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Opened 3 months ago
Closed 3 months ago
#18284 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-14.5-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/radhikakhera/Downloads/cryosparc_P24_J450_class_00_final_volume.mrc
Opened cryosparc_P24_J450_class_00_final_volume.mrc as #1, grid size
256,256,256, pixel 2.62, shown at level 0.126, step 1, values float32
> lighting soft
> set bgColor white
> volume #1 level 0.1647
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_j111/cryosparc_P4_J116_006_volume_map.mrc
Opened cryosparc_P4_J116_006_volume_map.mrc as #1, grid size 640,640,640,
pixel 1.05, shown at level 0.0623, step 4, values float32
> volume #1 step 1
> volume #1 level 0.1378
> ui tool show "Map Filter"
> volume gaussian #1 sDev 1
Opened cryosparc_P4_J116_006_volume_map.mrc gaussian as #2, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #2 color #fffc79
> volume #2 color #ffd479
> volume #2 level 0.0985
> volume #2 level 0.1071
> movie record
> roll x 1 2160
> wait 360
> stop
> wait 30
> volume level 0.009
> wait 10
> transparency #2 0
> wait 10
> color zone #2 near #1 distance 7
color zone: No atoms specified.
> volume #2 level 0.1209
> movie record
Already recording a movie
> stop
> movie stop
> movie record
> roll y 1 2160
> wait 360
> stop
> wait 50
> roll x 1 2160
> wait 360
> stop
> wait 30
> movie encode /Users/radhikakhera/Desktop/mab_b3_J116.mp4
Movie saved to /Users/radhikakhera/Desktop/mab_b3_J116.mp4
> graphics silhouettes true
> movie record
> roll y 1 2160
> wait 360
> stop
> wait 50
> roll x 1 2160
> wait 360
> stop
> wait 30
> movie encode /Users/radhikakhera/Desktop/mab_b3_J116.mp4
Movie saved to /Users/radhikakhera/Desktop/mab_b3_J116.mp4
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_j111/cryosparc_P4_J146_003_volume_map.mrc
Opened cryosparc_P4_J146_003_volume_map.mrc as #3, grid size 640,640,640,
pixel 1.05, shown at level 0.0406, step 4, values float32
> volume #3 step 1
> volume #3 level 0.1025
> ui tool show "Map Filter"
> volume gaussian #3 sDev 1
Opened cryosparc_P4_J146_003_volume_map.mrc gaussian as #4, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #4 level 0.06561
> volume #4 level 0.0858
> volume #4 level 0.06393
> volume #4 level 0.07234
> volume #4 level 0.05215
> volume #4 level 0.05888
> volume #4 level 0.05215
> volume #4 level 0.1178
> volume #4 level 0.04711
> volume #4 level 0.06729
> volume #4 level 0.09758
> volume #4 level 0.04038
> volume #2 level 0.0943
> volume #2 level 0.1315
> volume #2 level 0.09075
> volume #2 level 0.09607
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/J96/J96_006_volume_map_lp15.mrc
Opened J96_006_volume_map_lp15.mrc as #5, grid size 640,640,640, pixel 1.05,
shown at level 0.0267, step 4, values float32
> volume #5 step 1
> volume #5 level 0.01531
> ui tool show "Segment Map"
Segmenting J96_006_volume_map_lp15.mrc, density threshold 0.015315
Showing 173 region surfaces
388 watershed regions, grouped to 173 regions
Showing J96_006_volume_map_lp15.seg - 173 regions, 173 surfaces
> select add #6.29
1 model selected
> select add #6.5
2 models selected
> select add #6.20
3 models selected
> select add #6.1
4 models selected
> select add #6.145
5 models selected
> select add #6.106
6 models selected
> select add #6.42
7 models selected
> select add #6.4
8 models selected
Grouped 8 regions
Deleted 165 regions
Saving 1 regions to mrc file...
Opened J96_006_volume_map_lp15_region_537_7July25.mrc as #7, grid size
100,130,162, pixel 1.05, shown at step 1, values float32
Wrote J96_006_volume_map_lp15_region_537_7July25.mrc
> volume resample #7 onGrid #5
Opened J96_006_volume_map_lp15_region_537_7July25.mrc resampled as #8, grid
size 640,640,640, pixel 1.05, shown at step 1, values float32
> volume #8 level 0.05934
> hide #!6 models
> select add #6
2 models selected
> volume #8 level 0.02116
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/J96/J96_006_volume_map_lp15_region_537_7July25_resampled.mrc
> models #8
> close #6
Segmenting J96_006_volume_map_lp15_region_537_7July25_resampled.mrc, density
threshold 0.021160
Showing 9 region surfaces
59 watershed regions, grouped to 9 regions
Showing J96_006_volume_map_lp15_region_537_7July25_resampled.seg - 9 regions,
9 surfaces
> volume #8 level 0.01909
> close #6
> volume #8 level 0.01831
Segmenting J96_006_volume_map_lp15_region_537_7July25_resampled.mrc, density
threshold 0.018308
Showing 9 region surfaces
61 watershed regions, grouped to 9 regions
Showing J96_006_volume_map_lp15_region_537_7July25_resampled.seg - 9 regions,
9 surfaces
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/J96/J96_006_volume_map_lp15_ab.mrc
Opened J96_006_volume_map_lp15_ab.mrc as #9, grid size 640,640,640, pixel
1.05, shown at level 3.09e-06, step 4, values float32
> close #6
> volume #9 step 1
> volume #9 level 0.01831
> volume #9 level 0.02304
> ui tool show "Map Eraser"
> volume erase #8 center 311.13,381.37,327.75 radius 58.665
> volume erase #8 center 300.37,330.94,377.44 radius 58.665
> volume erase #8 center 318.31,282.53,301.59 radius 58.665
> volume erase #8 center 477.53,376.57,426.63 radius 58.665
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/J96/J96_006_volume_map_lp15_region_537_7July25_resampled_2.mrc
> models #8
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/cryosparc_P4_J96_003_volume_map.mrc
Opened cryosparc_P4_J96_003_volume_map.mrc as #6, grid size 640,640,640, pixel
1.05, shown at level 0.0375, step 4, values float32
> volume #6 step 1
> volume #6 level 0.0794
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/cryosparc_P4_J148_mask.mrc
Opened cryosparc_P4_J148_mask.mrc as #10, grid size 640,640,640, pixel 1.05,
shown at level 5e-05, step 4, values float32
> volume #10 step 1
> volume #10 level 0.06491
> volume #10 level 0.4217
> volume #10 level 0.5
> volume #10 level 1
> volume #10 level 0.5
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/cryosparc_P4_J109_mask.mrc
Opened cryosparc_P4_J109_mask.mrc as #11, grid size 640,640,640, pixel 1.05,
shown at level 5e-05, step 4, values float32
> volume #11 step 1
> volume #11 level 0.5
> volume #10 color #cccc9980
> volume #6 level 0.1143
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J149_class_00_00171_volume.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J149_class_01_00171_volume.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J149_class_02_00171_volume.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J149_class_03_00171_volume.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J149_class_04_00171_volume.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J149_class_05_00171_volume.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J149_class_06_00171_volume.mrc
Opened cryosparc_P4_J149_class_00_00171_volume.mrc as #12.1, grid size
100,100,100, pixel 6.72, shown at level 0.434, step 1, values float32
Opened cryosparc_P4_J149_class_01_00171_volume.mrc as #12.2, grid size
100,100,100, pixel 6.72, shown at level 0.468, step 1, values float32
Opened cryosparc_P4_J149_class_02_00171_volume.mrc as #12.3, grid size
100,100,100, pixel 6.72, shown at level 0.489, step 1, values float32
Opened cryosparc_P4_J149_class_03_00171_volume.mrc as #12.4, grid size
100,100,100, pixel 6.72, shown at level 0.463, step 1, values float32
Opened cryosparc_P4_J149_class_04_00171_volume.mrc as #12.5, grid size
100,100,100, pixel 6.72, shown at level 0.474, step 1, values float32
Opened cryosparc_P4_J149_class_05_00171_volume.mrc as #12.6, grid size
100,100,100, pixel 6.72, shown at level 0.466, step 1, values float32
Opened cryosparc_P4_J149_class_06_00171_volume.mrc as #12.7, grid size
100,100,100, pixel 6.72, shown at level 0.4, step 1, values float32
> volume #12.1 level 0.6966
> volume #12.2 level 0.9904
> volume #12.3 level 0.9248
> volume #12.3 level 1.306
> volume #12.4 level 1.219
> volume #12.5 level 0.9246
> volume #12.6 level 1.062
> volume #12.7 level 0.3034
> volume #12.2 level 1.219
> volume #12.3 level 1.644
> volume #12.4 level 1.089
> volume #12.4 level 0.7761
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J150_mask.mrc
Opened cryosparc_P4_J150_mask.mrc as #13, grid size 100,100,100, pixel 6.72,
shown at level 1, step 1, values float32
> volume #13 level 0.9153
> volume #13 level 0.5
> volume #13 color #99bfe577
> volume #13 color #99bfe578
> volume #13 level 1
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_149/cryosparc_P4_J151_mask.mrc
Opened cryosparc_P4_J151_mask.mrc as #14, grid size 100,100,100, pixel 6.72,
shown at level 1, step 1, values float32
> volume #14 level 0.5
> volume #14 level 0.4
> volume #14 color #cccc9982
> volume #13 level 0.4
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/refine_64/run_it003_half2_class001.mrc
Opened run_it003_half2_class001.mrc as #15, grid size 640,640,640, pixel 1.05,
shown at level 0.000641, step 4, values float32
> volume #15 step 1
> volume #15 level 0.0007905
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/refine_64/run_it015_half2_class001.mrc
Opened run_it015_half2_class001.mrc as #16, grid size 640,640,640, pixel 1.05,
shown at level 0.000518, step 4, values float32
> volume #16 step 1
> volume #16 level 0.002056
> volume #16 level 0.003081
> ui tool show "Map Filter"
[Repeated 1 time(s)]
> volume gaussian #16 sDev 1
Opened run_it015_half2_class001.mrc gaussian as #17, grid size 640,640,640,
pixel 1.05, shown at step 1, values float32
> volume #17 level 0.002091
> volume #17 level 0.0007783
> volume #17 level 0.003161
> volume #17 level 0.002285
> volume #17 level 0.002918
> open
> /Users/radhikakhera/Downloads/CP29_woodwardia_7b843_0/CP29_woodwardia_7b843_0_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
CP29_woodwardia_7b843_0_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb
#18
---
Chain | Description
A | No description available
> open
> /Users/radhikakhera/Downloads/CP29_woodwardia_7b843_0/CP29_woodwardia_7b843_0_unrelaxed_rank_002_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
CP29_woodwardia_7b843_0_unrelaxed_rank_002_alphafold2_ptm_model_2_seed_000.pdb
#19
---
Chain | Description
A | No description available
> open
> /Users/radhikakhera/Downloads/CP29_woodwardia_7b843_0/CP29_woodwardia_7b843_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
CP29_woodwardia_7b843_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#20
---
Chain | Description
A | No description available
> open
> /Users/radhikakhera/Downloads/CP29_woodwardia_7b843_0/CP29_woodwardia_7b843_0_unrelaxed_rank_004_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
CP29_woodwardia_7b843_0_unrelaxed_rank_004_alphafold2_ptm_model_4_seed_000.pdb
#21
---
Chain | Description
A | No description available
> open
> /Users/radhikakhera/Downloads/CP29_woodwardia_7b843_0/CP29_woodwardia_7b843_0_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
CP29_woodwardia_7b843_0_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
#22
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 4 time(s)]
> hide #22 models
> hide #21 models
> hide #20 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #18 models
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> show #18 models
> hide #19 models
> show #21 models
> hide #18 models
> hide #21 models
> show #20 models
> show #19 models
> show #18 models
> hide #19 models
> hide #20 models
> show #22 models
> hide #22 models
> hide #18 models
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/refine_64/run_class001.mrc
Opened run_class001.mrc as #23, grid size 640,640,640, pixel 1.05, shown at
level 0.00116, step 4, values float32
> volume #23 step 1
> volume #23 level 0.002772
> ui tool show "Map Filter"
> volume gaussian #23 sDev 1
Opened run_class001.mrc gaussian as #24, grid size 640,640,640, pixel 1.05,
shown at step 1, values float32
> volume #24 level 0.001218
> volume #24 level 0.002173
> volume #24 level 0.00246
> volume #24 level 0.002412
> open 7oui fromDatabase pdb format mmcif
Summary of feedback from opening 7oui fetched from pdb
---
warnings | Atom C4 is not in the residue template for AJP /A:412
Atom C4 is not in the residue template for AJP /B:624
Atom CAW is not in the residue template for AJP /S:319
Atom CAW is not in the residue template for AJP /G:618
Atom CAW is not in the residue template for AJP /N:619
Atom CAW is not in the residue template for AJP /N:620
Atom CAW is not in the residue template for AJP /Y:320
4 messages similar to the above omitted
Atom C4 is not in the residue template for AJP /a:413
Atom C4 is not in the residue template for AJP /b:624
Atom CAW is not in the residue template for AJP /s:319
Atom CAW is not in the residue template for AJP /g:618
Atom CAW is not in the residue template for AJP /n:619
Atom CAW is not in the residue template for AJP /n:620
Atom CAW is not in the residue template for AJP /y:320
4 messages similar to the above omitted
7oui title:
Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana
(digitonin-extracted) [more info...]
Chain information for 7oui #25
---
Chain | Description | UniProt
1 3 5 7 | Lhcb1.4 | Q39142_ARATH 2-267
2 6 | Lhcb3.1 | CB3_ARATH 26-268
4 8 | Chlorophyll a-b binding protein, chloroplastic | Q9LMQ2_ARATH 47-258
A a | Photosystem II protein D1 | PSBA_ARATH 2-353
B b | Photosystem II CP47 reaction center protein | PSBB_ARATH 1-508
C c | Photosystem II CP43 reaction center protein | PSBC_ARATH 15-473
D d | Photosystem II D2 protein | PSBD_ARATH 2-353
E e | Cytochrome b559 subunit alpha | PSBE_ARATH 1-83
F f | Cytochrome b559 subunit beta (PsbF) | PSBF_ARATH 1-39
G N Y g n y | Chlorophyll a-b binding protein 1, chloroplastic | CB1C_ARATH 36-267
H h | Photosystem II reaction center protein H | PSBH_ARATH 2-73
I i | Photosystem II reaction center protein I | PSBI_ARATH 1-36
K k | Photosystem II reaction center protein K | PSBK_ARATH 25-61
L l | Photosystem II reaction center protein L | PSBL_ARATH 1-38
M m | Photosystem II reaction center protein M | PSBM_ARATH 1-34
O o | Oxygen-evolving enhancer protein 1-1, chloroplastic | PSBO1_ARATH 86-332
R r | Chlorophyll a-b binding protein CP29.1, chloroplastic | CB4A_ARATH 41-290
S s | Chlorophyll a-b binding protein CP26, chloroplastic | CB5_ARATH 49-280
T t | Photosystem II reaction center protein T | PSBT_ARATH 1-33
U u | PsbTn | PST2_ARATH 76-103
W w | Photosystem II reaction center W protein, chloroplastic | PSBW_ARATH 80-133
X x | PsbX | A0A7G2E9B1_ARATH 75-116
Z z | Photosystem II reaction center protein Z | PSBZ_ARATH 1-62
Non-standard residues in 7oui #25
---
AJP — Digitonin
BCR — β-carotene
BCT — bicarbonate ion
CA — calcium ion
CHL — chlorophyll B
CL — chloride ion
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
FE2 — Fe (II) ion
HEM — protoporphyrin IX containing Fe (HEME)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-neoxanthin)
PHO — pheophytin A
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)
> select add #25
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.056527,0.03331,0.99785,-1.7913,0.94406,0.32345,-0.064277,-42.705,-0.3249,0.94566,-0.013162,64.01
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.056527,0.03331,0.99785,-8.0413,0.94406,0.32345,-0.064277,32.096,-0.3249,0.94566,-0.013162,119.35
> view matrix models
> #25,0.056527,0.03331,0.99785,32.208,0.94406,0.32345,-0.064277,-13.57,-0.3249,0.94566,-0.013162,141.55
> view matrix models
> #25,0.056527,0.03331,0.99785,15.886,0.94406,0.32345,-0.064277,94.752,-0.3249,0.94566,-0.013162,176.68
> view matrix models
> #25,0.056527,0.03331,0.99785,85.161,0.94406,0.32345,-0.064277,62.196,-0.3249,0.94566,-0.013162,194.88
> view matrix models
> #25,0.056527,0.03331,0.99785,113.97,0.94406,0.32345,-0.064277,91.123,-0.3249,0.94566,-0.013162,243.44
> ui tool show "Fit in Map"
> fitmap #25 inMap #24
Fit molecule 7oui (#25) to map run_class001.mrc gaussian (#24) using 85897
atoms
average map value = 0.004893, steps = 140
shifted from previous position = 15.2
rotated from previous position = 8.37 degrees
atoms outside contour = 21497, contour level = 0.0024123
Position of 7oui (#25) relative to run_class001.mrc gaussian (#24)
coordinates:
Matrix rotation and translation
0.06215869 0.05432059 0.99658696 106.19602763
0.88660006 0.45554331 -0.08012877 75.24914268
-0.45834117 0.88855476 -0.01984467 269.32888612
Axis 0.50036930 0.75153685 0.42991037
Axis point 116.78809510 0.00000000 116.55224618
Rotation angle (degrees) 104.54091700
Shift along axis 225.47701637
> volume #24 level 0.003272
> select subtract #25
Nothing selected
> volume #24 color #ffb2ff99
> volume #24 level 0.003559
> volume #24 color #ffb2ff
> volume #24 level 0.004371
> volume #24 color #ffb2ff85
> volume #24 color #ffb2ff8a
> show #!25 atoms
> style #!25 stick
Changed 85897 atom styles
> volume #24 level 0.003606
> volume #24 color #ffb2ff
> volume #24 level 0.002938
> volume #24 level 0.003511
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/refine_64/7oui_relative_tomap.pdb
> models #25 relModel #23
> select add #25/8:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #25/6:179
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #25/7:91
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #25/5:209
29 atoms, 25 bonds, 4 residues, 1 model selected
> select up
1008 atoms, 1030 bonds, 128 residues, 1 model selected
> select up
6410 atoms, 6622 bonds, 816 residues, 1 model selected
> select up
6413 atoms, 6622 bonds, 816 residues, 1 model selected
> select up
6676 atoms, 6900 bonds, 821 residues, 1 model selected
> select up
85897 atoms, 88812 bonds, 8855 residues, 1 model selected
> select down
6676 atoms, 6900 bonds, 821 residues, 1 model selected
> cartoon hide sel
> hide sel target a
> volume #24 level 0.002603
> volume #24 level 0.002269
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_73/run_it025_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_73/run_it025_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/class3d_73/run_it025_class003.mrc
Opened run_it025_class001.mrc as #26.1, grid size 256,256,256, pixel 1.05,
shown at level 0.00293, step 1, values float32
Opened run_it025_class002.mrc as #26.2, grid size 256,256,256, pixel 1.05,
shown at level 0.00291, step 1, values float32
Opened run_it025_class003.mrc as #26.3, grid size 256,256,256, pixel 1.05,
shown at level 0.00242, step 1, values float32
> select add #25
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> select subtract #25
Nothing selected
> hide #!25 models
> hide #!12 models
> hide #!8 models
> volume #26.1 level 0.003314
> volume #26.2 level 0.004202
> volume #26.2 level 0.003365
> volume #26.3 level 0.002582
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001.mrc
Opened run_class001.mrc as #1, grid size 576,576,576, pixel 1.05, shown at
level 0.014, step 4, values float32
> volume #1 step 1
> measure symmetry
Missing or invalid "volumes" argument: empty atom specifier
> measure symmetry #1
No symmetry found for run_class001.mrc
> volume #1 level 0.01681
> measure symmetry #1
No symmetry found for run_class001.mrc
> measure symmetry #1
No symmetry found for run_class001.mrc
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001_align.mrc
Opened run_class001_align.mrc as #2, grid size 576,576,576, pixel 1.05, shown
at level 0.0115, step 4, values float32
> volume #2 step 1
> volume #2 level 0.01581
> measure symmetry #2
No symmetry found for run_class001_align.mrc
> measure symmetry #2
No symmetry found for run_class001_align.mrc
> show axis
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show axes
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> view orient
> define axis
No atoms specified for axis computation
> volume #1 level 0.01441
> volume #1 level 0.01507
> volume #1 level 0.01725
> volume #1 level 0.01463
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/3drec/3dmodel_job077.mrc
Opened 3dmodel_job077.mrc as #3, grid size 640,640,640, pixel 1.05, shown at
level 0.000776, step 4, values float32
> volume #3 step 1
> volume #3 level 0.002068
> volume #3 level 0.003776
> volume #3 level 0.003473
> volume #3 level 0.002561
> volume #3 level 0.003321
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/3drec/3dmodel_job078.mrc
File size 1045430272 too small for grid size (640,640,640)
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/3drec/3dmodel_job078.mrc
Opened 3dmodel_job078.mrc as #4, grid size 640,640,640, pixel 1.05, shown at
level 0.00079, step 4, values float32
> volume #4 step 1
> volume #4 level 0.002903
> volume #4 level 0.003199
> volume #4 level 0.003749
> volume #4 level 0.003875
> volume #3 level 0.003625
> volume #4 level 0.003115
> volume #3 level 0.004118
> volume #3 level 0.003397
> volume #3 level 0.003625
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/refine_81/run_class001.mrc
Opened run_class001.mrc as #5, grid size 640,640,640, pixel 1.05, shown at
level 0.000803, step 4, values float32
> volume #5 step 1
> volume #5 level 0.003263
> volume #5 level 0.003842
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/refine_82/run_class001.mrc
Opened run_class001.mrc as #6, grid size 640,640,640, pixel 1.05, shown at
level 0.000935, step 4, values float32
> volume #6 step 1
> volume #6 level 0.00339
> volume #6 level 0.002163
> volume #5 level 0.002612
> ui tool show "Map Filter"
> volume gaussian #5 sDev 1
Opened run_class001.mrc gaussian as #7, grid size 640,640,640, pixel 1.05,
shown at step 1, values float32
> volume gaussian #6 sDev 1
Opened run_class001.mrc gaussian as #8, grid size 640,640,640, pixel 1.05,
shown at step 1, values float32
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/mask_83/mask.mrc
Opened mask.mrc as #9, grid size 640,640,640, pixel 1.05, shown at level
5e-05, step 4, values float32
> volume #9 step 1
> volume #9 level 0
> volume #9 color #99bfe581
> volume #9 level 0.03697
> volume #9 color #99bfe582
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/refine_88/run_class001.mrc
Opened run_class001.mrc as #10, grid size 640,640,640, pixel 1.05, shown at
level 0.000718, step 4, values float32
> volume #10 step 1
> volume #10 level 0.001228
> volume #10 level 0.003034
> volume gaussian #10 sDev 1
Opened run_class001.mrc gaussian as #11, grid size 640,640,640, pixel 1.05,
shown at step 1, values float32
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_178/run_class001.mrc
Opened run_class001.mrc as #1, grid size 240,240,240, pixel 1.05, shown at
level 0.0159, step 1, values float32
> volume #1 level 0.02158
> volume #1 level 0.02087
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/J59_005_volume_map_lp15.mrc
Opened J59_005_volume_map_lp15.mrc as #2, grid size 640,640,640, pixel 1.05,
shown at level 0.332, step 4, values float32
> hide #!2 models
> close #2
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001_clean_lp15.mrc
Opened run_class001_clean_lp15.mrc as #2, grid size 576,576,576, pixel 1.05,
shown at level 0.00345, step 4, values float32
> volume #2 step 1
> volume #2 level 0.009213
> ui tool show "Segment Map"
Segmenting run_class001_clean_lp15.mrc, density threshold 0.009213
Showing 84 region surfaces
210 watershed regions, grouped to 84 regions
Showing run_class001_clean_lp15.seg - 84 regions, 84 surfaces
> select add #3.12
1 model selected
> select add #3.28
2 models selected
> select add #3.33
3 models selected
> select add #3.14
4 models selected
> select add #3.16
5 models selected
> select add #3.18
6 models selected
> select add #3.80
7 models selected
> select add #3.2
8 models selected
> select add #3.21
9 models selected
> select add #3.46
10 models selected
> select add #3.26
11 models selected
> select add #3.75
12 models selected
> select add #3.11
13 models selected
Grouped 13 regions
> select add #3.61
2 models selected
> select add #3.39
3 models selected
> select add #3.55
4 models selected
Grouped 4 regions
> select add #3.81
2 models selected
Grouped 2 regions
> select add #3.72
2 models selected
> select add #3.65
3 models selected
Grouped 3 regions
Deleted 65 regions
> hide #!2 models
Saving 1 regions to mrc file...
Opened run_class001_clean_lp15_region_307_15July25.mrc as #4, grid size
71,137,130, pixel 1.05, shown at step 1, values float32
Wrote run_class001_clean_lp15_region_307_15July25.mrc
> volume resample #4 onGrid #2
Opened run_class001_clean_lp15_region_307_15July25.mrc resampled as #5, grid
size 576,576,576, pixel 1.05, shown at step 1, values float32
> close #3
> volume #5 level 0.009492
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001_align_lp15_1trimer_again_15Julay25.mrc
> models #5
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_179/mask.mrc
Opened mask.mrc as #3, grid size 576,576,576, pixel 1.05, shown at level
5e-05, step 4, values float32
> volume #3 step 1
> volume #3 color #ffb2b280
> volume #3 level 0
> volume #3 level 0.5
> volume #3 color #ffb2b2
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_180/mask.mrc
Opened mask.mrc as #6, grid size 576,576,576, pixel 1.05, shown at level
5e-05, step 4, values float32
> volume #6 step 1
> volume #6 level 0.5
> volume #6 color #b2ffb282
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/class3d_96/run_it025_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/class3d_96/run_it025_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/class3d_96/run_it025_class003.mrc
Opened run_it025_class001.mrc as #7.1, grid size 256,256,256, pixel 1.05,
shown at level 0.00307, step 1, values float32
Opened run_it025_class002.mrc as #7.2, grid size 256,256,256, pixel 1.05,
shown at level 0.00267, step 1, values float32
Opened run_it025_class003.mrc as #7.3, grid size 256,256,256, pixel 1.05,
shown at level 0.00358, step 1, values float32
> volume #7.1 level 0.001951
> volume #7.2 level 0.002084
> volume #7.2 level 0.001764
> volume #7.2 level 0.001126
> volume #7.3 level 0.001651
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/3drec/3dmodel_job090.mrc
Opened 3dmodel_job090.mrc as #8, grid size 256,256,256, pixel 1.05, shown at
level 0.00345, step 1, values float32
> volume #8 level 0.001585
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/mask_89/mask.mrc
Opened mask.mrc as #9, grid size 640,640,640, pixel 1.05, shown at level 1,
step 4, values float32
> volume #9 step 1
> volume #9 level 0.5731
> volume #9 level 0.5
> volume #9 level 0.8549
> volume #9 level 1
> volume #9 level 0.2403
> volume #5 level 0.00954
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_181/mask.mrc
Opened mask.mrc as #10, grid size 576,576,576, pixel 1.05, shown at level
5e-05, step 4, values float32
> volume #10 step 1
> volume #10 level 0.5
> volume #10 color #b2ffff84
> volume #10 color #b2ffff85
> volume #10 level 1
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/3drec/3dmodel_job182.mrc
Opened 3dmodel_job182.mrc as #11, grid size 240,240,240, pixel 1.05, shown at
level 0.0193, step 1, values float32
> volume #11 level 0.01604
> volume #11 level 0.009756
> volume #11 level 0.01005
> volume #11 level 0.01
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_183/mask.mrc
Opened mask.mrc as #12, grid size 240,240,240, pixel 1.05, shown at level 1,
step 1, values float32
> volume #12 level 0.6303
> volume #12 color #ffb2ff80
> volume #12 level 0.5
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_184/run_it025_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_184/run_it025_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_184/run_it025_class003.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_184/run_it025_class004.mrc
Opened run_it025_class001.mrc as #13.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0147, step 1, values float32
Opened run_it025_class002.mrc as #13.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0167, step 1, values float32
Opened run_it025_class003.mrc as #13.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0173, step 1, values float32
Opened run_it025_class004.mrc as #13.4, grid size 240,240,240, pixel 1.05,
shown at level 0.0171, step 1, values float32
> volume #13.1 level 0.01604
> volume #13.2 level 0.0176
> volume #13.3 level 0.01711
> volume #13.4 level 0.0176
> volume #13.2 level 0.01704
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_184/run_it025_class003_lp15.mrc
Opened run_it025_class003_lp15.mrc as #14, grid size 240,240,240, pixel 1.05,
shown at level 0.0188, step 1, values float32
> volume #14 level 0.01099
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_183/mask.mrc
Opened mask.mrc as #15, grid size 240,240,240, pixel 1.05, shown at level 1,
step 1, values float32
> volume #15 level 0.7949
> volume #15 color #b2b2b280
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_188/run_it007_half2_class001.mrc
Opened run_it007_half2_class001.mrc as #16, grid size 240,240,240, pixel 1.05,
shown at level 0.0138, step 1, values float32
> volume #16 level 0.0152
> volume #16 level 0.01358
> volume #16 level 0.01502
> volume #16 level 0.01322
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_188/run_it010_half2_class001.mrc
Opened run_it010_half2_class001.mrc as #17, grid size 240,240,240, pixel 1.05,
shown at level 0.0136, step 1, values float32
> volume #17 level 0.01283
> volume #17 level 0.0136
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001.mrc
Opened run_class001.mrc as #18, grid size 576,576,576, pixel 1.05, shown at
level 0.014, step 4, values float32
> volume #18 step 1
> volume #18 level 0.016
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/cryosparc_j59_map_12june25.mrc
Opened cryosparc_j59_map_12june25.mrc as #19, grid size 640,640,640, pixel
1.05, shown at level 0.155, step 4, values float32
> volume #19 step 1
> volume #19 level 0.474
> volume #19 level 0.5822
> volume #19 level 0.4968
> volume #19 level 0.6107
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_188/run_class001.mrc
Opened run_class001.mrc as #20, grid size 240,240,240, pixel 1.05, shown at
level 0.0166, step 1, values float32
> volume #20 level 0.01656
> volume #20 level 0.0189
> volume #20 level 0.01851
> ui tool show "Segment Map"
Segmenting run_class001_clean_lp15.mrc, density threshold 0.009213
Showing 84 region surfaces
210 watershed regions, grouped to 84 regions
Showing run_class001_clean_lp15.seg - 84 regions, 84 surfaces
> select add #21.33
1 model selected
> select add #21.12
2 models selected
> select add #21.14
3 models selected
> select add #21.81
4 models selected
> select add #21.16
5 models selected
> select add #21.67
6 models selected
> select add #21.28
7 models selected
Drag select of 287, 497 of 37276 triangles, 299, 428 of 31916 triangles, 226,
685 of 26332 triangles, 161, 386 of 22088 triangles, 289, 164 of 24176
triangles, 135, 78 of 23112 triangles, 139, 668 of 20596 triangles, 159, 266
of 15004 triangles, 134, 55 of 11920 triangles, 2 run_class001_clean_lp15.mrc
> select subtract #21.78
10 models selected
> select subtract #21.9
9 models selected
> select subtract #21.35
8 models selected
> select add #21.14
9 models selected
> select add #21.81
10 models selected
> select add #21.16
11 models selected
> select subtract #21.16
10 models selected
> select add #21.16
11 models selected
Grouped 9 regions
> select add #21.18
4 models selected
Grouped 2 regions
> select add #21.80
4 models selected
Grouped 2 regions
> select add #21.61
4 models selected
> select subtract #21.61
3 models selected
> select add #21.61
4 models selected
> select subtract #21.61
3 models selected
> select add #21.61
4 models selected
> select subtract #21.61
3 models selected
> select add #21.61
4 models selected
Grouped 2 regions
Deleted 72 regions
> hide #!2 models
> select subtract #2
1 model selected
Saving 1 regions to mrc file...
Opened run_class001_clean_lp15_region_cp29_16July25.mrc as #22, grid size
63,93,118, pixel 1.05, shown at step 1, values float32
Wrote run_class001_clean_lp15_region_cp29_16July25.mrc
> volume resample #22 onGrid #2
Opened run_class001_clean_lp15_region_cp29_16July25.mrc resampled as #23, grid
size 576,576,576, pixel 1.05, shown at step 1, values float32
> close #21
> volume #23 level 0.009563
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001_clean_lp15_region_cp29_16July25.mrc
> models #23
> volume #23 level 0.009
> volume #23 level 0.01
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_191/mask.mrc
Opened mask.mrc as #21, grid size 576,576,576, pixel 1.05, shown at level
5e-05, step 4, values float32
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_190/run_it012_half2_class001.mrc
Opened run_it012_half2_class001.mrc as #24, grid size 240,240,240, pixel 1.05,
shown at level 0.0135, step 1, values float32
> volume #24 level 0.01437
> volume #24 level 0.01261
> volume #24 level 0.01507
> volume #21 step 1
> volume #21 color #99bfe5c7
> show #!2 models
> undo
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_190/run_class001.mrc
Opened run_class001.mrc as #25, grid size 240,240,240, pixel 1.05, shown at
level 0.0162, step 1, values float32
> volume #25 level 0.01689
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_193/run_it014_half2_class001.mrc
Opened run_it014_half2_class001.mrc as #26, grid size 240,240,240, pixel 1.05,
shown at level 0.0133, step 1, values float32
> volume #26 level 0.01384
> volume #26 level 0.01192
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_193/run_class001.mrc
Opened run_class001.mrc as #27, grid size 240,240,240, pixel 1.05, shown at
level 0.0159, step 1, values float32
> volume #27 level 0.01882
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/3drec/3dmodel_job189.mrc
Opened 3dmodel_job189.mrc as #28, grid size 576,576,576, pixel 1.05, shown at
level 0.00389, step 4, values float32
> volume #28 step 1
> volume #28 level 0.01263
> volume #28 level 0.01574
> volume #28 level 0.01944
> show #!2 models
> hide #!2 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> volume #28 level 0.01248
> volume #28 level 0.01515
> volume #28 level 0.01307
> volume #28 level 0.01737
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_195/run_it010_half2_class001.mrc
Opened run_it010_half2_class001.mrc as #29, grid size 240,240,240, pixel 1.05,
shown at level 0.0138, step 1, values float32
> volume #29 level 0.01461
> volume #29 level 0.01501
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/3drec/3dmodel_job192.mrc
Opened 3dmodel_job192.mrc as #30, grid size 240,240,240, pixel 1.05, shown at
level 0.0165, step 1, values float32
> volume #30 level 0.01799
> volume #30 level 0.008319
> volume #30 level 0.009078
> volume #30 level 0.01846
> volume #30 level 0.01126
> volume #30 level 0.008319
> volume #30 level 0.009457
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_197/mask.mrc
Opened mask.mrc as #31, grid size 240,240,240, pixel 1.05, shown at level 1,
step 1, values float32
> volume #31 level 0.6747
> volume #31 color #b2ffb280
> volume #31 level 0.5453
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_195/run_class001.mrc
Opened run_class001.mrc as #32, grid size 240,240,240, pixel 1.05, shown at
level 0.0159, step 1, values float32
> volume #32 level 0.01866
> volume #32 level 0.01709
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/3drec/3dmodel_job196.mrc
Opened 3dmodel_job196.mrc as #33, grid size 576,576,576, pixel 1.05, shown at
level 0.00283, step 4, values float32
> volume #33 step 1
> volume #33 level 0.01806
> volume #33 level 0.01693
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #33 level 0.01073
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_159/mask.mrc
Opened mask.mrc as #34, grid size 576,576,576, pixel 1.05, shown at level
0.75, step 4, values float32
> volume #34 step 1
> volume #34 level 0.5
> volume #34 color #cccc99b0
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_199/run_it003_half2_class001.mrc
Opened run_it003_half2_class001.mrc as #35, grid size 576,576,576, pixel 1.05,
shown at level 0.00296, step 4, values float32
> volume #35 step 1
> volume #35 level 0.01512
> volume #35 level 0.01715
> volume #35 level 0.01786
> volume #35 level 0.01572
> volume #35 level 0.01858
> volume #35 level 0.0156
Segmenting run_class001_clean_lp15.mrc, density threshold 0.009213
Showing 84 region surfaces
210 watershed regions, grouped to 84 regions
Showing run_class001_clean_lp15.seg - 84 regions, 84 surfaces
> select add #36.34
1 model selected
> select add #36.15
2 models selected
> select add #36.19
3 models selected
> select add #36.22
4 models selected
Drag select of 251, 614 of 29140 triangles, 269, 54 of 26980 triangles, 291,
539 of 25084 triangles, 33, 10 of 17264 triangles, 47, 83 of 14184 triangles,
2 run_class001_clean_lp15.mrc
> select add #36.19
8 models selected
> select add #36.34
9 models selected
> select add #36.10
10 models selected
> select subtract #36.10
9 models selected
> select subtract #36.29
8 models selected
> select add #36.56
9 models selected
> select add #36.8
10 models selected
> select add #36.43
11 models selected
Grouped 9 regions
> select add #36.71
4 models selected
> select add #36.29
5 models selected
Grouped 3 regions
> select add #36.20
4 models selected
> select add #36.5
5 models selected
Grouped 3 regions
> select add #36.13
4 models selected
Grouped 2 regions
> select add #36.63
4 models selected
> select add #36.57
5 models selected
> select add #36.83
6 models selected
Grouped 4 regions
> select add #36.84
4 models selected
Grouped 2 regions
> select add #36.10
4 models selected
> select subtract #36.10
3 models selected
> select add #36.10
4 models selected
> select add #36.4
5 models selected
Grouped 3 regions
> select add #36.48
4 models selected
Grouped 2 regions
Deleted 63 regions
> hide #!2 models
Saving 1 regions to mrc file...
Opened run_class001_clean_lp15_other_trimer_16July25.mrc as #37, grid size
102,131,116, pixel 1.05, shown at step 1, values float32
Wrote run_class001_clean_lp15_other_trimer_16July25.mrc
> volume resample #37 onGrid #2
Opened run_class001_clean_lp15_other_trimer_16July25.mrc resampled as #38,
grid size 576,576,576, pixel 1.05, shown at step 1, values float32
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001_align_lp15_1trimer_again_15Julay25.mrc
> models #38
> close #36
> volume #38 level 0.009586
> volume #38 level 0.009332
Segmenting run_class001_align_lp15_1trimer_again_15Julay25.mrc, density
threshold 0.009332
Showing 24 region surfaces
57 watershed regions, grouped to 24 regions
Showing run_class001_align_lp15_1trimer_again_15Julay25.seg - 24 regions, 24
surfaces
> select add #36.13
3 models selected
> select add #36.10
4 models selected
> select add #36.5
5 models selected
> select add #36.6
6 models selected
> select add #36.8
7 models selected
> select add #36.9
8 models selected
> select add #36.7
9 models selected
> select add #36.22
10 models selected
> select add #36.19
11 models selected
> select add #36.3
12 models selected
> select add #36.24
13 models selected
> select add #36.12
14 models selected
> select add #36.15
15 models selected
> select add #36.23
16 models selected
> select add #36.20
17 models selected
> select add #36.17
18 models selected
Grouped 16 regions
> select add #36.21
4 models selected
> select add #36.18
5 models selected
Grouped 3 regions
> select add #36.1
4 models selected
> select add #36.4
5 models selected
Grouped 3 regions
> select add #36.16
4 models selected
Grouped 2 regions
Deleted 3 regions
Saving 1 regions to mrc file...
Opened run_class001_align_lp15_1trimer_again_15Julay25_region_85.mrc as #39,
grid size 75,131,112, pixel 1.05, shown at step 1, values float32
Wrote run_class001_align_lp15_1trimer_again_15Julay25_region_85.mrc
> volume resample #39 onGrid #2
Opened run_class001_align_lp15_1trimer_again_15Julay25_region_85.mrc resampled
as #40, grid size 576,576,576, pixel 1.05, shown at step 1, values float32
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001_align_lp15_1trimer_again_15Julay25_region_85.mrc
> models #40
> close #36
> volume #40 level 0.009451
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it006_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it006_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it006_class003.mrc
Opened run_it006_class001.mrc as #36.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0131, step 1, values float32
Opened run_it006_class002.mrc as #36.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0134, step 1, values float32
Opened run_it006_class003.mrc as #36.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0138, step 1, values float32
> volume #36.1 level 0.01513
> volume #36.2 level 0.01996
> volume #36.3 level 0.01719
> volume #36.2 level 0.01729
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_199/run_it008_half2_class001.mrc
Opened run_it008_half2_class001.mrc as #41, grid size 576,576,576, pixel 1.05,
shown at level 0.00236, step 4, values float32
> volume #41 step 1
> volume #41 level 0.01469
> volume #41 level 0.01625
> volume #41 level 0.01859
> save /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/reifne_160/run_class001_align_lp15_othertrimer_16July25.mrc
> models #40
> volume #40 level 0.009531
> volume #40 level 0.0095
> volume #40 level 0
> volume #40 level 0.008644
> volume #40 level 0.0098
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_199/run_it009_half2_class001.mrc
Opened run_it009_half2_class001.mrc as #42, grid size 576,576,576, pixel 1.05,
shown at level 0.00223, step 4, values float32
> volume #42 step 1
> volume #42 level 0.01498
> volume #42 level 0.01592
> volume #42 level 0.01797
> volume #42 level 0.01514
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it008_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it008_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it008_class003.mrc
Opened run_it008_class001.mrc as #43.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
Opened run_it008_class002.mrc as #43.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
Opened run_it008_class003.mrc as #43.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0136, step 1, values float32
> volume #43.1 level 0.01618
> volume #43.2 level 0.01966
> volume #43.3 level 0.01894
> volume #43.2 level 0.02006
> volume #43.3 level 0.0174
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_199/run_it011_half2_class001.mrc
Opened run_it011_half2_class001.mrc as #44, grid size 576,576,576, pixel 1.05,
shown at level 0.00194, step 4, values float32
> volume #44 step 1
> volume #44 level 0.01519
> volume #44 level 0.01388
> volume #44 level 0.01356
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it013_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it013_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it013_class003.mrc
Opened run_it013_class001.mrc as #45.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
Opened run_it013_class002.mrc as #45.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0131, step 1, values float32
Opened run_it013_class003.mrc as #45.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0136, step 1, values float32
> volume #45.1 level 0.01676
> volume #45.2 level 0.01814
> volume #45.2 level 0.01908
> volume #45.3 level 0.01597
> volume #45.3 level 0.01911
> volume #45.3 level 0.01782
> volume #45.2 level 0.02038
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it015_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it015_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it015_class003.mrc
Opened run_it015_class001.mrc as #46.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0133, step 1, values float32
Opened run_it015_class002.mrc as #46.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0131, step 1, values float32
Opened run_it015_class003.mrc as #46.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0134, step 1, values float32
> volume #46.1 level 0.01654
> volume #46.2 level 0.01744
> volume #46.2 level 0.01654
> volume #46.3 level 0.0167
> volume #46.3 level 0.01833
> volume #46.2 level 0.01817
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it018_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it018_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it018_class003.mrc
Opened run_it018_class001.mrc as #47.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0133, step 1, values float32
Opened run_it018_class002.mrc as #47.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
Opened run_it018_class003.mrc as #47.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0133, step 1, values float32
> volume #47.2 level 0.01739
[Repeated 1 time(s)]
> volume #47.3 level 0.01527
> volume #47.3 level 0.01721
> volume #47.3 level 0.01897
> volume #47.2 level 0.01813
> volume #47.2 level 0.01666
> volume #47.3 level 0.01509
> volume #47.2 level 0.01831
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_199/run_it015_half2_class001.mrc
Opened run_it015_half2_class001.mrc as #48, grid size 576,576,576, pixel 1.05,
shown at level 0.00174, step 4, values float32
> volume #48 step 1
> volume #48 level 0.01577
> volume #48 level 0.01542
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_199/run_it017_half2_class001.mrc
Opened run_it017_half2_class001.mrc as #49, grid size 576,576,576, pixel 1.05,
shown at level 0.00168, step 4, values float32
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it021_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it021_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it021_class003.mrc
Opened run_it021_class001.mrc as #50.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
Opened run_it021_class002.mrc as #50.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
Opened run_it021_class003.mrc as #50.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
> volume #50.2 level 0.01799
> volume #50.3 level 0.0188
> volume #50.1 level 0.01698
> volume #50.2 level 0.02165
> volume #50.2 level 0.01909
> volume #49 step 1
> volume #49 level 0.01532
> volume #49 level 0.01125
> volume #49 level 0.01638
Unsupported scale factor (0.000000) detected on Display0
[Repeated 1 time(s)]
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it025_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it025_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_200/run_it025_class003.mrc
Opened run_it025_class001.mrc as #51.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0133, step 1, values float32
Opened run_it025_class002.mrc as #51.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
Opened run_it025_class003.mrc as #51.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0131, step 1, values float32
> view matrix models #2,1,0,0,-24.883,0,1,0,13.39,0,0,1,-0.12375
> volume #51.2 level 0.01978
> volume #51.3 level 0.01704
> volume #51.3 level 0.01941
> volume #51.1 level 0.01703
[Repeated 1 time(s)]
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_199/run_class001.mrc
Opened run_class001.mrc as #52, grid size 576,576,576, pixel 1.05, shown at
level 0.0142, step 4, values float32
> volume #52 step 1
> volume #52 level 0.02076
> volume #52 level 0.01748
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_202/run_it015_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_202/run_it015_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/class3d_202/run_it015_class003.mrc
Opened run_it015_class001.mrc as #53.1, grid size 240,240,240, pixel 1.05,
shown at level 0.0133, step 1, values float32
Opened run_it015_class002.mrc as #53.2, grid size 240,240,240, pixel 1.05,
shown at level 0.0131, step 1, values float32
Opened run_it015_class003.mrc as #53.3, grid size 240,240,240, pixel 1.05,
shown at level 0.0132, step 1, values float32
> view matrix models #2,1,0,0,-1.7212,0,1,0,10.944,0,0,1,13.758
> volume #53.3 level 0.02164
> volume #53.3 level 0.02435
> volume #53.3 level 0.02503
> volume #53.3 level 0.02435
> volume #53.2 level 0.01961
> volume #53.1 level 0.01607
> volume #53.3 level 0.02147
> volume #51.2 level 0.01284
> volume #51.2 level 0.01704
> volume #51.2 level 0.008085
> volume #51.2 level 0.01723
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_197/mask.mrc
Opened mask.mrc as #54, grid size 240,240,240, pixel 1.05, shown at level 1,
step 1, values float32
> volume #54 level 0.767
> volume #54 color #ffb2b280
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/class3d_96/run_it025_class001.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/class3d_96/run_it025_class002.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/class3d_96/run_it025_class003.mrc
Opened run_it025_class001.mrc as #55.1, grid size 256,256,256, pixel 1.05,
shown at level 0.00307, step 1, values float32
Opened run_it025_class002.mrc as #55.2, grid size 256,256,256, pixel 1.05,
shown at level 0.00267, step 1, values float32
Opened run_it025_class003.mrc as #55.3, grid size 256,256,256, pixel 1.05,
shown at level 0.00358, step 1, values float32
> view matrix models #2,1,0,0,0.52758,0,1,0,-16.301,0,0,1,15.997
> volume #55.1 level 0.0007395
> volume #55.2 level 0.001192
> volume #55.3 level 0.00113
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_204/run_it004_half2_class001.mrc
Opened run_it004_half2_class001.mrc as #56, grid size 240,240,240, pixel 1.05,
shown at level 0.0111, step 1, values float32
> volume #56 level 0.01251
> volume #56 level 0.01803
> volume #56 level 0.01879
> volume #56 level 0.02002
> volume #56 level 0.01711
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_204/run_it005_half1_class001.mrc
Opened run_it005_half1_class001.mrc as #57, grid size 240,240,240, pixel 1.05,
shown at level 0.0112, step 1, values float32
> volume #57 level 0.01835
> volume #57 level 0.0176
> volume #57 level 0.01582
> volume #57 level 0.02057
> volume #57 level 0.01597
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_204/run_it006_half2_class001.mrc
Opened run_it006_half2_class001.mrc as #58, grid size 240,240,240, pixel 1.05,
shown at level 0.011, step 1, values float32
> volume #58 level 0.01656
> volume #58 level 0.01915
> volume #58 level 0.01552
> volume #58 level 0.0176
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_204/run_it007_half2_class001.mrc
Opened run_it007_half2_class001.mrc as #59, grid size 240,240,240, pixel 1.05,
shown at level 0.0108, step 1, values float32
> volume #59 level 0.01772
> volume #59 level 0.01704
> volume #59 level 0.01466
> volume #59 level 0.01857
> volume #59 level 0.01653
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_204/run_it009_half2_class001.mrc
Opened run_it009_half2_class001.mrc as #60, grid size 240,240,240, pixel 1.05,
shown at level 0.0108, step 1, values float32
> volume #60 level 0.01711
> volume #60 level 0.01548
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_204/run_it011_half2_class001.mrc
Opened run_it011_half2_class001.mrc as #61, grid size 240,240,240, pixel 1.05,
shown at level 0.0107, step 1, values float32
> volume #61 level 0.01575
> volume #61 level 0.01701
> volume #61 level 0.0145
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_204/run_class001.mrc
Opened run_class001.mrc as #62, grid size 240,240,240, pixel 1.05, shown at
level 0.0123, step 1, values float32
> volume #62 level 0.02359
> volume #62 level 0.02039
[Repeated 1 time(s)]
> ui tool show "Map Filter"
> volume gaussian #62 sDev 0.52
Opened run_class001.mrc gaussian as #63, grid size 240,240,240, pixel 1.05,
shown at step 1, values float32
> volume #63 level 0.01779
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/3drec/3dmodel_job205.mrc
Opened 3dmodel_job205.mrc as #64, grid size 576,576,576, pixel 1.05, shown at
level 0.00364, step 4, values float32
> volume #64 step 1
> volume #64 level 0.01613
> volume #64 level 0.01691
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/mask_159/mask.mrc
Opened mask.mrc as #65, grid size 576,576,576, pixel 1.05, shown at level
0.75, step 4, values float32
> volume #65 step 1
> volume #65 color #99bfe580
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_206/run_it013_half2_class001.mrc
Opened run_it013_half2_class001.mrc as #66, grid size 576,576,576, pixel 1.05,
shown at level 0.00181, step 4, values float32
> volume #66 step 1
> volume #66 level 0.01588
> view matrix models #2,1,0,0,1.683,0,1,0,-17.333,0,0,1,10.405
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refine_206/run_class001.mrc
Opened run_class001.mrc as #67, grid size 576,576,576, pixel 1.05, shown at
level 0.0145, step 4, values float32
> volume #67 step 1
> volume #67 level 0.02403
> volume #67 level 0.02022
> view matrix models #2,1,0,0,1.704,0,1,0,-17.444,0,0,1,10.511
> volume #67 level 0.02158
> open 7oui fromDatabase pdb format mmcif
Summary of feedback from opening 7oui fetched from pdb
---
warnings | Atom C4 is not in the residue template for AJP /A:412
Atom C4 is not in the residue template for AJP /B:624
Atom CAW is not in the residue template for AJP /S:319
Atom CAW is not in the residue template for AJP /G:618
Atom CAW is not in the residue template for AJP /N:619
Atom CAW is not in the residue template for AJP /N:620
Atom CAW is not in the residue template for AJP /Y:320
4 messages similar to the above omitted
Atom C4 is not in the residue template for AJP /a:413
Atom C4 is not in the residue template for AJP /b:624
Atom CAW is not in the residue template for AJP /s:319
Atom CAW is not in the residue template for AJP /g:618
Atom CAW is not in the residue template for AJP /n:619
Atom CAW is not in the residue template for AJP /n:620
Atom CAW is not in the residue template for AJP /y:320
4 messages similar to the above omitted
7oui title:
Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana
(digitonin-extracted) [more info...]
Chain information for 7oui #68
---
Chain | Description | UniProt
1 3 5 7 | Lhcb1.4 | Q39142_ARATH 2-267
2 6 | Lhcb3.1 | CB3_ARATH 26-268
4 8 | Chlorophyll a-b binding protein, chloroplastic | Q9LMQ2_ARATH 47-258
A a | Photosystem II protein D1 | PSBA_ARATH 2-353
B b | Photosystem II CP47 reaction center protein | PSBB_ARATH 1-508
C c | Photosystem II CP43 reaction center protein | PSBC_ARATH 15-473
D d | Photosystem II D2 protein | PSBD_ARATH 2-353
E e | Cytochrome b559 subunit alpha | PSBE_ARATH 1-83
F f | Cytochrome b559 subunit beta (PsbF) | PSBF_ARATH 1-39
G N Y g n y | Chlorophyll a-b binding protein 1, chloroplastic | CB1C_ARATH 36-267
H h | Photosystem II reaction center protein H | PSBH_ARATH 2-73
I i | Photosystem II reaction center protein I | PSBI_ARATH 1-36
K k | Photosystem II reaction center protein K | PSBK_ARATH 25-61
L l | Photosystem II reaction center protein L | PSBL_ARATH 1-38
M m | Photosystem II reaction center protein M | PSBM_ARATH 1-34
O o | Oxygen-evolving enhancer protein 1-1, chloroplastic | PSBO1_ARATH 86-332
R r | Chlorophyll a-b binding protein CP29.1, chloroplastic | CB4A_ARATH 41-290
S s | Chlorophyll a-b binding protein CP26, chloroplastic | CB5_ARATH 49-280
T t | Photosystem II reaction center protein T | PSBT_ARATH 1-33
U u | PsbTn | PST2_ARATH 76-103
W w | Photosystem II reaction center W protein, chloroplastic | PSBW_ARATH 80-133
X x | PsbX | A0A7G2E9B1_ARATH 75-116
Z z | Photosystem II reaction center protein Z | PSBZ_ARATH 1-62
Non-standard residues in 7oui #68
---
AJP — Digitonin
BCR — β-carotene
BCT — bicarbonate ion
CA — calcium ion
CHL — chlorophyll B
CL — chloride ion
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
FE2 — Fe (II) ion
HEM — protoporphyrin IX containing Fe (HEME)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-neoxanthin)
PHO — pheophytin A
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)
> select add #68
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 5 models selected
> show sel cartoons
> hide sel atoms
> view matrix models
> #2,1,0,0,-6.1592,0,1,0,-7.84,0,0,1,45.011,#68,1,0,0,-7.8631,0,1,0,9.604,0,0,1,34.501
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.34264,0.045843,-0.93835,284.56,0.76499,0.56616,0.307,-121.58,0.54533,-0.82302,0.15892,267.16,#68,0.34264,0.045843,-0.93835,294.64,0.76499,0.56616,0.307,-116.24,0.54533,-0.82302,0.15892,250.21
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.34264,0.045843,-0.93835,360.64,0.76499,0.56616,0.307,-114.1,0.54533,-0.82302,0.15892,382.48,#68,0.34264,0.045843,-0.93835,370.72,0.76499,0.56616,0.307,-108.75,0.54533,-0.82302,0.15892,365.52
> view matrix models
> #2,0.34264,0.045843,-0.93835,392.04,0.76499,0.56616,0.307,-11.117,0.54533,-0.82302,0.15892,344.31,#68,0.34264,0.045843,-0.93835,402.11,0.76499,0.56616,0.307,-5.7714,0.54533,-0.82302,0.15892,327.35
> ui tool show "Fit in Map"
> fitmap #68 inMap #67
Fit molecule 7oui (#68) to map run_class001.mrc (#67) using 85897 atoms
average map value = 0.02006, steps = 304
shifted from previous position = 29
rotated from previous position = 18.6 degrees
atoms outside contour = 49708, contour level = 0.02158
Position of 7oui (#68) relative to run_class001.mrc (#67) coordinates:
Matrix rotation and translation
0.18696087 0.00163473 -0.98236600 462.88558961
0.92991979 0.32208300 0.17751544 10.03861682
0.31669358 -0.94671003 0.05869675 418.21727544
Axis -0.57572007 -0.66525327 0.47537825
Axis point -46.58897045 0.00000000 466.17459826
Rotation angle (degrees) 102.48181215
Shift along axis -74.35934913
> select subtract #68
2 models selected
> volume #67 color #b2b2b273
> show atoms
> style stick
Changed 85897 atom styles
> volume #67 level 0.01696
> save /Users/radhikakhera/Desktop/image1.png supersample 3
> volume #67 level 0.01506
> volume #67 color #b2b2b2
> volume #67 level 0.02076
> view matrix models
> #2,0.34264,0.045843,-0.93835,386.35,0.76499,0.56616,0.307,7.585,0.54533,-0.82302,0.15892,328.13
> view matrix models
> #2,0.34264,0.045843,-0.93835,383.01,0.76499,0.56616,0.307,18.235,0.54533,-0.82302,0.15892,321.07
> volume #67 level 0.01941
> hide #!68 models
> show #!68 models
> select add /4:120
9 atoms, 8 bonds, 1 residue, 3 models selected
> select add /R:273
16 atoms, 14 bonds, 2 residues, 3 models selected
> select add /2:246
24 atoms, 21 bonds, 3 residues, 3 models selected
> select add /3:91
31 atoms, 27 bonds, 4 residues, 3 models selected
> select add /1:136
37 atoms, 32 bonds, 5 residues, 3 models selected
> select up
842 atoms, 865 bonds, 106 residues, 3 models selected
> select up
8237 atoms, 8500 bonds, 1051 residues, 3 models selected
> select up
8240 atoms, 8500 bonds, 1051 residues, 3 models selected
> select up
9413 atoms, 9749 bonds, 1074 residues, 3 models selected
> select down
8240 atoms, 8500 bonds, 1051 residues, 3 models selected
> select down
8237 atoms, 8500 bonds, 1051 residues, 3 models selected
> select down
842 atoms, 865 bonds, 106 residues, 3 models selected
> select subtract /R:269
834 atoms, 856 bonds, 105 residues, 3 models selected
> select clear
> select add /4:254
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add /2:242
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add /3:91
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add /1:136
25 atoms, 21 bonds, 4 residues, 1 model selected
> select up
507 atoms, 517 bonds, 65 residues, 1 model selected
> select up
6410 atoms, 6622 bonds, 816 residues, 1 model selected
> select up
6413 atoms, 6622 bonds, 816 residues, 1 model selected
> select up
6676 atoms, 6900 bonds, 821 residues, 1 model selected
> select up
85897 atoms, 88812 bonds, 8855 residues, 1 model selected
> select down
6676 atoms, 6900 bonds, 821 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> hide #!68 models
> show #!68 models
> hide #!68 models
> volume #67 level 0.02049
> show #!68 models
> hide #!68 models
> volume #67 level 0.01343
> volume #67 level 0.01913
> volume #67 level 0.01696
> show #!68 models
> hide sel atoms
> select add #68
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> select subtract #68
Nothing selected
> select add #68
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> hide sel atoms
> select subtract #68
Nothing selected
> ui mousemode right zoom
> volume #67 level 0.01587
> volume #67 level 0.01886
> volume #67 level 0.01723
> volume #67 level 0.01777
> show atoms
> volume #67 level 0.0156
> volume #67 color #b2b2b280
> show atoms
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Nina_25Nov24/refined_relative_tocryo_j59_12June25.pdb
Chain information for refined_relative_tocryo_j59_12June25.pdb #69
---
Chain | Description
A a | No description available
B b | No description available
C c | No description available
D d | No description available
E e | No description available
F f | No description available
G N Y g n y | No description available
H h | No description available
I i | No description available
J j | No description available
K k | No description available
L l | No description available
M m | No description available
O o | No description available
R r | No description available
S s | No description available
T t | No description available
V v | No description available
W w | No description available
X x | No description available
Z z | No description available
> hide #!67 models
> show #!67 models
> hide #!67 models
> show #!67 models
> hide #!68 models
> select add #69
70499 atoms, 73099 bonds, 989 pseudobonds, 7347 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #69,1,0,0,-65.588,0,1,0,7.8422,0,0,1,1.4778
> view matrix models #69,1,0,0,-58.063,0,1,0,-25.832,0,0,1,-14.454
> view matrix models #69,1,0,0,-59.906,0,1,0,-16.386,0,0,1,-13.402
> ui tool show "Fit in Map"
> fitmap #69 inMap #67
Fit molecule refined_relative_tocryo_j59_12June25.pdb (#69) to map
run_class001.mrc (#67) using 70499 atoms
average map value = 0.02481, steps = 96
shifted from previous position = 7.54
rotated from previous position = 1.25 degrees
atoms outside contour = 18474, contour level = 0.0156
Position of refined_relative_tocryo_j59_12June25.pdb (#69) relative to
run_class001.mrc (#67) coordinates:
Matrix rotation and translation
0.99999936 -0.00069211 -0.00088972 -64.76803038
0.00067254 0.99976186 -0.02181212 -13.39576328
0.00090460 0.02181151 0.99976169 -24.40645958
Axis 0.99866746 -0.04107696 0.03124070
Axis point 0.00000000 1017.85727216 -747.46525367
Rotation angle (degrees) 1.25149183
Shift along axis -64.89394214
> select subtract #69
Nothing selected
> hide #!67 models
> show #!67 models
> show #!68 models
> select add #68
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> hide sel atoms
> select subtract #68
Nothing selected
> ui mousemode right zoom
> volume #67 level 0.02104
> volume #67 level 0.0175
> select add #68
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> show sel atoms
> select subtract #68
Nothing selected
> volume #67 level 0.01397
> volume #67 level 0.01533
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/10Jan25_mab_B3/cryosparc/cryosparc_P2_J212_007_volume_map.mrc
Opened cryosparc_P2_J212_007_volume_map.mrc as #1, grid size 640,640,640,
pixel 1.05, shown at level 0.0627, step 4, values float32
> volume #1 step 1
> volume #1 level 0.08538
> volume #1 level 0.1646
> volume #1 level 0.1533
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/10Jan25_mab_B3/cryosparc/cryosparc_P2_J68__mask_solvent.mrc
Opened cryosparc_P2_J68__mask_solvent.mrc as #2, grid size 100,100,100, pixel
6.72, shown at level 1, step 1, values float32
> volume #2 level 1
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/10Jan25_mab_B3/cryosparc/cryosparc_P2_J65_class_00_00122_volume.mrc
Opened cryosparc_P2_J65_class_00_00122_volume.mrc as #3, grid size
320,320,320, pixel 2.1, shown at level 0.178, step 2, values float32
> close #3
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/10Jan25_mab_B3/cryosparc/cryosparc_P2_J65_class_00_00122_volume.mrc
Opened cryosparc_P2_J65_class_00_00122_volume.mrc as #3, grid size
320,320,320, pixel 2.1, shown at level 0.178, step 2, values float32
> volume #3 step 1
> volume #3 level 0.3517
> volume #3 level 0.4307
> volume #3 level 0.5255
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/25june25_L17_b3/cryosparc/cryosparc_P5_J11_class_01_00142_volume.mrc
Opened cryosparc_P5_J11_class_01_00142_volume.mrc as #4, grid size
320,320,320, pixel 2.1, shown at level 0.231, step 2, values float32
> volume #4 step 1
> volume #4 level 0.3361
> volume #4 level 0.756
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/15Jan25_F8_mAb/cryosparc/cryosparc_P6_J71_006_volume_map.mrc
Opened cryosparc_P6_J71_006_volume_map.mrc as #5, grid size 640,640,640, pixel
1.05, shown at level 0.295, step 4, values float32
> volume #5 step 1
> volume #5 level 0.6223
> volume #5 level 0.3825
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/15Jan25_F8_mAb/cryosparc/cryosparc_P6_J17_006_volume_map.mrc
Opened cryosparc_P6_J17_006_volume_map.mrc as #6, grid size 640,640,640, pixel
1.05, shown at level 0.0527, step 4, values float32
> volume #6 step 1
> volume #6 level 0.1229
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/15Jan25_F8_mAb/cryosparc/cryosparc_P6_J60_006_volume_map.mrc
Opened cryosparc_P6_J60_006_volume_map.mrc as #7, grid size 640,640,640, pixel
1.05, shown at level 0.0569, step 4, values float32
> volume #7 step 1
> volume #7 level 0.1546
> volume #7 level 0.1302
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/15Jan25_F8_mAb/cryosparc/cryosparc_P6_J71_006_volume_map.mrc
Opened cryosparc_P6_J71_006_volume_map.mrc as #8, grid size 640,640,640, pixel
1.05, shown at level 0.295, step 4, values float32
> volume #8 step 1
> volume #8 level 0.4527
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/15Jan25_F8_mAb/cryosparc/cryosparc_P6_J59_007_volume_map.mrc
Opened cryosparc_P6_J59_007_volume_map.mrc as #9, grid size 640,640,640, pixel
1.05, shown at level 0.123, step 4, values float32
> volume #9 step 1
> volume #9 level 0.4593
> volume #9 level 0.5609
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/25june25_L17_b3/cryosparc/cryosparc_P5_J11_class_01_00142_volume.mrc
Opened cryosparc_P5_J11_class_01_00142_volume.mrc as #1, grid size
320,320,320, pixel 2.1, shown at level 0.231, step 2, values float32
> volume #1 step 1
> volume #1 level 0.3916
> volume #1 level 1.121
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J8_001_volume_map.mrc
Opened cryosparc_P9_J8_001_volume_map.mrc as #1, grid size 640,640,640, pixel
1.05, shown at level 0.0648, step 4, values float32
> volume #1 step 1
> volume #1 level 0.2015
> volume #1 level 0.3136
> volume #1 level 0.3486
> volume #1 level 0.4468
> volume #1 level 0.4012
> volume #1 level 0.3381
> volume #1 level 0.1244
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J8_002_volume_map.mrc
Opened cryosparc_P9_J8_002_volume_map.mrc as #2, grid size 640,640,640, pixel
1.05, shown at level 0.0598, step 4, values float32
> volume #2 step 1
> volume #2 level 0.3343
> volume #2 level 0.4258
> ui tool show "Map Filter"
> volume gaussian #2 sDev 1
Opened cryosparc_P9_J8_002_volume_map.mrc gaussian as #3, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #3 level 0.08536
> volume #3 level 0.2786
> volume #3 level 0.3876
> volume #3 level 0.3138
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/10Jan25_mab_B3/cryosparc/cryosparc_P2_J212_007_volume_map.mrc
Opened cryosparc_P2_J212_007_volume_map.mrc as #4, grid size 640,640,640,
pixel 1.05, shown at level 0.0627, step 4, values float32
> volume #4 step 1
> volume #4 level 0.3188
> volume #4 level 0.1326
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J9_mask.mrc
Opened cryosparc_P9_J9_mask.mrc as #5, grid size 640,640,640, pixel 1.05,
shown at level 1, step 4, values float32
> volume #5 step 1
> volume #5 level 0.7687
> volume #5 color #ffb2ff82
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J8_003_volume_map.mrc
Opened cryosparc_P9_J8_003_volume_map.mrc as #6, grid size 640,640,640, pixel
1.05, shown at level 0.0627, step 4, values float32
> volume #6 step 1
> volume #6 level 0.1768
> volume #6 level 0.2681
> volume #6 level 0.4335
> volume #6 level 0.3251
> volume #6 level 0.5247
> volume #6 level 0.4905
> volume #6 level 0.4106
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J8_004_volume_map.mrc
Opened cryosparc_P9_J8_004_volume_map.mrc as #7, grid size 640,640,640, pixel
1.05, shown at level 0.0636, step 4, values float32
> volume #7 step 1
> volume #7 level 0.2889
> volume #7 level 0.4241
> volume #7 level 0.4973
> volume #7 level 0.4466
> volume #7 level 0.1481
> ui tool show "Map Filter"
> volume gaussian #7 sDev 1
Opened cryosparc_P9_J8_004_volume_map.mrc gaussian as #8, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #8 level 0.3557
> volume #8 level 0.3243
> volume #8 level 0.4152
> volume #8 level 0.3452
> volume #8 level 0.4082
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J8_005_volume_map.mrc
Opened cryosparc_P9_J8_005_volume_map.mrc as #9, grid size 640,640,640, pixel
1.05, shown at level 0.0543, step 4, values float32
> volume #9 step 1
> volume #9 level 0.335
> volume #9 level 0.4192
> volume #9 level 0.4248
> ui tool show "Map Filter"
> volume gaussian #9 sDev 1
Opened cryosparc_P9_J8_005_volume_map.mrc gaussian as #10, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume gaussian #9 sDev 1 modelId #10
Opened cryosparc_P9_J8_005_volume_map.mrc gaussian as #10, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #10 level 0.4209
> volume #10 level 0.368
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J8_007_volume_map.mrc
Opened cryosparc_P9_J8_007_volume_map.mrc as #11, grid size 640,640,640, pixel
1.05, shown at level 0.054, step 4, values float32
> volume #11 step 1
> volume #11 level 0.4131
[Repeated 1 time(s)]
> volume #11 level 0.2728
> volume #11 level 0.3907
> volume #11 level 0.4187
> volume #11 level 0.3458
> volume #11 level 0.4075
> volume #11 level 0.2391
> ui tool show "Map Filter"
> volume gaussian #11 sDev 1
Opened cryosparc_P9_J8_007_volume_map.mrc gaussian as #12, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #12 level 0.06554
> volume #12 level 0.1183
> volume #12 level 0.3609
> volume #12 level 0.4101
> volume #12 level 0.28
> volume #12 level 0.3644
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J16_000_volume_map.mrc
Opened cryosparc_P9_J16_000_volume_map.mrc as #13, grid size 640,640,640,
pixel 1.05, shown at level 0.0848, step 4, values float32
> volume #13 step 1
> volume #13 level 0.3535
> volume #13 level 0.2706
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J16_001_volume_map.mrc
Opened cryosparc_P9_J16_001_volume_map.mrc as #14, grid size 640,640,640,
pixel 1.05, shown at level 0.0594, step 4, values float32
> volume #14 step 1
> volume #14 level 0.2725
> volume #14 level 0.2867
> volume #14 level 0.2725
> volume #14 level 0.3208
> volume #14 level 0.3776
> volume #14 level 0.2185
> volume #14 level 0.2753
[Repeated 1 time(s)]
> volume #14 level 0.3293
> volume #14 level 0.1162
> volume #14 level 0.3293
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J16_004_volume_map.mrc
Opened cryosparc_P9_J16_004_volume_map.mrc as #15, grid size 640,640,640,
pixel 1.05, shown at level 0.0655, step 4, values float32
> volume #15 step 1
> volume #15 level 0.2952
> volume #15 level 0.3288
> volume #15 level 0.3961
> volume #15 level 0.3568
> ui tool show "Map Filter"
> volume gaussian #15 sDev 1
Opened cryosparc_P9_J16_004_volume_map.mrc gaussian as #16, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #16 level 0.3989
> volume #16 level 0.3382
> volume #16 level 0.2989
> volume #16 level 0.3667
> volume #16 level 0.4239
> volume #16 level 0.3274
> open 7oui fromDatabase pdb format mmcif
Summary of feedback from opening 7oui fetched from pdb
---
warnings | Atom C4 is not in the residue template for AJP /A:412
Atom C4 is not in the residue template for AJP /B:624
Atom CAW is not in the residue template for AJP /S:319
Atom CAW is not in the residue template for AJP /G:618
Atom CAW is not in the residue template for AJP /N:619
Atom CAW is not in the residue template for AJP /N:620
Atom CAW is not in the residue template for AJP /Y:320
4 messages similar to the above omitted
Atom C4 is not in the residue template for AJP /a:413
Atom C4 is not in the residue template for AJP /b:624
Atom CAW is not in the residue template for AJP /s:319
Atom CAW is not in the residue template for AJP /g:618
Atom CAW is not in the residue template for AJP /n:619
Atom CAW is not in the residue template for AJP /n:620
Atom CAW is not in the residue template for AJP /y:320
4 messages similar to the above omitted
7oui title:
Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana
(digitonin-extracted) [more info...]
Chain information for 7oui #17
---
Chain | Description | UniProt
1 3 5 7 | Lhcb1.4 | Q39142_ARATH 2-267
2 6 | Lhcb3.1 | CB3_ARATH 26-268
4 8 | Chlorophyll a-b binding protein, chloroplastic | Q9LMQ2_ARATH 47-258
A a | Photosystem II protein D1 | PSBA_ARATH 2-353
B b | Photosystem II CP47 reaction center protein | PSBB_ARATH 1-508
C c | Photosystem II CP43 reaction center protein | PSBC_ARATH 15-473
D d | Photosystem II D2 protein | PSBD_ARATH 2-353
E e | Cytochrome b559 subunit alpha | PSBE_ARATH 1-83
F f | Cytochrome b559 subunit beta (PsbF) | PSBF_ARATH 1-39
G N Y g n y | Chlorophyll a-b binding protein 1, chloroplastic | CB1C_ARATH 36-267
H h | Photosystem II reaction center protein H | PSBH_ARATH 2-73
I i | Photosystem II reaction center protein I | PSBI_ARATH 1-36
K k | Photosystem II reaction center protein K | PSBK_ARATH 25-61
L l | Photosystem II reaction center protein L | PSBL_ARATH 1-38
M m | Photosystem II reaction center protein M | PSBM_ARATH 1-34
O o | Oxygen-evolving enhancer protein 1-1, chloroplastic | PSBO1_ARATH 86-332
R r | Chlorophyll a-b binding protein CP29.1, chloroplastic | CB4A_ARATH 41-290
S s | Chlorophyll a-b binding protein CP26, chloroplastic | CB5_ARATH 49-280
T t | Photosystem II reaction center protein T | PSBT_ARATH 1-33
U u | PsbTn | PST2_ARATH 76-103
W w | Photosystem II reaction center W protein, chloroplastic | PSBW_ARATH 80-133
X x | PsbX | A0A7G2E9B1_ARATH 75-116
Z z | Photosystem II reaction center protein Z | PSBZ_ARATH 1-62
Non-standard residues in 7oui #17
---
AJP — Digitonin
BCR — β-carotene
BCT — bicarbonate ion
CA — calcium ion
CHL — chlorophyll B
CL — chloride ion
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
FE2 — Fe (II) ion
HEM — protoporphyrin IX containing Fe (HEME)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-neoxanthin)
PHO — pheophytin A
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)
> select add #17
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.98892,0.0551,-0.13783,16.995,-0.14239,0.089842,-0.98573,401.86,-0.041931,0.99443,0.096692,-24.735
> view matrix models
> #17,0.15629,0.3068,0.93885,-67.173,0.94149,0.24109,-0.23552,7.0327,-0.2986,0.92073,-0.25117,108.66
> view matrix models
> #17,-0.0093593,0.081442,0.99663,2.0768,0.90039,0.43424,-0.02703,-63.497,-0.43498,0.89711,-0.077394,108.66
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.0093593,0.081442,0.99663,137.08,0.90039,0.43424,-0.02703,-37.284,-0.43498,0.89711,-0.077394,269.51
> view matrix models
> #17,-0.0093593,0.081442,0.99663,149.82,0.90039,0.43424,-0.02703,28.079,-0.43498,0.89711,-0.077394,290.78
> view matrix models
> #17,-0.0093593,0.081442,0.99663,117.35,0.90039,0.43424,-0.02703,36.467,-0.43498,0.89711,-0.077394,277.06
> view matrix models
> #17,-0.0093593,0.081442,0.99663,111.07,0.90039,0.43424,-0.02703,72.396,-0.43498,0.89711,-0.077394,277.92
> ui tool show "Fit in Map"
> fitmap #17 inMap #16
Fit molecule 7oui (#17) to map cryosparc_P9_J16_004_volume_map.mrc gaussian
(#16) using 85897 atoms
average map value = 0.4614, steps = 104
shifted from previous position = 8.44
rotated from previous position = 4.7 degrees
atoms outside contour = 28739, contour level = 0.32744
Position of 7oui (#17) relative to cryosparc_P9_J16_004_volume_map.mrc
gaussian (#16) coordinates:
Matrix rotation and translation
0.06323899 0.05498459 0.99648258 105.69030922
0.88669032 0.45514465 -0.08138561 75.39740641
-0.45801867 0.88871820 -0.01997141 269.31450731
Axis 0.50106571 0.75126053 0.42958209
Axis point 116.57194049 0.00000000 116.80748621
Rotation angle (degrees) 104.52449534
Shift along axis 225.29357492
> fitmap #17 inMap #16
Fit molecule 7oui (#17) to map cryosparc_P9_J16_004_volume_map.mrc gaussian
(#16) using 85897 atoms
average map value = 0.4614, steps = 48
shifted from previous position = 0.0322
rotated from previous position = 0.00704 degrees
atoms outside contour = 28750, contour level = 0.32744
Position of 7oui (#17) relative to cryosparc_P9_J16_004_volume_map.mrc
gaussian (#16) coordinates:
Matrix rotation and translation
0.06317299 0.05500960 0.99648538 105.71025820
0.88664731 0.45523651 -0.08134042 75.38207932
-0.45811103 0.88866960 -0.02001546 269.32278135
Axis 0.50101849 0.75131151 0.42954800
Axis point 116.59426080 0.00000000 116.80099597
Rotation angle (degrees) 104.52503330
Shift along axis 225.28528080
> select subtract #17
Nothing selected
> ui mousemode right zoom
> volume #16 level 0.2631
> volume #16 color #b2ffb27c
> volume #16 color #b2ffb27a
> graphics silhouettes false
> graphics silhouettes true
> volume #16 level 0.381
> volume #16 color #d6d6d6
> volume #16 color #d6d6d6d6
> volume #16 level 0.4346
> show atoms
> style stick
Changed 85897 atom styles
> volume #16 level 0.3953
> volume #16 color #d6d6d6
> volume #16 level 0.3953
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J16_005_volume_map.mrc
Opened cryosparc_P9_J16_005_volume_map.mrc as #18, grid size 640,640,640,
pixel 1.05, shown at level 0.047, step 4, values float32
> volume #18 step 1
> volume #18 level 0.2183
> volume #18 level 0.4891
> volume #18 level 0.4228
> hide #!17 models
> volume gaussian #18 sDev 1
Opened cryosparc_P9_J16_005_volume_map.mrc gaussian as #19, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #19 level 0.3758
> show #!17 models
> hide atoms
> volume #19 color #99bfe59c
> volume #19 color #99bfe5
> volume #19 level 0.06245
> volume #19 level 0.3406
> volume #19 color #99bfe59c
> volume #19 level 0.4321
> show atoms
> volume #19 level 0.323
> volume #19 color #99bfe5
> hide atoms
> volume #19 level 0.323
> volume #19 color #99bfe5a7
> volume #19 color #99bfe5a6
> volume #19 level 0.3547
> volume #19 level 0.4533
> show atoms
> hide atoms
> volume #18 color #e5bf99bb
> volume #18 color #e5bf99ba
> volume #18 color #d6d6d6
> volume #18 color #d6d6d683
> volume #18 color #d6d6d682
> volume #18 level 0.4891
> show atoms
> hide atoms
> show atoms
[Repeated 1 time(s)]
> hide atoms
> show atoms
> hide atoms
> volume #18 color #d6d6d6
> volume #18 level 0.4228
> volume #18 level 0.2681
> volume #18 level 0.3786
> volume #18 level 0.3288
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/J96/J96_006_volume_map_lp15.mrc
Opened J96_006_volume_map_lp15.mrc as #20, grid size 640,640,640, pixel 1.05,
shown at level 0.0267, step 4, values float32
> volume #20 step 1
> volume #20 level 0.05423
> volume #20 level 0.05155
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J20_mask.mrc
Opened cryosparc_P9_J20_mask.mrc as #21, grid size 640,640,640, pixel 1.05,
shown at level 1, step 4, values float32
> volume #21 step 1
> volume #21 level 0.9305
> volume #21 color #b2b2b280
> volume #21 color #b2b2b2
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J21_mask.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J16_006_volume_map.mrc
Opened cryosparc_P9_J21_mask.mrc as #22.1, grid size 640,640,640, pixel 1.05,
shown at level 1, step 4, values float32
Opened cryosparc_P9_J16_006_volume_map.mrc as #22.2, grid size 640,640,640,
pixel 1.05, shown at level 0.0461, step 4, values float32
> volume #22.2 step 1
> volume #22.2 level 0.1063
> volume #22.2 level 0.1282
> volume #22.2 level 0.1556
> hide #!17 models
> volume #22.2 level 0.3198
> volume #22.2 level 0.2323
> volume #22.2 level 0.3636
> volume #22.2 level 0.3363
> volume #22.2 level 0.4184
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> volume #22.2 level 0.3636
> volume #22.2 level 0.3417
> volume #22.2 level 0.3855
> volume gaussian #22.2 sDev 1
Opened cryosparc_P9_J16_006_volume_map.mrc gaussian as #23, grid size
640,640,640, pixel 1.05, shown at step 1, values float32
> volume #22.1 step 1
> volume #22.1 level 0.8296
> volume #22.1 color #ffffb29e
> volume #23 level 0.2996
> volume #23 level 0.2892
> volume #23 level 0.4073
> volume #23 level 0.3274
> volume #23 level 0.383
> volume #23 level 0.06346
> volume #23 level 0.119
> show #!17 models
> volume #23 level 0.2996
> volume #23 color #b2b2ff8e
> volume #23 color #b2b2ff8f
> volume #23 level 0.3899
> volume #23 level 0.4073
> show atoms
> 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.
> segmentations create #20
Opened segmentation 1 of J96_006_volume_map_lp15.mrc as #27, grid size
640,640,640, pixel 1.05, shown at level 0.501, step 1, values float64
> close #27
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/28May25_L17_b3/cryosparc/J96/J96_006_volume_map_lp15.mrc format
> mrc
Opened J96_006_volume_map_lp15.mrc as #1, grid size 640,640,640, pixel 1.05,
shown at level 0.0267, step 4, values float32
> volume #1 step 1
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J22_006_volume_map.mrc
Opened cryosparc_P9_J22_006_volume_map.mrc as #2, grid size 640,640,640, pixel
1.05, shown at level 0.0493, step 4, values float32
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 1735, in <lambda>
sm.addAction("%d" % step, lambda s=step: self.data_step_cb(s))
^^^^^^^^^^^^^^^^^^^^
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 1808, in data_step_cb
self.plane_viewer.update_and_rerender()
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 817, in
update_and_rerender
self.view.drawing.parent.update_drawings()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'update_drawings'
AttributeError: 'NoneType' object has no attribute 'update_drawings'
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 817, in
update_and_rerender
self.view.drawing.parent.update_drawings()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb
self.plane_viewer.on_color_changed()
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 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb
self.plane_viewer.on_color_changed()
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 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J22_006_volume_map.mrc
> format mrc
Opened cryosparc_P9_J22_006_volume_map.mrc as #1, grid size 640,640,640, pixel
1.05, shown at level 0.0493, step 4, values float32
> volume #1 step 1
> volume #1 level 0.3146
> volume #1 level 0.4012
> volume #1 level 0.3795
> volume #1 level 0.4012
> open 7oui fromDatabase pdb format mmcif
Summary of feedback from opening 7oui fetched from pdb
---
warnings | Atom C4 is not in the residue template for AJP /A:412
Atom C4 is not in the residue template for AJP /B:624
Atom CAW is not in the residue template for AJP /S:319
Atom CAW is not in the residue template for AJP /G:618
Atom CAW is not in the residue template for AJP /N:619
Atom CAW is not in the residue template for AJP /N:620
Atom CAW is not in the residue template for AJP /Y:320
4 messages similar to the above omitted
Atom C4 is not in the residue template for AJP /a:413
Atom C4 is not in the residue template for AJP /b:624
Atom CAW is not in the residue template for AJP /s:319
Atom CAW is not in the residue template for AJP /g:618
Atom CAW is not in the residue template for AJP /n:619
Atom CAW is not in the residue template for AJP /n:620
Atom CAW is not in the residue template for AJP /y:320
4 messages similar to the above omitted
7oui title:
Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana
(digitonin-extracted) [more info...]
Chain information for 7oui #2
---
Chain | Description | UniProt
1 3 5 7 | Lhcb1.4 | Q39142_ARATH 2-267
2 6 | Lhcb3.1 | CB3_ARATH 26-268
4 8 | Chlorophyll a-b binding protein, chloroplastic | Q9LMQ2_ARATH 47-258
A a | Photosystem II protein D1 | PSBA_ARATH 2-353
B b | Photosystem II CP47 reaction center protein | PSBB_ARATH 1-508
C c | Photosystem II CP43 reaction center protein | PSBC_ARATH 15-473
D d | Photosystem II D2 protein | PSBD_ARATH 2-353
E e | Cytochrome b559 subunit alpha | PSBE_ARATH 1-83
F f | Cytochrome b559 subunit beta (PsbF) | PSBF_ARATH 1-39
G N Y g n y | Chlorophyll a-b binding protein 1, chloroplastic | CB1C_ARATH 36-267
H h | Photosystem II reaction center protein H | PSBH_ARATH 2-73
I i | Photosystem II reaction center protein I | PSBI_ARATH 1-36
K k | Photosystem II reaction center protein K | PSBK_ARATH 25-61
L l | Photosystem II reaction center protein L | PSBL_ARATH 1-38
M m | Photosystem II reaction center protein M | PSBM_ARATH 1-34
O o | Oxygen-evolving enhancer protein 1-1, chloroplastic | PSBO1_ARATH 86-332
R r | Chlorophyll a-b binding protein CP29.1, chloroplastic | CB4A_ARATH 41-290
S s | Chlorophyll a-b binding protein CP26, chloroplastic | CB5_ARATH 49-280
T t | Photosystem II reaction center protein T | PSBT_ARATH 1-33
U u | PsbTn | PST2_ARATH 76-103
W w | Photosystem II reaction center W protein, chloroplastic | PSBW_ARATH 80-133
X x | PsbX | A0A7G2E9B1_ARATH 75-116
Z z | Photosystem II reaction center protein Z | PSBZ_ARATH 1-62
Non-standard residues in 7oui #2
---
AJP — Digitonin
BCR — β-carotene
BCT — bicarbonate ion
CA — calcium ion
CHL — chlorophyll B
CL — chloride ion
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
FE2 — Fe (II) ion
HEM — protoporphyrin IX containing Fe (HEME)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-neoxanthin)
PHO — pheophytin A
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)
> select add #2
85897 atoms, 88812 bonds, 1002 pseudobonds, 8855 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.035341,-0.068019,0.99706,23.473,-0.37726,0.92296,0.076336,78.722,-0.92543,-0.37885,0.0069572,454.85
> view matrix models
> #2,0.12766,-0.076605,0.98886,7.857,-0.36221,0.92455,0.11838,67.372,-0.92331,-0.37328,0.090277,437.54
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.12766,-0.076605,0.98886,129.54,-0.36221,0.92455,0.11838,161.07,-0.92331,-0.37328,0.090277,582.5
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.24899,0.15288,0.95636,63.757,0.73779,0.60977,-0.28956,77.115,-0.62743,0.77769,0.039034,295.57
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.24899,0.15288,0.95636,84.979,0.73779,0.60977,-0.28956,124.6,-0.62743,0.77769,0.039034,322.84
> view matrix models
> #2,0.24899,0.15288,0.95636,55.184,0.73779,0.60977,-0.28956,129.5,-0.62743,0.77769,0.039034,318.93
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 7oui (#2) to map cryosparc_P9_J22_006_volume_map.mrc (#1) using
85897 atoms
average map value = 0.592, steps = 236
shifted from previous position = 13.5
rotated from previous position = 17.3 degrees
atoms outside contour = 34540, contour level = 0.40116
Position of 7oui (#2) relative to cryosparc_P9_J22_006_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.06275258 0.05555781 0.99648152 106.10558098
0.88772421 0.45316359 -0.08116935 75.53534280
-0.45607875 0.88969436 -0.02088283 268.96297642
Axis 0.50168586 0.75059860 0.43001516
Axis point 116.30229379 0.00000000 116.48186429
Rotation angle (degrees) 104.62451181
Shift along axis 225.58654901
> select subtract #2
Nothing selected
> volume #1 level 0.4012
> volume #1 color #b2b2b271
> volume #1 color #b2b2b2b0
> open 3jcu fromDatabase pdb format mmcif
3jcu title:
Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom
resolution [more info...]
Chain information for 3jcu #3
---
Chain | Description | UniProt
A a | Photosystem II protein D1 | PSBA_SPIOL 1-344
B b | Photosystem II CP47 reaction center protein | PSBB_SPIOL 1-508
C c | Photosystem II CP43 reaction center protein | PSBC_SPIOL 1-473
D d | Photosystem II D2 protein | PSBD_SPIOL 0-352
E e | Cytochrome b559 subunit alpha | PSBE_SPIOL 1-83
F f | Cytochrome b559 subunit beta | PSBF_SPIOL 7-45
G N Y g n y | Chlorophyll a-b binding protein, chloroplastic | CB2A_SPIOL -34-232
H h | Photosystem II reaction center protein H | PSBH_SPIOL 1-73
I i | Protein Photosystem II reaction center protein I | PSBI_SPIOL 1-36
J j | Photosystem II reaction center protein J | PSBJ_SPIOL 1-40
K k | Photosystem II reaction center protein K | PSBK_SPIOL 1-59
L l | Protein Photosystem II reaction center protein L | PSBL_SPIOL 1-38
M m | Photosystem II reaction center protein M | PSBM_SPIOL 1-34
O o | Oxygen-evolving enhancer protein 1, chloroplastic | PSBO_SPIOL 1-332
P p | Oxygen-evolving enhancer protein 2, chloroplastic | PSBP_SPIOL -80-186
Q q | Oxygen-evolving enhancer protein 3, chloroplastic | PSBQ_SPIOL -82-149
R r | Chlorophyll A-B Binding protein 29 kD (CP29) | F2Z293_SPIOL 1-243
S s | Chlorophyll A-B Binding protein 26 kD (CP26) | A0A0K9QUQ7_SPIOL -50-244
T t | Photosystem II Reaction Center protein Tc | PSBT_SPIOL 1-33
U u | Photosystem II Reaction Center Tn protein | A0A0K9RHP1_SPIOL -70-28
W w | Photosystem II reaction center W protein, chloroplastic | PSBW_SPIOL 1-137
X x | Photosystem II Reaction Center X protein | A0A0K9RTU3_SPIOL 1-117
Z z | Photosystem II reaction center protein Z | PSBZ_SPIOL 1-62
Non-standard residues in 3jcu #3
---
BCR — β-carotene
BCT — bicarbonate ion
CHL — chlorophyll B
CL — chloride ion
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
FE2 — Fe (II) ion
HEM — protoporphyrin IX containing Fe (HEME)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol, lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol, 9'-cis-neoxanthin)
OEX — Ca-MN4-O5 cluster
PHO — pheophytin A
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)
> select add #3
75994 atoms, 78658 bonds, 940 pseudobonds, 7970 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> view matrix models #3,1,0,0,279.56,0,1,0,308.96,0,0,1,340.33
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.35265,-0.030145,-0.93527,291.96,0.63114,0.74558,0.21395,306.13,0.69087,-0.66573,0.28196,349.85
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.35265,-0.030145,-0.93527,336.65,0.63114,0.74558,0.21395,317.89,0.69087,-0.66573,0.28196,332.48
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 3jcu (#3) to map cryosparc_P9_J22_006_volume_map.mrc (#1) using
75994 atoms
average map value = 0.7084, steps = 460
shifted from previous position = 26.4
rotated from previous position = 36 degrees
atoms outside contour = 19269, contour level = 0.40116
Position of 3jcu (#3) relative to cryosparc_P9_J22_006_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.08418809 0.00434068 -0.99644043 331.43026116
0.95941358 0.26974621 0.08223480 334.02232483
0.26914298 -0.96292167 0.01854491 353.58523140
Axis -0.55037075 -0.66644575 0.50293349
Axis point -225.88832512 0.00000000 414.74046519
Rotation angle (degrees) 108.28599632
Shift along axis -227.18742623
> select subtract #3
Nothing selected
> hide #!2 models
> show #!3 atoms
> style #!3 stick
Changed 75994 atom styles
> hide #!3 atoms
> volume #1 level 0.4568
> show #!3 atoms
> close session
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J24_class_01_00080_volume.mrc
> /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J24_class_02_00080_volume.mrc
Opened cryosparc_P9_J24_class_01_00080_volume.mrc as #1.1, grid size
320,320,320, pixel 2.1, shown at level 0.197, step 2, values float32
Opened cryosparc_P9_J24_class_02_00080_volume.mrc as #1.2, grid size
320,320,320, pixel 2.1, shown at level 0.0859, step 2, values float32
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J24_class_00_00080_volume.mrc
Opened cryosparc_P9_J24_class_00_00080_volume.mrc as #2, grid size
320,320,320, pixel 2.1, shown at level 0.306, step 2, values float32
> volume #1.1 step 1
> volume #1.1 level 0.7664
> ui mousemode right zoom
> volume #1.1 level 0.8845
> volume #1.2 step 1
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 1735, in <lambda>
sm.addAction("%d" % step, lambda s=step: self.data_step_cb(s))
^^^^^^^^^^^^^^^^^^^^
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 1808, in data_step_cb
self.plane_viewer.update_and_rerender()
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 817, in
update_and_rerender
self.view.drawing.parent.update_drawings()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'update_drawings'
AttributeError: 'NoneType' object has no attribute 'update_drawings'
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 817, in
update_and_rerender
self.view.drawing.parent.update_drawings()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> volume #1.2 level 0.1182
> volume #1.2 level 0.1527
> volume #1.2 level 0.2481
> volume #1.1 level 1.132
> open /Users/radhikakhera/Desktop/Niyogi/Niyogi/Results/cryo-
> maps/EM_maps/Merged_datasets_Cryosparc/cryosparc_P9_J34_volume_map_consensus.mrc
Opened cryosparc_P9_J34_volume_map_consensus.mrc as #3, grid size 144,144,144,
pixel 4.67, shown at level 0.524, step 1, values float32
> volume #3 level 1.275
> volume #3 level 2.702
> volume #3 level 2.073
[Repeated 1 time(s)]
> volume #3 level 2.103
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/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb
self.plane_viewer.on_color_changed()
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 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb
self.plane_viewer.on_color_changed()
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 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent
self._drag(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag
cb(event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb
cb(m)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb
self.plane_viewer.on_color_changed()
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 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'image_colors'
AttributeError: 'NoneType' object has no attribute 'image_colors'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
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: MacBookPro18,2
Model Number: Z150000H5LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 77 days, 16 hours, 51 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
MAG 27CQ6F:
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
babel: 2.16.0
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-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-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-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
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
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
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: 3.9.2
matplotlib-inline: 0.1.7
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: 1.26.4
openvr: 1.26.701
packaging: 23.2
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
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
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
tifffile: 2024.7.24
tinyarray: 1.2.4
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
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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