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Opened 3 years ago
Closed 3 years ago
#7110 closed defect (not a bug)
Coordset not recorded
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
When making a movie using a cxc script, movie encoding fails whereas when I enter the commands one after another into ChimeraX the movie records, encodes and saves properly. It seems like when I use the script ChimeraX is not waiting for the coordset command to complete before running movie encode and so there are no frames to make into a movie.
Commands used are below:
#########
# Setup #
#########
open 5ljo
open 5d0o
hide #1,2 atoms
# to allow display of backbone atoms
cartoon suppress false
show #1,2/A cartoons
color #1,2/A rgb(0.252,0.680,1.000)
color #1,2/B rgb(0.000,0.831,0.321)
color #1,2/C rgb(1.000,0.861,0.137)
color #1,2/D rgb(1.000,0.400,0.100)
color #1,2/E rgb(0.780,0.000,0.400)
### Align barrels ###
# mmaker #2/A:435-810 to #1/A:435-810
view matrix model #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
### Color EPR regions ###
color #1,2/A:424-447 green
color #1,2/A:454-518 red
color #1,2/A:348-423 dark orange
### Create Morph ###
morph #1,2 frames 40
### Show single mutant CA ###
show #3/A:501,755@CA
color #3/A:501,755@CA medium spring green
######################
# Lets make a movie! #
######################
### Render Settings ###
set bgColor white
lighting full
view matrix camera -0.95767,-0.27958,0.068542,182.67,0.068982,0.0082751,0.99758,422.6,-0.27948,0.96009,0.011362,160.72
### Morph Movie ###
movie record supersample 4 size 2000,2000
coordset #3 1,41
movie encode "~/Desktop/MORPH.mp4" quality good verbose true roundTrip true
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/run_it025_class001.mrc"
Opened run_it025_class001.mrc as #1, grid size 144,144,144, pixel 1.48, shown
at level 0.0002, step 1, values float32
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/run_it025_class002.mrc"
Opened run_it025_class002.mrc as #2, grid size 144,144,144, pixel 1.48, shown
at level 0.0203, step 1, values float32
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/run_it025_class003.mrc"
Opened run_it025_class003.mrc as #3, grid size 144,144,144, pixel 1.48, shown
at level 0.017, step 1, values float32
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/run_it025_class004.mrc"
Opened run_it025_class004.mrc as #4, grid size 144,144,144, pixel 1.48, shown
at level 0.0147, step 1, values float32
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/run_it025_class005.mrc"
Opened run_it025_class005.mrc as #5, grid size 144,144,144, pixel 1.48, shown
at level 0.0214, step 1, values float32
> volume #1 level 0.1007
> volume #4 level 0.01153
> volume #3 level 0.007107
> volume #3 level 0.008634
> close #1
> close #2
> close #3
> close #4
> close #5
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220606_BAM-
> LL-T571M/Models/run_it025_class001.mrc"
Opened run_it025_class001.mrc as #1, grid size 144,144,144, pixel 1.36, shown
at level 0.0116, step 1, values float32
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220606_BAM-
> LL-T571M/Models/run_it025_class002.mrc"
Opened run_it025_class002.mrc as #2, grid size 144,144,144, pixel 1.36, shown
at level 0.0146, step 1, values float32
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220606_BAM-
> LL-T571M/Models/run_it025_class003.mrc"
Opened run_it025_class003.mrc as #3, grid size 144,144,144, pixel 1.36, shown
at level 0.0152, step 1, values float32
> volume #2 level 0.01287
> volume #1 level 0.006768
> volume #1 level 0.007772
> tile
1 model tiled
> tile
3 models tiled
> volume #1 level 0.007716
> ~tile
> view matrix
camera position:
0.85112,-0.32668,-0.41095,-117.94,0.33724,-0.2597,0.90489,583,-0.40233,-0.90876,-0.11087,42.919
model positions:
#1,0.98366,0.17998,-0.004556,-16.299,-0.17991,0.98172,-0.062185,26.145,-0.0067195,0.061989,0.99805,-5.4685,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.98366,0.17998,-0.004556,-16.299,-0.17991,0.98172,-0.062185,26.145,-0.0067195,0.061989,0.99805,-5.4685,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,0.98366,0.17998,-0.004556,-16.299,-0.17991,0.98172,-0.062185,26.145,-0.0067195,0.061989,0.99805,-5.4685,#3.1,1,0,0,0,0,1,0,0,0,0,1,0
> volume #2 color #ffe580
> volume #3 color #ffe580
> volume #2 color #a7dbdb
> lighting soft
> set bgColor white
> graphics silhouettes false
> hide #!3 models
> show #!3 models
> show #!2 models
> save "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June 2022/Rendering/BAM-LL_T571M_latOpen.png" width
> 2000 height 2000 supersample 10 transparentBackground true
> hide #!2 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> save "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June 2022/Rendering/BAM-LL_T571M_latOpen.png" width
> 2000 height 2000 supersample 10 transparentBackground true
> hide #!2 models
> show #!3 models
> save "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June 2022/Rendering/BAM-LL_T571M_latClosed.png" width
> 2000 height 2000 supersample 10 transparentBackground true
> hide #!3 models
> show #!1 models
> volume #1 level 0.008887
> close #1-3
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/022_latclosed_PP.mrc"
Opened 022_latclosed_PP.mrc as #1, grid size 144,144,144, pixel 1.48, shown at
level 0.0317, step 1, values float32
> volume #1 level 0.05283
> open 7BNQ
7bnq title:
Lateral-closed conformation of the lid-locked BAM complex (BamA E435C S665C,
BamBDCE) by cryoEM [more info...]
Chain information for 7bnq #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> hide atoms
> show cartoons
> ui tool show Matchmaker
> select add #2
11617 atoms, 11870 bonds, 1 pseudobond, 1488 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
11617 atoms, 11870 bonds, 1 pseudobond, 1488 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-52.158,0,1,0,-31.924,0,0,1,2.4361
> view matrix models #2,1,0,0,-34.382,0,1,0,-57.731,0,0,1,-54.81
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.031136,0.87193,0.48865,-108.26,-0.99676,-0.06339,0.049597,269.72,0.07422,-0.48552,0.87107,38.966
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.031136,0.87193,0.48865,-111.77,-0.99676,-0.06339,0.049597,273.49,0.07422,-0.48552,0.87107,37.358
> view matrix models
> #2,-0.031136,0.87193,0.48865,-110.14,-0.99676,-0.06339,0.049597,272.23,0.07422,-0.48552,0.87107,28.124
> fitmap #2 inMap #1
Fit molecule 7bnq (#2) to map 022_latclosed_PP.mrc (#1) using 11617 atoms
average map value = 0.05414, steps = 92
shifted from previous position = 6.5
rotated from previous position = 8.2 degrees
atoms outside contour = 6068, contour level = 0.052827
Position of 7bnq (#2) relative to 022_latclosed_PP.mrc (#1) coordinates:
Matrix rotation and translation
-0.04604096 0.93162043 0.36050465 -95.44998373
-0.99755037 -0.06190445 0.03257452 273.69723581
0.05266393 -0.35812178 0.93218845 5.76768226
Axis -0.19610685 0.15451816 -0.96833168
Axis point 77.04723239 177.29904118 0.00000000
Rotation angle (degrees) 95.04156930
Shift along axis 55.42455927
> save /Users/samuelhaysom/Desktop/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/7bnq_rel022_latclosed_PP.pdb relModel #1
> view matrix models
> #2,-0.046041,0.93162,0.3605,-83.851,-0.99755,-0.061904,0.032575,276.07,0.052664,-0.35812,0.93219,9.2852
> fitmap #2 inMap #1
Fit molecule 7bnq (#2) to map 022_latclosed_PP.mrc (#1) using 11617 atoms
average map value = 0.02073, steps = 72
shifted from previous position = 8.72
rotated from previous position = 3.29 degrees
atoms outside contour = 9837, contour level = 0.052827
Position of 7bnq (#2) relative to 022_latclosed_PP.mrc (#1) coordinates:
Matrix rotation and translation
-0.04343597 0.93925907 0.34044930 -90.22888184
-0.99354763 -0.07634677 0.08387059 270.86624481
0.10476842 -0.33460959 0.93651482 -6.68540856
Axis -0.21012414 0.11833832 -0.97048642
Axis point 79.71102072 171.75222468 0.00000000
Rotation angle (degrees) 95.25761460
Shift along axis 57.50121998
> ui mousemode right select
Drag select of 1 022_latclosed_PP.mrc , 61 residues
> select clear
Drag select of 1 022_latclosed_PP.mrc , 12 residues
> select clear
> fitmap #2 inMap #1
Fit molecule 7bnq (#2) to map 022_latclosed_PP.mrc (#1) using 11617 atoms
average map value = 0.02072, steps = 44
shifted from previous position = 0.0221
rotated from previous position = 0.0109 degrees
atoms outside contour = 9839, contour level = 0.052827
Position of 7bnq (#2) relative to 022_latclosed_PP.mrc (#1) coordinates:
Matrix rotation and translation
-0.04361510 0.93923521 0.34049220 -90.21865608
-0.99353514 -0.07653342 0.08384844 270.88376985
0.10481244 -0.33463391 0.93650120 -6.68897924
Axis -0.21012891 0.11833983 -0.97048520
Axis point 79.70091305 171.74843354 0.00000000
Rotation angle (degrees) 95.26852948
Shift along axis 57.50544306
> volume #1 level 0.04386
> close #1
> close #2
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/7bnq_rel022_latclosed_PP.pdb"
> "/Users/samuelhaysom/Library/CloudStorage/OneDrive-UniversityofLeeds/PhD
> Mechanistic Biology
> (2018-22)/Computing/BAM_Fab_suppressors_PROCESS/220528_BAM-
> LL-P518L/Models/022_latclosed_PP.mrc"
Chain information for 7bnq_rel022_latclosed_PP.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Opened 022_latclosed_PP.mrc as #2, grid size 144,144,144, pixel 1.48, shown at
level 0.0317, step 1, values float32
> hide atoms
> show cartoons
> transparency 50
> volume #2 level 0.06179
> lighting soft
Drag select of 6 residues, 2 022_latclosed_PP.mrc
> select clear
> fitmap #1 inMap #2
Fit molecule 7bnq_rel022_latclosed_PP.pdb (#1) to map 022_latclosed_PP.mrc
(#2) using 11617 atoms
average map value = 0.05415, steps = 44
shifted from previous position = 0.0295
rotated from previous position = 0.0101 degrees
atoms outside contour = 7138, contour level = 0.06179
Position of 7bnq_rel022_latclosed_PP.pdb (#1) relative to 022_latclosed_PP.mrc
(#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00000675 -0.00007691 0.02952584
0.00000676 0.99999999 0.00015920 -0.01013269
0.00007691 -0.00015920 0.99999998 -0.01093232
Axis -0.89977648 -0.43467802 0.03817463
Axis point 0.00000000 -63.26881416 125.29490211
Rotation angle (degrees) 0.01013740
Shift along axis -0.02257953
> volume #2 level 0.04258
> fitmap #1 inMap #2
Fit molecule 7bnq_rel022_latclosed_PP.pdb (#1) to map 022_latclosed_PP.mrc
(#2) using 11617 atoms
average map value = 0.05414, steps = 44
shifted from previous position = 0.0347
rotated from previous position = 0.00937 degrees
atoms outside contour = 4797, contour level = 0.042583
Position of 7bnq_rel022_latclosed_PP.pdb (#1) relative to 022_latclosed_PP.mrc
(#2) coordinates:
Matrix rotation and translation
0.99999999 0.00010070 -0.00009557 -0.00379871
-0.00010070 0.99999999 0.00003745 0.00290811
0.00009557 -0.00003744 0.99999999 -0.00438886
Axis -0.26040247 -0.66462432 -0.70033211
Axis point 42.93567253 32.21789906 -0.00000000
Rotation angle (degrees) 0.00823862
Shift along axis 0.00213005
> volume #2 level 0.05411
> volume #2 level 0.05475
> volume #2 level 0.04642
> select /A:546
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:549
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:550
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 11 residues, 2 022_latclosed_PP.mrc
> select clear
> select /A:522
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
Drag select of 19 residues, 2 022_latclosed_PP.mrc
> ui mousemode right zoom
> select clear
> select /A:518
7 atoms, 7 bonds, 1 residue, 1 model selected
> volume #2 level 0.07139
> close #2
> close #1
> open 5ljo
Summary of feedback from opening 5ljo fetched from pdb
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
5ljo title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for 5ljo #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECO57
E | Outer membrane protein assembly factor BamE | BAME_ECOL6
> open 5d0o
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> hide #1,2 atoms
> cartoon suppressBackboneDisplay false # to allow display of backbone atoms
Expected a keyword
> show #1,2/A cartoons
> color #1,2/A rgb(0.252,0.680,1.000)
> color #1,2/B rgb(0.000,0.831,0.321)
> color #1,2/C rgb(1.000,0.861,0.137)
> color #1,2/D rgb(1.000,0.400,0.100)
> color #1,2/E rgb(0.780,0.000,0.400)
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> color #1,2/A:424-447 green
> color #1,2/A:454-518 red
> color #1,2/A:348-423 dark orange
> morph #1,2 frames 40
Computed 41 frame morph #3
> coordset #3 1,41
> show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a
> color #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA grey
> show #3/A:435,499,501,535,564,751,793@CA target a
> color #3/A:435,499,501,535,564,751,793@CA grey
> color #3/A:435,436,501,465
> color #3/A:755,795,434,495,465
> close session
> open 5ljo
Summary of feedback from opening 5ljo fetched from pdb
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
5ljo title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for 5ljo #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECO57
E | Outer membrane protein assembly factor BamE | BAME_ECOL6
> open 5d0o
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> hide #1,2 atoms
> cartoon suppressBackboneDisplay false # to allow display of backbone atoms
Expected a keyword
> show #1,2/A cartoons
> color #1,2/A rgb(0.252,0.680,1.000)
> color #1,2/B rgb(0.000,0.831,0.321)
> color #1,2/C rgb(1.000,0.861,0.137)
> color #1,2/D rgb(1.000,0.400,0.100)
> color #1,2/E rgb(0.780,0.000,0.400)
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> color #1,2/A:424-447 green
> color #1,2/A:454-518 red
> color #1,2/A:348-423 dark orange
> morph #1,2 frames 40
Computed 41 frame morph #3
> coordset #3 1,41
> show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a
> cartoon suppressBackboneDisplay false
> hide #1,2 atoms
> show #1,2/A cartoons
> show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a
> color #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA grey
> show #3/A:435,499,501,535,564,751,793@CA target a
> color #3/A:435,499,501,535,564,751,793@CA grey
> color #3/A:435,436,501,465@CA hot pink
> color #3/A:755,795,434,495,465@CA misty rose
> show #3/A:434,436,464,465,495,498,500,550,697,755,764,795,798,799@CA target
> a
> color #3/A:755,795,434,495,465,801@CA misty rose
> show #3/A:434,436,464,465,495,498,500,550,697,755,764,795,798,799,801@CA
> target a
> hide #3:/B-E
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3:/B-E targ c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3/B-E target c
> lighting soft
> view matrix camera
> -0.95767,-0.27958,0.068542,182.67,0.068982,0.0082751,0.99758,422.6,-0.27948,0.96009,0.011362,160.72
> set bgColor white
> lighting full
> view matrix camera
> -0.95767,-0.27958,0.068542,182.67,0.068982,0.0082751,0.99758,422.6,-0.27948,0.96009,0.011362,160.72
> movie record
> coordset #3 1,41
> movie encode "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June
> 2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4" quality good
> verbose true roundTrip true
Movie encoding failed because no images were recorded.
> coordset #3 1,41
> movie encode "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June
> 2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4" quality good
> verbose true roundTrip true
Movie encoding failed because no images were recorded.
> movie record
> coordset #3 1,41
> movie encode "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June
> 2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4" quality good
> verbose true roundTrip true
/Applications/ChimeraX-1.4.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/j9/pfzrsc1x6k3835z8ktp_dpbc0000gn/T/chimovie_qh6g-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /Users/samuelhaysom/Library/CloudStorage/OneDrive-
UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
Reports/OMP Symposium/June
2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with Apple clang version 11.0.0 (clang-1100.0.33.16)
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'/var/folders/j9/pfzrsc1x6k3835z8ktp_dpbc0000gn/T/chimovie_qh6g-%05d.ppm':
Duration: 00:00:03.28, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1197x918, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7f8caa00ac00] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7f8caa00ac00] profile High, level 3.2
[libx264 @ 0x7f8caa00ac00] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=18 lookahead_threads=3
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/samuelhaysom/Library/CloudStorage/OneDrive-
UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
Reports/OMP Symposium/June
2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1196x918, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 50 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 82 fps= 77 q=-1.0 Lsize= 2112kB time=00:00:03.16 bitrate=5475.8kbits/s
speed=2.96x
video:2110kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.085371%
[libx264 @ 0x7f8caa00ac00] frame I:1 Avg QP: 9.74 size: 73375
[libx264 @ 0x7f8caa00ac00] frame P:24 Avg QP:23.36 size: 41331
[libx264 @ 0x7f8caa00ac00] frame B:57 Avg QP:28.92 size: 19213
[libx264 @ 0x7f8caa00ac00] consecutive B-frames: 1.2% 17.1% 3.7% 78.0%
[libx264 @ 0x7f8caa00ac00] mb I I16..4: 75.1% 1.8% 23.1%
[libx264 @ 0x7f8caa00ac00] mb P I16..4: 0.9% 0.9% 2.3% P16..4: 4.4% 6.9% 10.6%
0.0% 0.0% skip:74.1%
[libx264 @ 0x7f8caa00ac00] mb B I16..4: 0.1% 0.2% 0.2% B16..8: 6.3% 6.9% 8.2%
direct: 2.4% skip:75.7% L0:43.9% L1:40.0% BI:16.1%
[libx264 @ 0x7f8caa00ac00] 8x8 transform intra:14.9% inter:11.0%
[libx264 @ 0x7f8caa00ac00] coded y,uvDC,uvAC intra: 33.6% 44.6% 42.3% inter:
10.0% 10.6% 8.8%
[libx264 @ 0x7f8caa00ac00] i16 v,h,dc,p: 90% 5% 5% 0%
[libx264 @ 0x7f8caa00ac00] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 5% 4% 89% 1% 0% 0%
0% 0% 0%
[libx264 @ 0x7f8caa00ac00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 20% 13% 23% 8% 7% 8%
6% 8% 8%
[libx264 @ 0x7f8caa00ac00] i8c dc,h,v,p: 71% 10% 14% 6%
[libx264 @ 0x7f8caa00ac00] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x7f8caa00ac00] ref P L0: 56.0% 13.0% 19.8% 11.3%
[libx264 @ 0x7f8caa00ac00] ref B L0: 86.0% 11.6% 2.4%
[libx264 @ 0x7f8caa00ac00] ref B L1: 95.9% 4.1%
[libx264 @ 0x7f8caa00ac00] kb/s:5269.44
Movie saved to
/Users/samuelhaysom/.../Rendering/EPR_singlePositions_which_work_MORPH.mp4
> movie record supersample 4 size 2000,2000
> coordset #3 1,41
> movie encode "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June
> 2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4" quality good
> verbose true roundTrip true
/Applications/ChimeraX-1.4.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/j9/pfzrsc1x6k3835z8ktp_dpbc0000gn/T/chimovie_E45b-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /Users/samuelhaysom/Library/CloudStorage/OneDrive-
UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
Reports/OMP Symposium/June
2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with Apple clang version 11.0.0 (clang-1100.0.33.16)
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'/var/folders/j9/pfzrsc1x6k3835z8ktp_dpbc0000gn/T/chimovie_E45b-%05d.ppm':
Duration: 00:00:03.28, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 2000x2000, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7fec91009a00] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7fec91009a00] profile High, level 5.0
[libx264 @ 0x7fec91009a00] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=18 lookahead_threads=3
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/samuelhaysom/Library/CloudStorage/OneDrive-
UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
Reports/OMP Symposium/June
2022/Rendering/EPR_singlePositions_which_work_MORPH.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
2000x2000, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 20 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 41 fps= 41 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 55 fps= 36 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 76 fps= 37 q=25.0 size= 443kB time=00:00:00.44 bitrate=8247.7kbits/s
speed=0.215x frame= 82 fps= 31 q=-1.0 Lsize= 2228kB time=00:00:03.16
bitrate=5775.4kbits/s speed=1.21x
video:2226kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.077383%
[libx264 @ 0x7fec91009a00] frame I:1 Avg QP: 9.49 size:104518
[libx264 @ 0x7fec91009a00] frame P:31 Avg QP:21.06 size: 46923
[libx264 @ 0x7fec91009a00] frame B:50 Avg QP:25.70 size: 14395
[libx264 @ 0x7fec91009a00] consecutive B-frames: 1.2% 39.0% 40.2% 19.5%
[libx264 @ 0x7fec91009a00] mb I I16..4: 73.5% 15.9% 10.5%
[libx264 @ 0x7fec91009a00] mb P I16..4: 0.3% 0.5% 0.6% P16..4: 2.7% 4.1% 4.2%
0.0% 0.0% skip:87.6%
[libx264 @ 0x7fec91009a00] mb B I16..4: 0.0% 0.1% 0.0% B16..8: 4.3% 3.3% 1.7%
direct: 0.8% skip:89.6% L0:36.2% L1:34.5% BI:29.2%
[libx264 @ 0x7fec91009a00] 8x8 transform intra:24.4% inter:28.9%
[libx264 @ 0x7fec91009a00] coded y,uvDC,uvAC intra: 17.9% 25.1% 22.7% inter:
3.9% 4.4% 3.3%
[libx264 @ 0x7fec91009a00] i16 v,h,dc,p: 93% 3% 4% 0%
[libx264 @ 0x7fec91009a00] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 21% 4% 70% 1% 1% 1%
1% 1% 1%
[libx264 @ 0x7fec91009a00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 20% 13% 24% 8% 8% 7%
6% 7% 6%
[libx264 @ 0x7fec91009a00] i8c dc,h,v,p: 80% 7% 9% 3%
[libx264 @ 0x7fec91009a00] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x7fec91009a00] ref P L0: 64.9% 14.5% 13.8% 6.8%
[libx264 @ 0x7fec91009a00] ref B L0: 89.2% 9.3% 1.5%
[libx264 @ 0x7fec91009a00] ref B L1: 99.3% 0.7%
[libx264 @ 0x7fec91009a00] kb/s:5558.29
Movie saved to
/Users/samuelhaysom/.../Rendering/EPR_singlePositions_which_work_MORPH.mp4
> close session
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June 2022/Rendering/EPR_L501C_S755C_MORPH.cxc"
> open 5ljo
Summary of feedback from opening 5ljo fetched from pdb
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
5ljo title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for 5ljo #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECO57
E | Outer membrane protein assembly factor BamE | BAME_ECOL6
> open 5d0o
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> hide #1,2 atoms
> cartoon suppressBackboneDisplay false # to allow display of backbone atoms
Expected a keyword
> close session
> open "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June 2022/Rendering/EPR_L501C_S755C_MORPH.cxc"
> open 5ljo
Summary of feedback from opening 5ljo fetched from pdb
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
5ljo title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for 5ljo #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECO57
E | Outer membrane protein assembly factor BamE | BAME_ECOL6
> open 5d0o
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> hide #1,2 atoms
> cartoon suppressBackboneDisplay false
> show #1,2/A cartoons
> color #1,2/A rgb(0.252,0.680,1.000)
> color #1,2/B rgb(0.000,0.831,0.321)
> color #1,2/C rgb(1.000,0.861,0.137)
> color #1,2/D rgb(1.000,0.400,0.100)
> color #1,2/E rgb(0.780,0.000,0.400)
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> color #1,2/A:424-447 green
> color #1,2/A:454-518 red
> color #1,2/A:348-423 dark orange
> morph #1,2 frames 40
Computed 41 frame morph #3
> coordset #3 1,41
> show #3/A:501,755@CA
> color #3/A:501,755@CA medium spring green
> set bgColor white
> lighting full
> view matrix camera
> -0.95767,-0.27958,0.068542,182.67,0.068982,0.0082751,0.99758,422.6,-0.27948,0.96009,0.011362,160.72
> movie record supersample 4 size 2000,2000
> coordset #3 1,41
> movie encode "/Users/samuelhaysom/Library/CloudStorage/OneDrive-
> UniversityofLeeds/PhD Mechanistic Biology (2018-22)/Presentations and
> Reports/OMP Symposium/June 2022/Rendering/EPR_L501C_S755C_MORPH.mp4" quality
> good verbose true roundTrip true
Movie encoding failed because no images were recorded.
OpenGL version: 4.1 ATI-4.7.101
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14242.0.0,0)
OS Loader Version: 540.60.2~89
Software:
System Software Overview:
System Version: macOS 12.1 (21C52)
Kernel Version: Darwin 21.2.0
Time since boot: 6:41
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 555X:
Chipset Model: Radeon Pro 555X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00e3
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501P-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PA302W:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 61105085TW
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Coordset not recorded |
comment:2 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
You need to put a wait command after your coordset command in the script
### Morph Movie ### movie record supersample 4 size 2000,2000 coordset #3 1,41 wait 41 movie encode "~/Desktop/MORPH.mp4" quality good verbose true roundTrip true
When running a command script ChimeraX does not render any graphics frames except when a wait command is used. A better name for the "wait" command would be "drawframes". And you tell it how many frames to draw. Here are a few more tricky details. The "coordset #3 1,41" command returns immediately -- it does not wait for the 41 sets of coordinates to be shown. Instead it says that over the next 41 drawn frames it will keep advancing to the next coordinate set. Other commands that operate for a specified number of frames work similarly. The command returns immediately. The reason for that is so that two commands can operate simultaneously. For instance if you wanted to rotate the scene and at the same time play through the coordinates you could use
turn y 3 41 coordset #3 1,41 wait 41
If instead you wanted the rotation to happen first, then after it stops you play through the coordinates then you would use
turn y 3 41 wait 41 coordset #3 1,41 wait 41
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Reported by Samual Haysom