![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 weeks ago
Closed 3 weeks ago
#20011 closed defect (duplicate)
ffmpeg: Permission Denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| 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: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/apadavan/Documents/Daphnia_Model_Building/Daphnia-
> Figures/Daphnia-Prep-2-021726.cxs
Opened composite_map.ccp4 as #2, grid size 245,254,396, pixel 0.88,0.88,0.88,
shown at level 2.78, step 1, values float32
Opened cryosparc_P33_J165_005_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.88, shown at level 0.15, step 1, values float32
Opened cryosparc_P33_J122_004_volume_map_sharp.mrc as #4, grid size
600,600,600, pixel 0.88, shown at level 0.578, step 1, values float32
Log from Thu Feb 19 15:22:31 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/apadavan/Documents/Daphnia_Model_Building/Daphnia-
> Figures/Daphnia-Model-Map.cxs
Opened composite_map.ccp4 as #2, grid size 245,254,396, pixel 0.88,0.88,0.88,
shown at level 2.78, step 1, values float32
Log from Tue Dec 9 17:07:25 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/apadavan/Documents/Daphnia_Model_Building/CombineFocusedMaps_15/composite_map.ccp4
Opened composite_map.ccp4 as #1, grid size 245,254,396, pixel 0.88,0.88,0.88,
shown at level 5.3, step 2, values float32
> volume #1 step 1
> volume #1 level 2.283
> volume #1 level 1.989
[Repeated 1 time(s)]
> ui tool show "Hide Dust"
> surface dust #1 size 5.28
> set bgColor white
> lighting soft
> surface dust #1 size 6
[Repeated 2 time(s)]
> open
> /Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_31/pdb_extract_out_coot-39_real_space_refined_031.cif
Summary of feedback from opening
/Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_31/pdb_extract_out_coot-39_real_space_refined_031.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 6347
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "3S", on line 226
Invalid residue range for struct_conf "2": invalid chain "3S", on line 227
Invalid residue range for struct_conf "3": invalid chain "3S", on line 228
Invalid residue range for struct_conf "4": invalid chain "3H", on line 229
Invalid residue range for struct_conf "5": invalid chain "3H", on line 230
315 messages similar to the above omitted
Bad residue range for struct_conf "329" on line 554
Bad residue range for struct_conf "330" on line 555
Bad residue range for struct_conf "331" on line 556
Bad residue range for struct_conf "332" on line 557
Bad residue range for struct_conf "333" on line 558
9 messages similar to the above omitted
Invalid residue range for struct_conf "343": invalid entity "AM", on line 568
Invalid residue range for struct_conf "344": invalid entity "AM", on line 569
Invalid residue range for struct_conf "345": invalid entity "AM", on line 570
Invalid residue range for struct_conf "346": invalid entity "AM", on line 571
Invalid residue range for struct_conf "347": invalid entity "AM", on line 572
Bad residue range for struct_conf "350" on line 575
Bad residue range for struct_conf "351" on line 576
Bad residue range for struct_conf "353" on line 578
Bad residue range for struct_conf "354" on line 579
Bad residue range for struct_conf "355" on line 580
Invalid residue range for struct_conf "356": invalid chain "B2", on line 581
Invalid residue range for struct_conf "357": invalid chain "B2", on line 582
Invalid residue range for struct_conf "358": invalid chain "B2", on line 583
Invalid residue range for struct_conf "359": invalid chain "B3", on line 584
Invalid residue range for struct_conf "360": invalid chain "B3", on line 585
34 messages similar to the above omitted
Bad residue range for struct_conf "401" on line 626
Bad residue range for struct_conf "402" on line 627
Bad residue range for struct_conf "403" on line 628
Bad residue range for struct_conf "404" on line 629
Invalid residue range for struct_conf "405": invalid chain "C2", on line 630
Invalid residue range for struct_conf "406": invalid chain "C2", on line 631
Invalid residue range for struct_conf "407": invalid chain "C2", on line 632
Invalid residue range for struct_conf "408": invalid chain "C2", on line 633
Invalid residue range for struct_conf "409": invalid chain "S1", on line 634
115 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "3A", on line
6101
Invalid sheet range for struct_sheet_range "1 2": invalid chain "3A", on line
6102
Invalid sheet range for struct_sheet_range "2 1": invalid chain "3A", on line
6103
Invalid sheet range for struct_sheet_range "2 2": invalid chain "3A", on line
6104
Invalid sheet range for struct_sheet_range "2 3": invalid chain "3A", on line
6105
130 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 111617
Skipping chem_comp category: Missing column 'type' on line 112100
Skipping chem_comp category: Missing column 'type' on line 112123
Skipping chem_comp category: Missing column 'type' on line 112744
Skipping chem_comp category: Missing column 'type' on line 112767
7 messages similar to the above omitted
note | Fetching CCD CUA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CUA/CUA.cif
Chain information for pdb_extract_out_coot-39_real_space_refined_031.cif #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
3A 3L | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G | No description available
3H 3S | No description available
3J | No description available
3M | No description available
3N | No description available
3O | No description available
3Q | No description available
3R | No description available
3T | No description available
3U | No description available
4 | No description available
4A | No description available
4B | No description available
4C | No description available
4D | No description available
4E | No description available
4F | No description available
4H | No description available
4I | No description available
4J | No description available
4K | No description available
4L | No description available
4M | No description available
4N | No description available
5 | No description available
6 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AB | No description available
AC | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C2 | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
V1 | No description available
V2 | No description available
> hide atoms
> show cartoons
> hide #!1 models
> show #!1 models
> open
> /Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_31/pdb_extract_out_coot-39_real_space_refined_031.pdb
Summary of feedback from opening
/Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_31/pdb_extract_out_coot-39_real_space_refined_031.pdb
---
warnings | Ignored bad PDB record found on line 864
SSBOND 1 CYS 3S 20 CYS 3S 64
Ignored bad PDB record found on line 865
SSBOND 2 CYS 3S 26 CYS 3S 60
Ignored bad PDB record found on line 866
SSBOND 3 CYS 3S 36 CYS 3S 50
Ignored bad PDB record found on line 867
SSBOND 4 CYS 3H 20 CYS 3H 64
Ignored bad PDB record found on line 868
SSBOND 5 CYS 3H 26 CYS 3H 60
7 messages similar to the above omitted
Chain information for pdb_extract_out_coot-39_real_space_refined_031.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
3A 3L | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G | No description available
3H 3S | No description available
3J | No description available
3M | No description available
3N | No description available
3O | No description available
3Q | No description available
3R | No description available
3T | No description available
3U | No description available
4 | No description available
4A | No description available
4B | No description available
4C | No description available
4D | No description available
4E | No description available
4F | No description available
4H | No description available
4I | No description available
4J | No description available
4K | No description available
4L | No description available
4M | No description available
4N | No description available
5 | No description available
6 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AB | No description available
AC | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C2 | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
V1 | No description available
V2 | No description available
> hide #!2 models
> hide #!3 atoms
> show #!3 cartoons
> hide #!1 models
> graphics silhouettes true
> show #!1 models
> close #2
> close #3
> close #1
> open
> /Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_31/pdb_extract_out_coot-39_real_space_refined_031.pdb
Summary of feedback from opening
/Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_31/pdb_extract_out_coot-39_real_space_refined_031.pdb
---
warnings | Ignored bad PDB record found on line 864
SSBOND 1 CYS 3S 20 CYS 3S 64
Ignored bad PDB record found on line 865
SSBOND 2 CYS 3S 26 CYS 3S 60
Ignored bad PDB record found on line 866
SSBOND 3 CYS 3S 36 CYS 3S 50
Ignored bad PDB record found on line 867
SSBOND 4 CYS 3H 20 CYS 3H 64
Ignored bad PDB record found on line 868
SSBOND 5 CYS 3H 26 CYS 3H 60
7 messages similar to the above omitted
Chain information for pdb_extract_out_coot-39_real_space_refined_031.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
3A 3L | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G | No description available
3H 3S | No description available
3J | No description available
3M | No description available
3N | No description available
3O | No description available
3Q | No description available
3R | No description available
3T | No description available
3U | No description available
4 | No description available
4A | No description available
4B | No description available
4C | No description available
4D | No description available
4E | No description available
4F | No description available
4H | No description available
4I | No description available
4J | No description available
4K | No description available
4L | No description available
4M | No description available
4N | No description available
5 | No description available
6 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AB | No description available
AC | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C2 | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
V1 | No description available
V2 | No description available
> hide atoms
> show cartoons
> select /3A:34-475
3419 atoms, 3483 bonds, 442 residues, 1 model selected
> select /3L:34-475
3419 atoms, 3483 bonds, 442 residues, 1 model selected
> select /3B:32-439
2974 atoms, 3013 bonds, 408 residues, 1 model selected
> select /3B:32-439
2974 atoms, 3013 bonds, 408 residues, 1 model selected
> select /3M:31-439
2980 atoms, 3019 bonds, 409 residues, 1 model selected
> select /3C:8-377
2982 atoms, 3090 bonds, 370 residues, 1 model selected
> select /3N:9-377
2972 atoms, 3079 bonds, 369 residues, 1 model selected
> select /3D:68-304
1888 atoms, 1945 bonds, 237 residues, 1 model selected
> select /3O:69-303
1871 atoms, 1928 bonds, 235 residues, 1 model selected
> select /3D:68-304
1888 atoms, 1945 bonds, 237 residues, 1 model selected
> select /3O:69-303
1871 atoms, 1928 bonds, 235 residues, 1 model selected
> select /3E:79-148
502 atoms, 510 bonds, 70 residues, 1 model selected
> select /3F:9-108
853 atoms, 872 bonds, 100 residues, 1 model selected
> select /3Q:13-110
841 atoms, 860 bonds, 98 residues, 1 model selected
> select /3G:4-74
587 atoms, 602 bonds, 71 residues, 1 model selected
> select /3R:4-73
578 atoms, 593 bonds, 70 residues, 1 model selected
> select /3H:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3H:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3H:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3H:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3H:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3S:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3H:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3S:9-74
518 atoms, 525 bonds, 66 residues, 1 model selected
> select /3J:5-57
434 atoms, 443 bonds, 53 residues, 1 model selected
> select /3U:25-59
294 atoms, 302 bonds, 35 residues, 1 model selected
> color #1/V1 #DC050C
> color #1/V2 #E8601C
> color #1/S1 #F1932D
> color #1/S2 #F6C141
> color #1/S3 #F7F056
> color #1/S7 #CAE0AB
> color #1/S8 #90C987
> color #1/1 #7BAFDE
> color #1/2 #D1BBD7
> color #1/3 #4EB265
> color #1/4 #AE76A3
> color #1/4L #1965B0
> color #1/5 #882E72
> color #1/6 #52FFD2
> color #1/A1 #B8221E
> color #1/A2 #2E8B57
> color #1/A3 #69B190
> color #1/A5 #95211b
> color #1/A6 #DF4828
> color #1/A7 #4D8AC6
> color #1/A8 #FF99FF
> color #1/A9 #6F4C9B
> color #1/AL #59A5A9
> color #1/AM #FEDA8B
> color #1/AN #D1B541
> color #1/AO #BEBC48
> color #1/AB #B58FC2
> color #1/AC #B58FC2
> color #1/B1 #DA2222
> color #1/B2 #E78C35
> color #1/B3 #77B77D
> color #1/B4 #D1B541
> color #1/B5 #4A7BB7
> color #1/B6 #D1B541
> color #1/B7 #DDAA3C
> color #1/B8 #E67932
> color #1/B9 #E49C39
> color #1/BL #95211B
> color #1/BM #E4632D
> color #1/C2 #8CBC68
> color #1/S4 #8C4E99
> color #1/S5 #60AB9E
> color #1/S6 #721E17
> color #1/3A /3L #7BAFDE
> color #1/3B /3M #1965B0
> color #1/3C /3N #AE76A3
> color #1/3D /3O #F1932D
> color #1/3E /3P #285e34
> color #1/3F /3Q #5289C7
> color #1/3G /3R #90C987
> color #1/3H /3S #F7F056
> color #1/3J /3U #882E72
> color #1/3K /3V #F6C141
> select clear
> select
> ::name="ATPA"::name="CU"::name="CUA4"::name="FESS"::name="FESV"::name="FMN"::name="HEA"::name="HEC3"::name="HEM"::name="HEM3"::name="MG4"::name="NDPA"::name="SF4"::name="SF4S"::name="SF4V"::name="ZN4"::name="ZNS"
550 atoms, 528 bonds, 137 pseudobonds, 24 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 550 atom styles
> select clear
> select
> ::name="ATPA"::name="CU"::name="CUA4"::name="FESS"::name="FESV"::name="FMN"::name="HEA"::name="HEC3"::name="HEM"::name="HEM3"::name="MG4"::name="NDPA"::name="SF4"::name="SF4S"::name="SF4V"::name="ZN4"::name="ZNS"
550 atoms, 528 bonds, 137 pseudobonds, 24 residues, 2 models selected
> color sel byhetero
> select clear
> cartoon style modeHelix tube sides 20
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> cartoon style xsection oval modeHelix default
> color #1/4A #6B8E23
> color #1/4B #D2691E
> color #1/4C #663399
> color #1/4D #8B0000
> color #1/4E #006400
> color #1/4F #191970
> color #1/4H #FFA500
> color #1/4I #FF4500
> color #1/4J #2E8B57
> color #1/4K #1E90FF
> color #1/4M #B22222
> color #1/4N #F4A460
> select
> ::name="ATPA"::name="CU"::name="CUA4"::name="FESS"::name="FESV"::name="FMN"::name="HEA"::name="HEC3"::name="HEM"::name="HEM3"::name="MG4"::name="NDPA"::name="SF4"::name="SF4S"::name="SF4V"::name="ZN4"::name="ZNS"
550 atoms, 528 bonds, 137 pseudobonds, 24 residues, 2 models selected
> color sel byhetero
> select clear
> open
> /Users/apadavan/Documents/Daphnia_Model_Building/CombineFocusedMaps_15/composite_map.ccp4
Opened composite_map.ccp4 as #2, grid size 245,254,396, pixel 0.88,0.88,0.88,
shown at level 5.3, step 2, values float32
> volume #2 step 1
> volume #2 level 2.776
> ui tool show "Hide Dust"
> surface dust #2 size 6.5
> select add #1
104746 atoms, 107359 bonds, 220 pseudobonds, 13220 residues, 3 models selected
> color zone #2 near sel range 4.0
Expected a keyword
> color zone #2 near sel distance 3.5
> select clear
> transparency 70
> select
> ::name="ATPA"::name="CU"::name="CUA4"::name="FESS"::name="FESV"::name="FMN"::name="HEA"::name="HEC3"::name="HEM"::name="HEM3"::name="MG4"::name="NDPA"::name="SF4"::name="SF4S"::name="SF4V"::name="ZN4"::name="ZNS"
550 atoms, 528 bonds, 137 pseudobonds, 24 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 550 atom styles
> style sel stick
Changed 550 atom styles
> style sel ball
Changed 550 atom styles
> style sel stick
Changed 550 atom styles
> select clear
> save /Users/apadavan/Documents/Daphnia_Model_Building/Daphnia-
> Figures/Daphnia-Model-Map.cxs
——— End of log from Tue Dec 9 17:07:25 2025 ———
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!2 models
> open /Users/apadavan/Documents/Daphnia_Model_Building/Daphnia-
> Figures/cryosparc_P33_J165_005_volume_map_sharp.mrc
Opened cryosparc_P33_J165_005_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.88, shown at level 0.0808, step 4, values float32
> volume #3 step 1
> volume #3 level 0.1918
> hide #!2 models
> select add #1
104746 atoms, 107359 bonds, 220 pseudobonds, 13220 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,16.091,0,1,0,22.583,0,0,1,7.8558
> view matrix models #1,1,0,0,124.95,0,1,0,177.39,0,0,1,89.896
> view matrix models #1,1,0,0,141.31,0,1,0,162.66,0,0,1,76.355
> view matrix models #1,1,0,0,147.69,0,1,0,148.14,0,0,1,66.945
> view matrix models #1,1,0,0,148.7,0,1,0,142.2,0,0,1,73.846
> view matrix models #1,1,0,0,149.41,0,1,0,140.58,0,0,1,76.465
> view matrix models #1,1,0,0,157.4,0,1,0,147.58,0,0,1,84.098
> view matrix models #1,1,0,0,154.54,0,1,0,143.77,0,0,1,82.488
> view matrix models #1,1,0,0,158.41,0,1,0,141.03,0,0,1,79.143
> view matrix models #1,1,0,0,163.01,0,1,0,139.13,0,0,1,76.814
> view matrix models #1,1,0,0,161.39,0,1,0,138.24,0,0,1,75.753
> view matrix models #1,1,0,0,162.59,0,1,0,134.37,0,0,1,80.332
> view matrix models #1,1,0,0,161.96,0,1,0,135.51,0,0,1,79.774
> select subtract #1
Nothing selected
> fitmap #1 inMap #3
Fit molecule pdb_extract_out_coot-39_real_space_refined_031.pdb (#1) to map
cryosparc_P33_J165_005_volume_map_sharp.mrc (#3) using 104746 atoms
average map value = 0.1295, steps = 316
shifted from previous position = 10.5
rotated from previous position = 12 degrees
atoms outside contour = 85110, contour level = 0.19182
Position of pdb_extract_out_coot-39_real_space_refined_031.pdb (#1) relative
to cryosparc_P33_J165_005_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99783126 0.05072189 -0.04195324 167.29407168
-0.05799802 0.97889733 -0.19594958 185.36709852
0.03112898 0.19795782 0.97971613 63.89752363
Axis 0.94890157 -0.17605111 -0.26190038
Axis point 0.00000000 -356.55446853 1082.66241183
Rotation angle (degrees) 11.97938102
Shift along axis 109.37673924
> volume #3 level 0.1668
> ui tool show "Hide Dust"
> surface dust #3 size 6.5
> show #!2 models
> select add #2
2 models selected
> view matrix models #2,1,0,0,124.17,0,1,0,148.6,0,0,1,91.335
> view matrix models #2,1,0,0,155.21,0,1,0,140.43,0,0,1,81.14
> view matrix models #2,1,0,0,158.25,0,1,0,140.84,0,0,1,76.691
> view matrix models #2,1,0,0,158.1,0,1,0,140.76,0,0,1,76.806
> select subtract #2
Nothing selected
> select add #2
2 models selected
> fitmap #2 inMap #3
Fit map composite_map.ccp4 in map cryosparc_P33_J165_005_volume_map_sharp.mrc
using 698479 points
correlation = 0.7858, correlation about mean = 0.2066, overlap = 5.03e+05
steps = 288, shift = 12.5, angle = 12 degrees
Position of composite_map.ccp4 (#2) relative to
cryosparc_P33_J165_005_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99782067 0.05082425 -0.04208085 167.32297178
-0.05811431 0.97894953 -0.19565413 185.28902968
0.03125106 0.19767324 0.97976970 63.91812864
Axis 0.94852997 -0.17684382 -0.26271116
Axis point 0.00000000 -357.46360931 1084.14064994
Rotation angle (degrees) 11.96623566
Shift along axis 109.15162885
> select subtract #2
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide cartoons #1/V1
Expected ',' or a keyword
> select #1/A1
557 atoms, 571 bonds, 69 residues, 1 model selected
> select #1/3A-3K
14200 atoms, 14529 bonds, 6 pseudobonds, 1818 residues, 2 models selected
> hide #!3 models
> hide ~ sel cartoons
> select clear
> show #1//3A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> /3B
Unknown command: /3B
> /3C
Unknown command: /3C
> /3D
Unknown command: /3D
> /3E
Unknown command: /3E
> /3F
Unknown command: /3F
> /3G
Unknown command: /3G
> /3H
Unknown command: /3H
> /3J
Unknown command: /3J
> /3K /3L
Unknown command: /3K /3L
> /3M
Unknown command: /3M
> /3N
Unknown command: /3N
> /3O
Unknown command: /3O
> /3P
Unknown command: /3P
> /3Q
Unknown command: /3Q
> /3R
Unknown command: /3R
> /3S
Unknown command: /3S
> /3U
Unknown command: /3U
> /3V cartoon
Unknown command: /3V cartoon
> show #1 cartoons
> select #1/3A-3V
28006 atoms, 28653 bonds, 12 pseudobonds, 3601 residues, 2 models selected
> hide ~ sel cartoons
> select add #1
104746 atoms, 107359 bonds, 220 pseudobonds, 13220 residues, 3 models selected
> select subtract #1
Nothing selected
> hide atoms
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #3 level 0.1418
> open /Users/apadavan/Downloads/cryosparc_P33_J122_004_volume_map_sharp.mrc
Opened cryosparc_P33_J122_004_volume_map_sharp.mrc as #4, grid size
600,600,600, pixel 0.88, shown at level 0.258, step 4, values float32
> volume #4 step 1
> volume #4 level 0.5777
> select add #4
2 models selected
> view matrix models #4,1,0,0,-6.2618,0,1,0,-11.237,0,0,1,-3.7229
> select subtract #4
Nothing selected
> select add #4
2 models selected
> select clear
> fitmap #4 inMap #3
Fit map cryosparc_P33_J122_004_volume_map_sharp.mrc in map
cryosparc_P33_J165_005_volume_map_sharp.mrc using 207947 points
correlation = 0.969, correlation about mean = 0.7743, overlap = 5.975e+04
steps = 308, shift = 5.98, angle = 11.8 degrees
Position of cryosparc_P33_J122_004_volume_map_sharp.mrc (#4) relative to
cryosparc_P33_J165_005_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99794632 0.05215311 -0.03719125 -6.65985490
-0.05838718 0.97940527 -0.19327767 71.15707486
0.02634528 0.19505223 0.98043896 -51.00612266
Axis 0.95010058 -0.15545054 -0.27045149
Axis point 0.00000000 299.91005585 333.31206755
Rotation angle (degrees) 11.79218406
Shift along axis -3.59425542
> surface dust #3 size 6.5
[Repeated 1 time(s)]
> surface dust #4 size 6.5
> hide #!3 models
> volume #4 color #b2ffff47
> graphics silhouettes false
> graphics silhouettes true
> volume #4 color #b2ffff4c
> volume #3 color #ffffb257
> volume #3 color #ffffb2
> volume #3 color #ffffb263
> open
> /Users/apadavan/Documents/Paramecium_Model_Building/CICIII2CIV/7TGH_Aligned.pdb
Summary of feedback from opening
/Users/apadavan/Documents/Paramecium_Model_Building/CICIII2CIV/7TGH_Aligned.pdb
---
warnings | Cannot find LINK/SSBOND residue ZN (101 )
Cannot find LINK/SSBOND residue ZN (101 )
Cannot find LINK/SSBOND residue ZN (402 )
Cannot find LINK/SSBOND residue ZN (402 )
Cannot find LINK/SSBOND residue ZN (201 )
3 messages similar to the above omitted
Chain information for 7TGH_Aligned.pdb #5
---
Chain | Description
1 | No description available
1B | No description available
2 | No description available
2B | No description available
3 | No description available
3A 3a | No description available
3B 3b | No description available
3C 3c | No description available
3D 3d | No description available
3E 3e | No description available
3F 3f | No description available
3G 3g | No description available
3H 3h | No description available
3I 3i | No description available
3J 3j | No description available
3M | No description available
3l | No description available
3m | No description available
4 | No description available
4L | No description available
5 | No description available
5B | No description available
6 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AB | No description available
AC | No description available
AL | No description available
AM | No description available
AN | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C | No description available
C1 | No description available
C2 | No description available
C3 | No description available
C4 | No description available
FX | No description available
J1 | No description available
P1 | No description available
P2 | No description available
R | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
T1 | No description available
T2 | No description available
T3 | No description available
T4 | No description available
T5 | No description available
T6 | No description available
T7 | No description available
T8 | No description available
T9 | No description available
TA | No description available
TB | No description available
TC | No description available
TD | No description available
TE | No description available
TX | No description available
V1 | No description available
V2 | No description available
X1 | No description available
> hide atoms
> show cartoons
> select #5/3A-3M /3a-3m
42334 atoms, 43475 bonds, 42 pseudobonds, 5084 residues, 3 models selected
> select add #5
153366 atoms, 157249 bonds, 98 pseudobonds, 18397 residues, 3 models selected
> select clear
> select add #5
153366 atoms, 157249 bonds, 98 pseudobonds, 18397 residues, 3 models selected
> view matrix models #5,1,0,0,-73.441,0,1,0,15.978,0,0,1,-145.34
> view matrix models #5,1,0,0,-146.51,0,1,0,31.91,0,0,1,-302.44
> view matrix models #5,1,0,0,-138.21,0,1,0,40.197,0,0,1,-315.93
> view matrix models #5,1,0,0,-124.37,0,1,0,45.717,0,0,1,-348.55
> view matrix models #5,1,0,0,-224.94,0,1,0,-155.95,0,0,1,-308.83
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.96481,-0.25472,0.065348,-155.06,0.25786,0.96512,-0.045191,-238.14,-0.051558,0.060451,0.99684,-304.48
> view matrix models
> #5,0.74972,-0.63276,0.19374,6.6784,0.65585,0.74951,-0.090037,-322.02,-0.088236,0.19457,0.97691,-323.64
> view matrix models
> #5,0.56772,-0.468,0.67726,-224.58,0.34604,0.88214,0.3195,-444.04,-0.74696,0.052975,0.66275,195.32
> view matrix models
> #5,0.46013,-0.43901,0.77172,-235.58,0.21815,0.89846,0.38104,-423.77,-0.86063,-0.0069815,0.50918,350.15
> view matrix models
> #5,0.84106,-0.51123,0.17683,-68.482,0.54078,0.80269,-0.25148,-201.69,-0.013373,0.30713,0.95157,-383.63
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.84106,-0.51123,0.17683,-66.919,0.54078,0.80269,-0.25148,-123.19,-0.013373,0.30713,0.95157,-363.46
> select subtract #5
Nothing selected
> mmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb_extract_out_coot-39_real_space_refined_031.pdb, chain S1 (#1)
with 7TGH_Aligned.pdb, chain S1 (#5), sequence alignment score = 1969.3
RMSD between 546 pruned atom pairs is 1.139 angstroms; (across all 679 pairs:
2.757)
> select #5/3A-3M /3a-3m
42334 atoms, 43475 bonds, 42 pseudobonds, 5084 residues, 3 models selected
> mmaker sel to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb_extract_out_coot-39_real_space_refined_031.pdb, chain 3A (#1)
with 7TGH_Aligned.pdb, chain 3b (#5), sequence alignment score = 921.5
RMSD between 338 pruned atom pairs is 1.128 angstroms; (across all 440 pairs:
2.760)
> select add #5
153366 atoms, 157249 bonds, 98 pseudobonds, 18397 residues, 3 models selected
> select subtract #5
Nothing selected
> select clear
> select #1/3A-3V #5/3A-3M /3a-3m
70340 atoms, 72128 bonds, 54 pseudobonds, 8685 residues, 5 models selected
> hide ~sel cartoons
> select clear
> volume #3 color #ffffb2fa
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> mmaker #5/3A to #1/3M
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb_extract_out_coot-39_real_space_refined_031.pdb, chain 3M (#1)
with 7TGH_Aligned.pdb, chain 3A (#5), sequence alignment score = 546.2
RMSD between 163 pruned atom pairs is 1.154 angstroms; (across all 391 pairs:
6.309)
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> open "/Users/apadavan/Desktop/Mouse_Data_Processing /MouseSC-XL-
> Refinement/RealSpaceRefine_158/pdb_extract_25225_aligned-to-153-Comp-
> Map_real_space_refined_154_real_space_refined_156-coot-1_real_space_refined_157-coot6_real_space_refined_158.pdb"
Summary of feedback from opening /Users/apadavan/Desktop/Mouse_Data_Processing
/MouseSC-XL-Refinement/RealSpaceRefine_158/pdb_extract_25225_aligned-
to-153-Comp-
Map_real_space_refined_154_real_space_refined_156-coot-1_real_space_refined_157-coot6_real_space_refined_158.pdb
---
warnings | Ignored bad PDB record found on line 300
SSBOND 1 CYS A8 46 CYS A8 56
Ignored bad PDB record found on line 301
SSBOND 2 CYS A8 88 CYS A8 100
Ignored bad PDB record found on line 302
SSBOND 3 CYS AM 18 CYS AM 75
Ignored bad PDB record found on line 303
SSBOND 4 CYS AM 95 CYS AM 115
Ignored bad PDB record found on line 304
SSBOND 5 CYS S5 33 CYS S5 66
13 messages similar to the above omitted
Chain information for pdb_extract_25225_aligned-to-153-Comp-
Map_real_space_refined_154_real_space_refined_156-coot-1_real_space_refined_157-coot6_real_space_refined_158.pdb
#6
---
Chain | Description
1 | No description available
1a | No description available
2 2a | No description available
3 | No description available
3A 3L | No description available
3B 3M | No description available
3C 3N | No description available
3D | No description available
3E | No description available
3F | No description available
3G | No description available
3H 3S | No description available
3J | No description available
3K | No description available
3O | No description available
3P | No description available
3Q | No description available
3R | No description available
3T | No description available
3U | No description available
3V | No description available
3a | No description available
4 4a | No description available
4L | No description available
4l | No description available
5 5a | No description available
6 | No description available
6a | No description available
A | No description available
A1 | No description available
A2 a2 | No description available
A3 a3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 a9 | No description available
AB ab | No description available
AC ac | No description available
AL al | No description available
AM am | No description available
AN an | No description available
AO ao | No description available
B | No description available
B1 b1 | No description available
B2 | No description available
B3 | No description available
B4 b4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 b8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C1 | No description available
C2 c2 | No description available
S1 s1 | No description available
S2 | No description available
S3 | No description available
S4 s4 | No description available
S5 s5 | No description available
S6 s6 | No description available
S7 s7 | No description available
S8 | No description available
V1 | No description available
V2 | No description available
V3 | No description available
a1 | No description available
a5 | No description available
a6 | No description available
a7 | No description available
a8 | No description available
b2 | No description available
b3 | No description available
b5 | No description available
b6 | No description available
b7 | No description available
b9 | No description available
bl | No description available
bm | No description available
c1 | No description available
s2 | No description available
s3 | No description available
s8 | No description available
v1 | No description available
v2 | No description available
v3 | No description available
> hide #!1,6 atoms
> show #6/3A-3V cartoons
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> close #6
> open "/Users/apadavan/Desktop/Mouse_Data_Processing /MouseSC-XL-
> Refinement/RealSpaceRefine_158/pdb_extract_25225_aligned-to-153-Comp-
> Map_real_space_refined_154_real_space_refined_156-coot-1_real_space_refined_157-coot6_real_space_refined_158.cif"
Summary of feedback from opening /Users/apadavan/Desktop/Mouse_Data_Processing
/MouseSC-XL-Refinement/RealSpaceRefine_158/pdb_extract_25225_aligned-
to-153-Comp-
Map_real_space_refined_154_real_space_refined_156-coot-1_real_space_refined_157-coot6_real_space_refined_158.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 1493
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "3", on line 295
Invalid residue range for struct_conf "2": invalid chain "3", on line 296
Invalid residue range for struct_conf "3": invalid chain "3", on line 297
Invalid residue range for struct_conf "4": invalid chain "3", on line 298
Invalid residue range for struct_conf "5": invalid chain "3", on line 299
111 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "15 1": invalid chain "5", on line
1491
Missing or incorrect sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 164644
Skipping chem_comp category: Missing column 'type' on line 165329
Skipping chem_comp category: Missing column 'type' on line 165356
Skipping chem_comp category: Missing column 'type' on line 165643
Skipping chem_comp category: Missing column 'type' on line 166226
9 messages similar to the above omitted
notes | Fetching CCD 2MR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/2MR/2MR.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD DGT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/DGT/DGT.cif
Fetching CCD EHZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/EHZ/EHZ.cif
Fetching CCD 3PC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/3PC/3PC.cif
Chain information for pdb_extract_25225_aligned-to-153-Comp-
Map_real_space_refined_154_real_space_refined_156-coot-1_real_space_refined_157-coot6_real_space_refined_158.cif
#6
---
Chain | Description
1 | No description available
1a | No description available
2 2a | No description available
3 | No description available
3A 3L | No description available
3B 3M | No description available
3C 3N | No description available
3D | No description available
3E | No description available
3F | No description available
3G | No description available
3H 3S | No description available
3J | No description available
3K | No description available
3O | No description available
3P | No description available
3Q | No description available
3R | No description available
3T | No description available
3U | No description available
3V | No description available
3a | No description available
4 4a | No description available
4L | No description available
4l | No description available
5 5a | No description available
6 | No description available
6a | No description available
A | No description available
A1 | No description available
A2 a2 | No description available
A3 a3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 a9 | No description available
AB ab | No description available
AC ac | No description available
AL al | No description available
AM am | No description available
AN an | No description available
AO ao | No description available
B | No description available
B1 b1 | No description available
B2 | No description available
B3 | No description available
B4 b4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 b8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C1 | No description available
C2 c2 | No description available
S1 s1 | No description available
S2 | No description available
S3 | No description available
S4 s4 | No description available
S5 s5 | No description available
S6 s6 | No description available
S7 s7 | No description available
S8 | No description available
V1 | No description available
V2 | No description available
V3 | No description available
a1 | No description available
a5 | No description available
a6 | No description available
a7 | No description available
a8 | No description available
b2 | No description available
b3 | No description available
b5 | No description available
b6 | No description available
b7 | No description available
b9 | No description available
bl | No description available
bm | No description available
c1 | No description available
s2 | No description available
s3 | No description available
s8 | No description available
v1 | No description available
v2 | No description available
v3 | No description available
> hide atoms
> show cartoons
Computing secondary structure
> hide #!1 models
> hide #!4 models
> hide #!5 models
> close #5
> show #!1 models
> select add #6
162887 atoms, 167122 bonds, 1170 pseudobonds, 20233 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.89722,0.41077,-0.1621,-10.604,-0.36618,0.89722,0.24679,14,0.24681,-0.16207,0.95542,-1.7882
> view matrix models
> #6,0.037963,0.99886,-0.028924,-3.6354,-0.56484,0.045326,0.82396,43.993,0.82433,-0.014942,0.56591,-22.055
> view matrix models
> #6,0.90998,0.14366,-0.38898,56.171,-0.018946,0.95149,0.3071,-41.753,0.41423,-0.27209,0.86855,6.1617
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.90998,0.14366,-0.38898,215.18,-0.018946,0.95149,0.3071,8.1765,0.41423,-0.27209,0.86855,117.97
> view matrix models
> #6,0.90998,0.14366,-0.38898,328.23,-0.018946,0.95149,0.3071,54.88,0.41423,-0.27209,0.86855,216.49
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.73957,-0.56064,0.37244,307.78,0.66323,0.70133,-0.26127,98.53,-0.11473,0.44025,0.89052,189.1
> view matrix models
> #6,0.59645,-0.17038,0.78436,211.41,0.72616,0.53087,-0.43688,139.88,-0.34195,0.83015,0.44036,241.71
> view matrix models
> #6,0.71515,0.42018,0.55858,164.6,0.12794,0.70695,-0.6956,229.11,-0.68716,0.56892,0.45181,310.08
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.71515,0.42018,0.55858,114.19,0.12794,0.70695,-0.6956,216.7,-0.68716,0.56892,0.45181,169.87
> select clear
> mmaker #6/3A-3V to #1/3A-3V
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb_extract_out_coot-39_real_space_refined_031.pdb, chain 3A (#1)
with pdb_extract_25225_aligned-to-153-Comp-
Map_real_space_refined_154_real_space_refined_156-coot-1_real_space_refined_157-coot6_real_space_refined_158.cif,
chain 3A (#6), sequence alignment score = 1555.8
RMSD between 428 pruned atom pairs is 0.722 angstroms; (across all 441 pairs:
0.924)
> hide cartoons
> show #1/3A-3V cartoons
> show #6/3A-3V cartoons
> show #!3 models
> lighting soft
> volume #3 color #ffffb2
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 color #ffffb28d
> volume #3 color #ffffb28c
> hide #!4 models
> hide #!6 models
> select #1/3K
Nothing selected
> select #1/3V
Nothing selected
> open
> /Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_45/pdb_extract_out_coot-39_real_space_refined_031_real_space_refined_045.cif
Summary of feedback from opening
/Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_45/pdb_extract_out_coot-39_real_space_refined_031_real_space_refined_045.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 6765
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "3S", on line 226
Invalid residue range for struct_conf "2": invalid chain "3S", on line 227
Invalid residue range for struct_conf "3": invalid chain "3S", on line 228
Invalid residue range for struct_conf "4": invalid chain "3H", on line 229
Invalid residue range for struct_conf "5": invalid chain "3H", on line 230
315 messages similar to the above omitted
Bad residue range for struct_conf "329" on line 554
Bad residue range for struct_conf "330" on line 555
Bad residue range for struct_conf "331" on line 556
Bad residue range for struct_conf "332" on line 557
Bad residue range for struct_conf "333" on line 558
9 messages similar to the above omitted
Invalid residue range for struct_conf "343": residue in non-polymer entity
"AM", on line 568
Invalid residue range for struct_conf "344": residue in non-polymer entity
"AM", on line 569
Invalid residue range for struct_conf "345": residue in non-polymer entity
"AM", on line 570
Invalid residue range for struct_conf "346": residue in non-polymer entity
"AM", on line 571
Invalid residue range for struct_conf "347": residue in non-polymer entity
"AM", on line 572
Bad residue range for struct_conf "350" on line 575
Bad residue range for struct_conf "351" on line 576
Bad residue range for struct_conf "353" on line 578
Bad residue range for struct_conf "354" on line 579
Bad residue range for struct_conf "355" on line 580
Invalid residue range for struct_conf "356": invalid chain "B2", on line 581
Invalid residue range for struct_conf "357": invalid chain "B2", on line 582
Invalid residue range for struct_conf "358": invalid chain "B2", on line 583
Invalid residue range for struct_conf "359": invalid chain "B3", on line 584
Invalid residue range for struct_conf "360": invalid chain "B3", on line 585
34 messages similar to the above omitted
Bad residue range for struct_conf "401" on line 626
Bad residue range for struct_conf "402" on line 627
Bad residue range for struct_conf "403" on line 628
Bad residue range for struct_conf "404" on line 629
Invalid residue range for struct_conf "405": invalid chain "C2", on line 630
Invalid residue range for struct_conf "406": invalid chain "C2", on line 631
Invalid residue range for struct_conf "407": invalid chain "C2", on line 632
Invalid residue range for struct_conf "408": invalid chain "C2", on line 633
Invalid residue range for struct_conf "409": invalid chain "S1", on line 634
115 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "3A", on line
6519
Invalid sheet range for struct_sheet_range "1 2": invalid chain "3A", on line
6520
Invalid sheet range for struct_sheet_range "2 1": invalid chain "3A", on line
6521
Invalid sheet range for struct_sheet_range "2 2": invalid chain "3A", on line
6522
Invalid sheet range for struct_sheet_range "2 3": invalid chain "3A", on line
6523
130 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 112035
Skipping chem_comp category: Missing column 'type' on line 112518
Skipping chem_comp category: Missing column 'type' on line 112541
Skipping chem_comp category: Missing column 'type' on line 113162
Skipping chem_comp category: Missing column 'type' on line 113185
7 messages similar to the above omitted
notes | Fetching CCD CU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/CU/CU.cif
Fetching CCD HEA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/HEA/HEA.cif
Fetching CCD CUA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CUA/CUA.cif
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif
Chain information for
pdb_extract_out_coot-39_real_space_refined_031_real_space_refined_045.cif #5
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
3A 3L | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G | No description available
3H 3S | No description available
3J | No description available
3M | No description available
3N | No description available
3O | No description available
3Q | No description available
3R | No description available
3T | No description available
3U | No description available
4 | No description available
4A | No description available
4B | No description available
4C | No description available
4D | No description available
4E | No description available
4F | No description available
4H | No description available
4I | No description available
4J | No description available
4K | No description available
4L | No description available
4M | No description available
4N | No description available
5 | No description available
6 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AB | No description available
AC | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C2 | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
V1 | No description available
V2 | No description available
> hide #!1 models
> hide #!5 atoms
> show #!5 cartoons
> hide #!5 models
> close #5
> open
> /Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_45/pdb_extract_out_coot-39_real_space_refined_031_real_space_refined_045.pdb
Summary of feedback from opening
/Users/apadavan/Documents/Daphnia_Model_Building/RealSpaceRefine_45/pdb_extract_out_coot-39_real_space_refined_031_real_space_refined_045.pdb
---
warnings | Ignored bad PDB record found on line 864
SSBOND 1 CYS 3S 20 CYS 3S 64
Ignored bad PDB record found on line 865
SSBOND 2 CYS 3S 26 CYS 3S 60
Ignored bad PDB record found on line 866
SSBOND 3 CYS 3S 36 CYS 3S 50
Ignored bad PDB record found on line 867
SSBOND 4 CYS 3H 20 CYS 3H 64
Ignored bad PDB record found on line 868
SSBOND 5 CYS 3H 26 CYS 3H 60
7 messages similar to the above omitted
Chain information for
pdb_extract_out_coot-39_real_space_refined_031_real_space_refined_045.pdb #5
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
3A 3L | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G | No description available
3H 3S | No description available
3J | No description available
3M | No description available
3N | No description available
3O | No description available
3Q | No description available
3R | No description available
3T | No description available
3U | No description available
4 | No description available
4A | No description available
4B | No description available
4C | No description available
4D | No description available
4E | No description available
4F | No description available
4H | No description available
4I | No description available
4J | No description available
4K | No description available
4L | No description available
4M | No description available
4N | No description available
5 | No description available
6 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AB | No description available
AC | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BL | No description available
BM | No description available
C2 | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
V1 | No description available
V2 | No description available
> hide #!5 atoms
> show #!5 cartoons
> close #6
> close #5
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 color #b2ffff
> hide #!4 models
> show #!4 models
> volume #3 color #ffffb2
> volume #3 level 0.06689
> volume #3 level 0.1363
> volume #3 level 0.1
> volume #3 level 0.15
> volume #3 level 0.1944
> volume #3 level 0.15
> save /Users/apadavan/Documents/Daphnia_Model_Building/Daphnia-
> Figures/Daphnia-Prep-2-021726.cxs includeMaps true
——— End of log from Thu Feb 19 15:22:31 2026 ———
> view name session-start
opened ChimeraX session
> volume #3 color #ffffb2c1
> volume #3 color #ffffb2ac
> volume #4 color #b2ffff80
> volume #3 color #ffffb2
> volume #4 color #b2ffff
> ui tool show "Side View"
> rock y 120 cycle 120
> stop
> rock y 120 cycle 120
> movie record
> stop
> turn y 2 180
> stop
> movie stop
> view
[Repeated 1 time(s)]
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
Drag select of 3599 residues
> show #!3 models
> volume zone #3 range 3.5 newMap true
Missing required "near_atoms" argument
> volume zone #3 nearAtoms sel range 3.5 newMap true
Opened cryosparc_P33_J165_005_volume_map_sharp.mrc zone as #5, grid size
600,600,600, pixel 0.88, shown at step 1, values float32
> hide #!1 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!5 models
> show #!4 models
> volume zone #4 nearAtoms sel range 3.5 newMap true
Opened cryosparc_P33_J122_004_volume_map_sharp.mrc zone as #6, grid size
600,600,600, pixel 0.88, shown at step 1, values float32
> show #!5 models
> hide #!6 models
> select clear
> show #!6 models
> hide #!6 models
> volume #5 level 0.1333
> volume #5 color #fffc79
> volume #5 color #d4fb79
> lighting soft
> volume #5 color #929000
> volume #6 color #009193
> volume #6 level 0.5087
> ui tool show "Hide Dust"
> surface dust #5 size 5.28
> surface dust #6 size 5.28
> volume #5 color #fffb00
> lighting soft
> volume #5 color #fefc7e
> volume #6 color #63ecf3
> volume #6 color #65f1f8
> volume #5 color #fefc7e95
> volume #5 color #fefc7e8b
> volume #5 color #fefc7e82
> volume #6 color #65f1f886
> volume #6 color #65f1f887
> turn y 2 270
> turn y 2 180
> turn y 1 180
> turn y 2 180
> rock y 2 180
> stop
> rock y 120
> stop
> rock y 180
> stop
> rock y 270
> stop
> turn y 4 180
> rock y 4 180
> stop
> rock y 200
> stop
> rock 270
Expected an axis vector or a keyword
> rock y 270
> stop
> rock y 360
> stop
> rock y 180 30
> stop
[Repeated 1 time(s)]
> rock y
> rock y 60
> rock y 270
> rock y 270 cycle 270
> rock y 270
> stop
> rock y 360
> rock y 360 720
> rock y 360
> rock y 360 360
> stop
> turn y 2 360
[Repeated 1 time(s)]
> movie record supersample 3
> turn y 2 360
> movie stop
> movie encode /Users/apadavan/Desktop/Dataset-2-CIII-density.mp4 quality high
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: Z12R000LXLL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 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: 25 days, 2 hours, 23 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP VH240a:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission Denied |
comment:2 by , 3 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Abhilash,
--Eric