id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
7110	Coordset not recorded	bssfh@…	Tom Goddard	"{{{
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

}}}
"	defect	closed	normal		Input/Output		not a bug						all	ChimeraX