bonds, 1456 residues, 1 model selected
> select clear
> rainbow polymers palette pubugn
> rainbow polymers palette
Missing "palette" keyword's argument
> rainbow polymers palette pubu
> help palette
> pastel2-4
Unknown command: palette pastel2-4
> Set1-9 (3-9)
Unknown command: palette Set1-9 (3-9)
> Set1-9 (3-9)
Unknown command: Set1-9 (3-9)
> colour: #1, #2 Set1-9 (3-9)
Unknown command: colour: #1, #2 Set1-9 (3-9)
> undo
[Repeated 4 time(s)]
> select clear
> hide #1 models
Drag select of 5 atoms, 23 residues, 7 bonds
> select clear
> select ::name="ACO"::name="ADP"::name="HOH"::name="ZN"
329 atoms, 328 bonds, 25 residues, 1 model selected
> ui tool show Contacts
> contacts resSeparation 5 intraMol false ignoreHiddenModels true select true
> reveal true
540 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true select true reveal true
No contacts
> contacts resSeparation 5 intraRes true intraModel false intraMol false
> ignoreHiddenModels true select true reveal true
No contacts
> contacts resSeparation 5 intraRes true intraModel false intraMol false
> ignoreHiddenModels true select true reveal true
No contacts
> contacts resSeparation 5 intraRes true intraModel false ignoreHiddenModels
> true select true reveal true
No contacts
> contacts resSeparation 5 interModel false intraRes true intraModel false
> ignoreHiddenModels true select true reveal true
No contacts
> contacts resSeparation 5 interModel false intraRes true ignoreHiddenModels
> true select true reveal true
7794 contacts
> contacts intraModel false ignoreHiddenModels true
No contacts
Restriction atom specifier must not be blank
> contacts sel distanceOnly 3.4999999999999996 intraModel false
> ignoreHiddenModels true
No distances
> contacts sel distanceOnly 3.4999999999999996 intraModel false
> ignoreHiddenModels true
No distances
> hide sel target a
> undo
[Repeated 2 time(s)]
> select clear
> undo
[Repeated 5 time(s)]
> select ~sel
61656 atoms, 61496 bonds, 8677 residues, 2 models selected
> hide sel target a
> undo
> select #1/A#2/A
16398 atoms, 16715 bonds, 2176 residues, 2 models selected
> hide sel target a
> select
65836 atoms, 67119 bonds, 8713 residues, 2 models selected
> hide sel target a
> select ::name="ACO"::name="ADP"::name="HOH"::name="ZN"
329 atoms, 328 bonds, 25 residues, 1 model selected
> show sel target ab
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> hbonds sel reveal true
107 hydrogen bonds found
> hide #1 models
> view sel
> view orient
> view sel
> view
> view sel
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 1 model selected
> view sel
> select clear
> select ::name="ACO"
204 atoms, 212 bonds, 5 pseudobonds, 4 residues, 2 models selected
> ui tool show "Side View"
> select ::name="ZN"
4 atoms, 4 residues, 1 model selected
> select ::name="ZN"
4 atoms, 4 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 3.5 resSeparation 5 intraModel false
> ignoreHiddenModels true showDist true reveal true
No distances
> save D:/AIIMS/PCOX/pcoxcomplex.cxs
> save "D:/AIIMS/PCOX/figures and chimera sessions/pcoxcomplex.cxs"
> open E:/analysis/pcox/Complex/Final/cryosparc_P1_J295_007_volume_map.mrc
Opened cryosparc_P1_J295_007_volume_map.mrc as #5, grid size 360,360,360,
pixel 0.86, shown at level 0.0236, step 2, values float32
> surface dust #5 size 8.6
> volume #5 level 0.01648
> select
65836 atoms, 67119 bonds, 107 pseudobonds, 8713 residues, 7 models selected
> view sel
> select clear
> volume #5 level 0.02751
> fitmap #2 inMap #5
Fit molecule refined_real_space_44a.pdb (#2) to map
cryosparc_P1_J295_007_volume_map.mrc (#5) using 31924 atoms
average map value = 0.007838, steps = 108
shifted from previous position = 1.5
rotated from previous position = 6.7 degrees
atoms outside contour = 28936, contour level = 0.027513
Position of refined_real_space_44a.pdb (#2) relative to
cryosparc_P1_J295_007_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.00689020 -0.12151460 0.99256573 21.25947727
-0.99843689 -0.05421872 -0.01356867 326.50528931
0.05546443 -0.99110773 -0.12095108 321.25745677
Axis -0.60592548 0.58086022 -0.54355839
Axis point 0.00000000 308.33509978 15.01658273
Rotation angle (degrees) 126.23013415
Shift along axis 2.15008871
> ui mousemode right "move picked models"
> select #2/C:253
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> color zone #5 near sel & #2 distance 5.16
> surface dust #5 size 8.6
> transparency 50
> undo
[Repeated 4 time(s)]
> view sel
> select clear
[Repeated 1 time(s)]
> ui mousemode right rotate
[Repeated 1 time(s)]
> ui mousemode right translate
Drag select of 57 atoms, 280 residues, 56 bonds, 5 pseudobonds
> ui mousemode right rotate
> ui mousemode right select
Drag select of 5 atoms, 34 residues, 4 bonds
Drag select of 20 residues
> ui mousemode right translate
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> select add #4
169 atoms, 107 pseudobonds, 20 residues, 2 models selected
> select add #5
169 atoms, 107 pseudobonds, 20 residues, 6 models selected
> select subtract #5
169 atoms, 107 pseudobonds, 20 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models #5,1,0,0,-9.8838,0,1,0,19.501,0,0,1,-139.96
> view matrix models #5,1,0,0,45.934,0,1,0,-4.5956,0,0,1,147.2
> view matrix models
> #2,0.013171,-0.0072541,0.99989,25.368,-0.99761,-0.067923,0.012648,345.87,0.067824,-0.99766,-0.0081314,236.23
> view matrix models #5,1,0,0,41.533,0,1,0,1.7199,0,0,1,98.732
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.013171,-0.0072541,0.99989,-100.71,-0.99761,-0.067923,0.012648,417.76,0.067824,-0.99766,-0.0081314,260.96,#4,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #2,0.013171,-0.0072541,0.99989,-70.94,-0.99761,-0.067923,0.012648,423.85,0.067824,-0.99766,-0.0081314,254.6,#4,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.88956,-0.16604,0.42557,182.32,-0.38701,-0.22104,-0.89519,493.56,0.24271,-0.96103,0.13237,200.1,#4,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #2,-0.44619,-0.0507,0.8935,23.376,-0.88031,-0.15494,-0.44839,490.53,0.16118,-0.98662,0.024503,233.38,#4,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #2,0.56458,-0.015869,0.82522,-127.94,-0.82378,0.051351,0.56458,293.03,-0.051335,-0.99855,0.015919,269.46,#4,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "move planes"
> volume #5 region 0,0,0,359,359,359
[Repeated 2 time(s)]
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right "move picked models"
[Repeated 1 time(s)]
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.92862,-0.28543,-0.23704,309.43,0.21287,-0.93314,0.28971,327.47,-0.30389,0.21857,0.9273,-20.931,#4,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #2,-0.94506,-0.27344,-0.17915,301.15,0.22505,-0.94169,0.25013,333.04,-0.2371,0.19606,0.95149,-31.533,#4,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.94506,-0.27344,-0.17915,419.01,0.22505,-0.94169,0.25013,218.01,-0.2371,0.19606,0.95149,94.704,#4,1,0,0,0,0,1,0,0,0,0,1,0
> fitmap #2 inMap #5
Fit molecule refined_real_space_44a.pdb (#2) to map
cryosparc_P1_J295_007_volume_map.mrc (#5) using 31924 atoms
average map value = 0.05344, steps = 252
shifted from previous position = 21.8
rotated from previous position = 23.2 degrees
atoms outside contour = 6419, contour level = 0.027513
Position of refined_real_space_44a.pdb (#2) relative to
cryosparc_P1_J295_007_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.99999998 0.00008865 0.00000174 309.59368022
-0.00008865 -0.99999998 -0.00005294 309.62657216
0.00000174 -0.00005294 0.99999998 0.00946573
Axis 0.00000212 0.00002787 -1.00000000
Axis point 154.80370240 154.80642466 0.00000000
Rotation angle (degrees) 179.99492059
Shift along axis -0.00018059
> volume #5 level 0.01861
> view matrix models
> #2,-1,8.8652e-05,1.7402e-06,348.52,-8.8653e-05,-1,-5.2939e-05,312.47,1.7353e-06,-5.2939e-05,1,101.27,#4,1,0,0,0,0,1,0,0,0,0,1,0
> fitmap #2 inMap #5
Fit molecule refined_real_space_44a.pdb (#2) to map
cryosparc_P1_J295_007_volume_map.mrc (#5) using 31924 atoms
average map value = 0.05344, steps = 80
shifted from previous position = 3.8
rotated from previous position = 0.000291 degrees
atoms outside contour = 2198, contour level = 0.018613
Position of refined_real_space_44a.pdb (#2) relative to
cryosparc_P1_J295_007_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.99999998 0.00009279 0.00000470 309.58612851
-0.00009279 -0.99999998 -0.00005298 309.62863598
0.00000469 -0.00005298 0.99999998 0.00903865
Axis 0.00000051 0.00002783 -1.00000000
Axis point 154.80024667 154.80713668 0.00000000
Rotation angle (degrees) 179.99468367
Shift along axis -0.00026475
> fitmap #2 inMap #5
Fit molecule refined_real_space_44a.pdb (#2) to map
cryosparc_P1_J295_007_volume_map.mrc (#5) using 31924 atoms
average map value = 0.05344, steps = 44
shifted from previous position = 0.00716
rotated from previous position = 0.00382 degrees
atoms outside contour = 2195, contour level = 0.018613
Position of refined_real_space_44a.pdb (#2) relative to
cryosparc_P1_J295_007_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.99999997 0.00015434 -0.00000589 309.57154740
-0.00015434 -0.99999997 -0.00007608 309.63918711
-0.00000591 -0.00007608 0.99999998 0.01398657
Axis 0.00000467 0.00003884 -1.00000000
Axis point 154.79772084 154.80764933 0.00000000
Rotation angle (degrees) 179.99115721
Shift along axis -0.00051389
> ui mousemode right "translate selected models"
> ui mousemode right pivot
> transparency 50
> color #5 #aaffffff models
> volume style mesh
> volume style surface
> volume style mesh
> transparency 50
> volume style image
[Repeated 1 time(s)]
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume show
> volume hide
> volume show
> volume style surface
> transparency 0
> transparency 50
> surface dust #5 size 8.6
> select ::name="ACO"::name="ADP"::name="HOH"::name="ZN"
329 atoms, 328 bonds, 5 pseudobonds, 25 residues, 2 models selected
> save "D:/AIIMS/PCOX/figures and chimera sessions/pcoxcomplex.cxs"
> volume #5 change image level -0.002114,0 level 0.02359,0.8 level 0.1489,1
> volume #5 level 0.03463
> volume #5 step 1
> color #5 #f6f6f6ff models
> color #5 #aaffffff models
> color #5 #aaff7fff models
> color #5 #ffff7fff models
> color #5 yellow models
> color #5 #ffff7fff models
> transparency 50
> color #2 red
> color #2 #aa00ffff
> color #2 #55ffffff
> color #2 #ffaa00ff
> color #2 yellow
> color #2 #ffff7fff
> color #2 #ff55ffff
> color #2 #ffaaffff
> color #4 #aa0000ff models
> color #4 #5500ffff models
> color #4 lime models
> color #4 #00aaffff models
> color #5 #ffffff80 models
> color #5 #bebebe80 models
> color #5 #9a9a9a80 models
> color #5 #a6a6a680 models
> color #5 #9d9d9d80 models
> volume #5 level 0.03057
> ui tool show "Color Zone"
> color zone #5 near #2 distance 21.55
[Repeated 1 time(s)]
> color single #5
> color zone #5 near #2 distance 1.44
> select ::name="ACO"::name="ADP"::name="HOH"::name="ZN"
329 atoms, 328 bonds, 5 pseudobonds, 25 residues, 2 models selected
> color (#2 & sel) red
> color zone #5 near #2 distance 1.34
> color zone #5 near #2 distance 1.24
> color zone #5 near #2 distance 1.34
> color zone #5 near #2 distance 1.44
> color zone #5 near #2 distance 1.54
> color zone #5 near #2 distance 1.64
> color zone #5 near #2 distance 1.74
> color zone #5 near #2 distance 1.84
> color zone #5 near #2 distance 1.94
> color zone #5 near #2 distance 2.04
> color zone #5 near #2 distance 2.14
> color zone #5 near #2 distance 2.24
> color zone #5 near #2 distance 2.34
> volume #5 level 0.035
> volume #5 level 0.03205
> volume #5 level 0.02798
> transparency 0
> transparency 50
> transparency 0
> hide #2 models
> show #2 models
> hide #!5 models
> show #!5 models
> save "D:/AIIMS/PCOX/figures and chimera sessions/pcoxcomplex2.cxs"
> save "D:/AIIMS/PCOX/figures and chimera sessions/colormapcomplex.cxs"
——— End of log from Tue Jun 3 15:19:52 2025 ———
opened ChimeraX session
> hide #!5 models
> hide #3 models
> hide #4 models
> select subtract #3
329 atoms, 328 bonds, 5 pseudobonds, 25 residues, 2 models selected
> select add #4
329 atoms, 328 bonds, 107 pseudobonds, 25 residues, 2 models selected
> select subtract #4
329 atoms, 328 bonds, 25 residues, 1 model selected
> select subtract #3
329 atoms, 328 bonds, 25 residues, 1 model selected
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> sequence chain #2/D
Alignment identifier is 2/D
> select #1/A:456
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:1-456
3446 atoms, 3507 bonds, 456 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange red
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> sequence chain #2/D
Alignment identifier is 2/D
> select #2/A:456
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:1-456
3446 atoms, 3507 bonds, 456 residues, 1 model selected
> color sel fire brick
> color sel coral
> color sel fire brick
> color sel tomato
> color sel orange red
> select #2/A:488
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> color sel gold
> select #2/A:489
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:489-980
3704 atoms, 3787 bonds, 492 residues, 1 model selected
> color sel dark orange
> select #2/A:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:981-1045
517 atoms, 522 bonds, 65 residues, 1 model selected
> color sel gold
> select #2/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1-456
3422 atoms, 3483 bonds, 456 residues, 1 model selected
> color sel yellow green
> select #2/B:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> color sel sea green
> select #2/B:489
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:489-980
3704 atoms, 3787 bonds, 492 residues, 1 model selected
> color sel olive
> select #2/B:981-983
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #2/B:981-1045
517 atoms, 522 bonds, 65 residues, 1 model selected
> color sel sea green
> color sel medium sea green
> select #2/B:488
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:458-488
244 atoms, 249 bonds, 31 residues, 1 model selected
> select #2/B:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:457-489
257 atoms, 262 bonds, 33 residues, 1 model selected
> select #2/B:490
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:489-490
15 atoms, 15 bonds, 2 residues, 1 model selected
> select
> #2/B:12-24,34-36,40-43,57-61,64-73,90-95,112-117,122-125,178-181,183-188,249-266,295-304,309-316,399-412,422-429,432-436,459-472,485-488,502-509,511-520,545-558,572-578,584-594,617-630,648-657,682-694,711-724,740-748,760-762,771-778,789-805,807-809,819-821,827-839,847-859,867-869,871-882,889-891,894-896,901-908,941-948,952-962,964-977,985-989,1042-1044
2982 atoms, 2996 bonds, 382 residues, 1 model selected
> select #2/B:488
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> color sel medium sea green
> color sel dark turquoise
> select #2/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:1-456
3423 atoms, 3484 bonds, 456 residues, 1 model selected
> color sel dark turquoise
> select #2/C:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/C:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> color sel cornflower blue
[Repeated 3 time(s)]
> color sel dodger blue
> color sel medium spring green
> select #2/C:489
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:489-980
3704 atoms, 3787 bonds, 492 residues, 1 model selected
> color sel steel blue
> color sel teal
> select #2/C:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:981-1045
517 atoms, 522 bonds, 65 residues, 1 model selected
> color sel dodger blue
> color sel medium spring green
> select #2/C:509
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:509-980
3554 atoms, 3634 bonds, 472 residues, 1 model selected
> color sel dodger blue
> color sel cornflower blue
> color sel royal blue
> color sel dodger blue
> select #2/D:456
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/D:1-456
3424 atoms, 3485 bonds, 456 residues, 1 model selected
> color sel slate blue
> select #2/D:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/D:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> color sel hot pink
> select #2/D:489
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/D:489-980
3704 atoms, 3787 bonds, 492 residues, 1 model selected
> color sel medium purple
> color sel pale violet red
> select #2/D:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/D:981-1045
517 atoms, 522 bonds, 65 residues, 1 model selected
> color sel deep pink
> color sel hot pink
> color sel magenta
> color sel dark violet
> color sel deep pink
> select #2/D:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/D:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> color sel deep pink
> save "D:/AIIMS/PCOX/figures and chimera sessions/COLORED DOMAINS.cxs"
> includeMaps true
> show #!5 models
> select ::name="ACO"
204 atoms, 212 bonds, 5 pseudobonds, 4 residues, 2 models selected
> color (#2 & sel) red
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 1 model selected
> color sel yellow
> select ::name="ZN"
4 atoms, 4 residues, 1 model selected
> color sel blue
> ui tool show "Color Zone"
> color zone #5 near #2 distance 2.04
> color zone #5 near #2 distance 2.14
> color zone #5 near #2 distance 2.24
> color zone #5 near #2 distance 2.34
> color zone #5 near #2 distance 2.44
> color zone #5 near #2 distance 2.54
> color zone #5 near #2 distance 2.64
> color zone #5 near #2 distance 2.74
> color zone #5 near #2 distance 2.84
> color zone #5 near #2 distance 2.94
> color zone #5 near #2 distance 3.04
> color zone #5 near #2 distance 3.14
> color zone #5 near #2 distance 3.24
> color zone #5 near #2 distance 3.34
> color zone #5 near #2 distance 3.44
> color zone #5 near #2 distance 3.54
> color zone #5 near #2 distance 3.64
> color zone #5 near #2 distance 3.74
> color zone #5 near #2 distance 3.84
> color zone #5 near #2 distance 3.94
> color zone #5 near #2 distance 4.04
> color zone #5 near #2 distance 4.14
> volume #5 step 2
> volume #5 step 4
> volume #5 step 8
> volume #5 step 1
> volume #5 level 0.02613
> volume #5 level 0.0132
> volume #5 level 0.01504
> volume #5 style mesh
> volume #5 style surface
> volume #5 level 0.018
> hide sel cartoons
> select
65836 atoms, 67119 bonds, 107 pseudobonds, 8713 residues, 6 models selected
> select clear
> select
65836 atoms, 67119 bonds, 107 pseudobonds, 8713 residues, 6 models selected
> hide sel & #2 cartoons
> select clear
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting soft
> color zone #5 near #2 distance 4.24
> color zone #5 near #2 distance 4.34
> color zone #5 near #2 distance 4.44
> color zone #5 near #2 distance 4.54
> color zone #5 near #2 distance 4.64
> color zone #5 near #2 distance 4.74
> color zone #5 near #2 distance 4.84
> color zone #5 near #2 distance 4.94
> color zone #5 near #2 distance 5.04
> show #2 cartoons
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/B:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chartreuse
> color sel dark goldenrod
> color sel salmon
> color sel green
> color sel chartreuse
> color sel cyan
> color sel deep sky blue
> color sel cyan
> color sel sea green
> color sel forest green
> select #2/B:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:981-1040
479 atoms, 484 bonds, 60 residues, 1 model selected
> select #2/B:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:981-1045
517 atoms, 522 bonds, 65 residues, 1 model selected
> color sel forest green
> select #2/C:488
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:457-488
249 atoms, 254 bonds, 32 residues, 1 model selected
> color sel blue
> color sel indigo
> color sel royal blue
> color sel blue
> color sel light pink
> color sel light green
> color sel midnight blue
> color sel indigo
> color sel dark blue
> color sel medium blue
> color sel blue
> select #2/C:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:981-1045
517 atoms, 522 bonds, 65 residues, 1 model selected
> color sel blue
> save "D:/AIIMS/PCOX/figures and chimera sessions/COLORED DOMAINS.cxs"
> select clear
> show #!5 models
> color zone #5 near #2 distance 5.14
> color zone #5 near #2 distance 5.24
> color zone #5 near #2 distance 5.14
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/C
Destroying pre-existing alignment with identifier 2/C
Alignment identifier is 2/C
> select #2/C:489
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:489-913
3202 atoms, 3272 bonds, 425 residues, 1 model selected
> select #2/C:980
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:489-980
3704 atoms, 3787 bonds, 492 residues, 1 model selected
> ui tool show "Color Actions"
> color sel teal
> show #!5 models
> color zone #5 near #2 distance 5.24
> hide sel cartoons
> hide #2 models
> lighting full
> lighting soft
> show #2 models
> hide #!5 models
> select clear
> show #!5 models
> hide #2 models
> save "D:/AIIMS/PCOX/figures and chimera sessions/FULLDOMAINCOLOREDMAP-
> BD.tif" width 12850 height 8000 supersample 3 transparentBackground true
> show #2 models
> hide #!5 models
> show #!5 models
> hide #2 models
> save "D:/AIIMS/PCOX/figures and chimera sessions/FULLDOMAINCOLOREDMAP-SIDE
> VEIW.tif" width 12850 height 8000 supersample 3 transparentBackground true
> view
> view orient
> save "D:/AIIMS/PCOX/figures and chimera sessions/FULLDOMAINCOLOREDMAP.tif"
> width 12850 height 8000 supersample 3 transparentBackground true
> view orient
[Repeated 1 time(s)]
> OREINT X90
Unknown command: OREINT X90
> help help:user
No help found for 'help:user ORIENT'
> save "D:/AIIMS/PCOX/figures and chimera sessions/sideviewmap.tif" width
> 12850 height 8000 supersample 3 transparentBackground true
> save "D:/AIIMS/PCOX/figures and chimera sessions/FULLDOMAINCOLOREDMAP-
> AC.tif" width 12850 height 8000 supersample 3 transparentBackground true
> save "D:/AIIMS/PCOX/figures and chimera sessions/ALLDOMAIN COLOURED
> COMPLEX.cxs" includeMaps true
> toolshed show
Downloading bundle DiffFit-0.7.0-py3-none-any.whl
Installed ChimeraX-QScore (1.1)
Installed DiffFit (0.7.0)
> save "D:/AIIMS/PCOX/figures and chimera sessions/1.cxs" includeMaps true
> transparency 0
> select add #5
3 models selected
> transparency sel 50
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting simple
> show #1 models
> hide #1 models
> show #2 models
> select add #4
107 pseudobonds, 4 models selected
> hide #2 cartoons
> volume #5 level 0.02218
> volume #5 level 0.02826
> volume #5 level 0.02446
> volume #5 step 2
> undo
[Repeated 9 time(s)]
> show #2 models
> color zone #5 near #2 distance 5.24
> hide #!5 models
> show #1 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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> color bychain
> undo
> select add #1
33912 atoms, 34568 bonds, 4508 residues, 1 model selected
> select subtract #3
33912 atoms, 34568 bonds, 4508 residues, 1 model selected
> color sel bychain
> select add #2
65836 atoms, 67119 bonds, 68 pseudobonds, 8713 residues, 3 models selected
> select subtract #2
33912 atoms, 34568 bonds, 4508 residues, 1 model selected
> select subtract #1
Nothing selected
> select subtract #3
Nothing selected
> show surfaces
> select add #1
33912 atoms, 34568 bonds, 4508 residues, 1 model selected
> select add #2
65836 atoms, 67119 bonds, 68 pseudobonds, 8713 residues, 7 models selected
> show sel surfaces
> select subtract #3
65836 atoms, 67119 bonds, 68 pseudobonds, 8713 residues, 11 models selected
> select subtract #2
33912 atoms, 34568 bonds, 4508 residues, 9 models selected
> select subtract #1
4 models selected
> select subtract #3
Nothing selected
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> hide #!1 models
> undo
[Repeated 9 time(s)]
> select add #1
33912 atoms, 34568 bonds, 4508 residues, 1 model selected
> select subtract #1
4 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> show #!2 models
> lighting full
[Repeated 1 time(s)]
> lighting flat
> lighting soft
> show cartoons
> hide surfaces
> hide #!2 models
> show #!2 models
> hide #!1 models
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> graphics silhouettes false
> select add #1
33912 atoms, 34568 bonds, 4508 residues, 1 model selected
> show #!1 models
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select subtract #1
4 models selected
> hide #!1 models
> show #!1 models
> save "D:/AIIMS/PCOX/figures and chimera sessions/2.cxs" includeMaps true
> matchmaker #2/A,B,C,D to #1/A,B,C,D atoms name CA
Expected a keyword
> matchmaker #2/A,B,C,D to #1/A,B,C,D atoms name CA
Expected a keyword
> matchmaker #2/A,B,C,D to #1/A,B,C,D atoms CA
Expected a keyword
> select add #1
33912 atoms, 34568 bonds, 4508 residues, 1 model selected
> select subtract #3
33912 atoms, 34568 bonds, 4508 residues, 5 models selected
> select add #2
65836 atoms, 67119 bonds, 68 pseudobonds, 8713 residues, 7 models selected
> select subtract #3
65836 atoms, 67119 bonds, 68 pseudobonds, 8713 residues, 11 models selected
> select add #4
65836 atoms, 67119 bonds, 107 pseudobonds, 8713 residues, 11 models selected
> select subtract #3
65836 atoms, 67119 bonds, 107 pseudobonds, 8713 residues, 11 models selected
> select subtract #4
65836 atoms, 67119 bonds, 8713 residues, 10 models selected
> select subtract #3
65836 atoms, 67119 bonds, 8713 residues, 10 models selected
> 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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> help help:user/tools/matchmaker.html
> rotaion #1#2
Unknown command: measure rotaion #1#2
> rotaion #1;#2
Unknown command: measure rotaion #1;#2
> rotaion
Unknown command: measure rotaion
> 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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> 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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> matchmaker #2/A,B,C,D to #1/A,B,C,D atoms name CA
Expected a keyword
> matchmaker #2/A,B,C,D to #1/A,B,C,D
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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> matchmaker #2/A,B,C,D to #1/A,B,C,D
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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> matchmaker #2/A,B,C,D to #1/A,B,C,D
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 Native-Pcox.pdb, chain A (#1) with refined_real_space_44a.pdb,
chain D (#2), sequence alignment score = 4638.3
RMSD between 688 pruned atom pairs is 1.164 angstroms; (across all 1045 pairs:
3.037)
> rmsd #2 #1 per-residue true report true log tru
Expected a keyword
> rmsd #2 #1 per-residue true report true log true
Expected a keyword
> rmsd #2 to #1 per-residue true report true log true
Expected a keyword
> rmsd #2 to #1
Number of atoms from first atom spec (31924) differs from number in second
(33912)
> rotation #2 to #1
Unknown command: rotation #2 to #1
> help help:user
> measure rotation #2 toModel #1
Position of refined_real_space_44a.pdb #2 relative to Native-Pcox.pdb #1
coordinates:
Matrix rotation and translation
0.01317096 -0.00725408 0.99988693 -0.18587334
-0.99761035 -0.06792331 0.01264820 323.02717972
0.06782388 -0.99766415 -0.00813137 302.93103244
Axis -0.59633963 0.55015277 -0.58456050
Axis point 0.00000000 302.12144724 1.93425451
Rotation angle (degrees) 122.10292758
Shift along axis 0.74362526
> save "D:/AIIMS/PCOX/figures and chimera sessions/3.cxs" includeMaps true
> close session
> toolshed show
> ui tool show "Volume Viewer"
> view # clip false
Expected an objects specifier or a view name or a keyword
> ui tool show "Show Volume Menu"
> help help:user
[Repeated 1 time(s)]
>
Incomplete command: vseries
> open
> E:/analysis/cryosparc_P1_J443_00364_volume_series/J443_class_00_00364_volume.mrc
> E:/analysis/cryosparc_P1_J443_00364_volume_series/J443_class_01_00364_volume.mrc
> E:/analysis/cryosparc_P1_J443_00364_volume_series/J443_class_02_00364_volume.mrc
> E:/analysis/cryosparc_P1_J443_00364_volume_series/J443_class_03_00364_volume.mrc
> E:/analysis/cryosparc_P1_J443_00364_volume_series/J443_class_04_00364_volume.mrc
Opened J443_class_00_00364_volume.mrc as #1.1, grid size 72,72,72, pixel 4.3,
shown at level 0.289, step 1, values float32
Opened J443_class_01_00364_volume.mrc as #1.2, grid size 72,72,72, pixel 4.3,
shown at level 0.289, step 1, values float32
Opened J443_class_02_00364_volume.mrc as #1.3, grid size 72,72,72, pixel 4.3,
shown at level 0.29, step 1, values float32
Opened J443_class_03_00364_volume.mrc as #1.4, grid size 72,72,72, pixel 4.3,
shown at level 0.287, step 1, values float32
Opened J443_class_04_00364_volume.mrc as #1.5, grid size 72,72,72, pixel 4.3,
shown at level 0.292, step 1, values float32
> vseries1
Unknown command: vseries1
> vseries#1
Unknown command: vseries#1
> display vseries#1
> show vseries#1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> display vseries #1to1.5 map
> show vseries #1to1.5 map
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> volume #1.1 level 0.05749
> volume #1.2 level 0.179
> volume #1.2 level 0.09775
> volume #1.2 level 0.1265
> volume #1.5 level 0.1539
> volume #1.5 level 0.05151
> volume #1.4 level 0.04228
> volume #1.3 level 0.03951
> volume #1.2 level 0.04188
> volume #1.4 step 2
> volume #1.4 step 1
> ui tool show "Volume Viewer"
> volume #1.4 level 0.162
> volume #1.5 level 0.2043
> volume #1.2 level 0.1976
> volume #1.3 level 0.216
> volume #1.2 level 0.1655
> volume #1.1 level 0.1477
> ui tool show "Show Volume Menu"
> toolshed show
Downloading bundle ChimeraX_EMalign-0.1.3-py3-none-any.whl
Installed ChimeraX-EMalign (0.1.3)
Downloading bundle ChimeraX_LigandRecognizer-0.2-py3-none-any.whl
Installed ChimeraX-LigandRecognizer (0.2)
Downloading bundle ChimeraX_PDBImages-1.2-py3-none-any.whl
Downloading bundle seqcrow-1.8.21-py3-none-any.whl
Installed SEQCROW (1.8.21)
> style ball
Changed 0 atom styles
> toolshed show
Downloading bundle MolecularDynamicsViewer-1.6-py3-none-any.whl
Installed MolecularDynamicsViewer (1.6)
QWebEngineUrlScheme::registerScheme: Too late to register scheme "kmd"
Downloading bundle ChimeraX_OME_Zarr-0.5.5-py3-none-any.whl
Installed ChimeraX-OME-Zarr (0.5.5)
> style ball
Changed 0 atom styles
> style ball
Changed 0 atom styles
> volume #1.1 level 0.197
> volume #1.3 level 0.2074
> volume #1.5 level 0.1897
> volume #1.3 level 0.1953
> volume #1.1 level 0.1749
> volume #1.3 level 0.1884
> volume #1.4 level 0.1464
> volume #1.5 level 0.1767
Downloading bundle ChimeraX_PDBImages-1.2-py3-none-any.whl
Installed ChimeraX-PDBImages (1.2)
> volume #1.4 level 0.1377
> volume #1.5 level 0.09866
> volume #1.5 level 0.1149
> volume #1.3 level 0.1572
> volume #1.2 level 0.135
> volume #1.2 level 0.1993
> volume #1.3 level 0.2299
> volume #1.1 level 0.2004
> volume #1.4 level 0.1915
> volume #1.5 level 0.2157
> volume #1.1 level 0.09662
> volume #1.2 level 0.1113
> volume #1.2 level 0.1011
> volume #1.3 level 0.09489
> volume #1.4 level 0.0579
> surface dust #1.1 size 43
> surface dust #1.2 size 43
> surface dust #1.3 size 43
> surface dust #1.4 size 43
> surface dust #1.5 size 43
> volume #1.4 level 0.06831
> volume #1.3 level 0.1087
> volume #1.4 level 0.1603
> volume #1.4 level 0.1846
> volume #1.3 level 0.1866
> volume #1.1 level 0.1834
> volume #1.2 level 0.1807
> volume #1.4 level 0.1811
> volume #1.5 level 0.1881
> volume #1.5 level 0.1767
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 154.8 tiltedSlabSpacing 4.3 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 154.8 tiltedSlabSpacing 4.3 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.3 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 154.8 tiltedSlabSpacing 4.3 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.4 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 154.8 tiltedSlabSpacing 4.3 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.5 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 154.8 tiltedSlabSpacing 4.3 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.1 orthoplanes xyz positionPlanes 36,36,36 style image region all
> mousemode rightMode "move planes"
> volume #1.2 orthoplanes xyz positionPlanes 36,36,36 style image region all
> mousemode rightMode "move planes"
> volume #1.3 orthoplanes xyz positionPlanes 36,36,36 style image region all
> mousemode rightMode "move planes"
> volume #1.4 orthoplanes xyz positionPlanes 36,36,36 style image region all
> mousemode rightMode "move planes"
> volume #1.5 orthoplanes xyz positionPlanes 36,36,36 style image region all
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
Hide dust shortcut requires a displayed map surface
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 5 maps.
> volume style surface
> volume #1.1 change image level -0.03214,0 level 0.4322,0.8 level 0.6744,1
> volume #1.1 level 0.1868
> volume #1.1 level 0.146
> volume #1.1 level 0.08131
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.5 models
> show #!1.4 models
> show #!1.3 models
> show #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.4 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.5 models
> toolshed show
> ui tool show "Hide Dust"
> ui tool show "Map Coordinates"
> ui tool show "Measure and Color Blobs"
> surface dust #1.1 size 25.8
> ui tool show "Map Statistics"
> measure mapstats
Map J443_class_00_00364_volume.mrc #1.1, minimum -0.2165, maximum 0.6851, mean
0.001955, SD 0.04873, RMS 0.04877
Map J443_class_01_00364_volume.mrc #1.2, minimum -0.2221, maximum 0.6752, mean
0.001952, SD 0.04881, RMS 0.04885
Map J443_class_02_00364_volume.mrc #1.3, minimum -0.2097, maximum 0.7077, mean
0.002038, SD 0.04903, RMS 0.04907
Map J443_class_03_00364_volume.mrc #1.4, minimum -0.2544, maximum 0.6654, mean
0.001514, SD 0.04857, RMS 0.0486
Map J443_class_04_00364_volume.mrc #1.5, minimum -0.2023, maximum 0.6594, mean
0.002121, SD 0.04888, RMS 0.04892
> select add #1
16 models selected
> select add #1
16 models selected
> ui tool show "Map Coordinates"
> ui tool show "Map Statistics"
> measure mapstats sel
Map J443_class_00_00364_volume.mrc #1.1, minimum -0.2165, maximum 0.6851, mean
0.001955, SD 0.04873, RMS 0.04877
Map J443_class_01_00364_volume.mrc #1.2, minimum -0.2221, maximum 0.6752, mean
0.001952, SD 0.04881, RMS 0.04885
Map J443_class_02_00364_volume.mrc #1.3, minimum -0.2097, maximum 0.7077, mean
0.002038, SD 0.04903, RMS 0.04907
Map J443_class_03_00364_volume.mrc #1.4, minimum -0.2544, maximum 0.6654, mean
0.001514, SD 0.04857, RMS 0.0486
Map J443_class_04_00364_volume.mrc #1.5, minimum -0.2023, maximum 0.6594, mean
0.002121, SD 0.04888, RMS 0.04892
> ui tool show "Marker Placement"
> ui tool show Orthopick
> ui tool show Orthoplanes
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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.
> ui tool show Segmentations
> ui view fourup
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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.
> segmentations create #1.1
Opened segmentation 1 of J443_class_00_00364_volume.mrc as #5, grid size
72,72,72, pixel 4.3, shown at level 0.501, step 1, values float64
OpenGL version: 3.3.0 NVIDIA 555.99
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Micro-Star International Co., Ltd.
Model: GF63 Thin 11UC
OS: Microsoft Windows 11 Home Single Language (Build 26120)
Memory: 8,276,946,944
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-US
Installed Packages:
aiobotocore: 2.22.0
aiohappyeyeballs: 2.6.1
aiohttp: 3.12.9
aioitertools: 0.12.0
aiosignal: 1.3.2
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asciitree: 0.3.3
asttokens: 3.0.0
attrs: 25.3.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.0.0
botocore: 1.37.3
build: 1.2.1
certifi: 2024.8.30
cffi: 1.17.1
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-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: 0.1.3
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-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-OME-Zarr: 0.5.5
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.2
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-QScore: 1.1
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
click: 8.2.1
cloudpickle: 3.1.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cryptography: 45.0.3
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
dask: 2025.5.1
debugpy: 1.8.9
decorator: 5.1.1
Deprecated: 1.2.18
DiffFit: 0.7.0
docutils: 0.21.2
executing: 2.1.0
fasteners: 0.19
filelock: 3.15.4
finufft: 2.3.1
fonttools: 4.55.3
frozenlist: 1.6.2
fsspec: 2025.5.1
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
imageio: 2.37.0
imagesize: 1.4.1
importlib_metadata: 8.7.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jmespath: 1.0.1
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
lazy_loader: 0.4
line_profiler: 4.1.3
locket: 1.0.0
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
multidict: 6.4.4
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numcodecs: 0.15.1
numexpr: 2.10.2
numpy: 1.26.4
numpy: 1.26.4
ome-zarr: 0.11.1
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
partd: 1.4.2
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
propcache: 0.3.1
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pycparser: 2.22
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
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
pyspnego: 0.11.2
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
PyYAML: 6.0.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
s3fs: 2025.5.1
scikit-image: 0.25.2
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.8.21
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
smbprotocol: 1.15.0
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
sspilib: 0.3.1
stack-data: 0.6.3
superqt: 0.6.3
sympy: 1.14.0
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
toolz: 1.0.0
torch: 2.2.1
tornado: 6.4.2
traitlets: 5.14.3
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-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
wrapt: 1.17.2
yarl: 1.20.0
zarr: 2.18.7
zipp: 3.22.0
Change History (2)
comment:1 by , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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