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Opened 17 months ago
Closed 17 months ago
#15249 closed defect (can't reproduce)
movie encode failure
| 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/kaylie/UFL Dropbox/Kaylie Padgett-
> Pagliai/Kaylie/NB290/NB290pg65/050824_InteractingResidues.cxs"
Log from Wed May 8 12:41:32 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/kaylie/Dropbox
> (UFL)/Kaylie/NB290/NB290pg65/050324_InteractingResidues.cxs"
Log from Fri May 3 12:11:38 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/kaylie/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs" format
> session
Log from Fri Feb 16 09:15:12 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs"
Log from Thu Feb 15 15:26:57 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs"
Log from Mon Feb 12 13:43:19 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs"
Log from Mon Feb 12 13:28:33 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions.cxs"
Log from Mon Feb 12 10:40:44 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction 020524/Kaylie_021224/YoaA_Chi_2.cxs"
Log from Mon Feb 12 07:54:31 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/YoaA_chi_AlphaFold_prediction_2/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
B | No description available
C | No description available
> sequence chain #1/B
Alignment identifier is 1/B
> select /B
4940 atoms, 5028 bonds, 636 residues, 1 model selected
> toolshed show
> ui tool show Toolbar
> ui tool show "Change Chain IDs"
> changechains sel YoaA_2
Chain IDs of 636 residues changed
> select /C
1174 atoms, 1200 bonds, 147 residues, 1 model selected
> select /C
1174 atoms, 1200 bonds, 147 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel Chi_2
Chain IDs of 147 residues changed
> save .cxs
'.cxs' has only compression suffix; cannot determine format from suffix
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction 020524/Kaylie_021224/YoaA_Chi_2.cxs"
——— End of log from Mon Feb 12 07:54:31 2024 ———
opened ChimeraX session
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction 020524/Chi-Psi_pdb3sxu.ent"
Chi-Psi_pdb3sxu.ent title:
Structure of the E. Coli SSB-DNA polymerase III interface [more info...]
Chain information for Chi-Psi_pdb3sxu.ent #2
---
Chain | Description | UniProt
A | DNA polymerase III subunit χ | HOLC_ECOLI 1-147
B | DNA polymerase III subunit ψ | HOLD_ECOLI 2-137
C | SSB peptide |
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best_model.pdb, chain Chi_2 (#1) with Chi-Psi_pdb3sxu.ent, chain A
(#2), sequence alignment score = 746
RMSD between 141 pruned atom pairs is 0.621 angstroms; (across all 146 pairs:
1.148)
> select #1//chain_id='Chi_2'
1174 atoms, 1200 bonds, 147 residues, 1 model selected
> select #1//chain_id='Chi_2'
1174 atoms, 1200 bonds, 147 residues, 1 model selected
> color sel #011993ff
> color sel #929000ff
> color sel #fffb00ff
> ui tool show "Color Actions"
> color sel goldenrod
> color sel dark goldenrod
> color sel goldenrod
> select #2/A
1356 atoms, 1192 bonds, 336 residues, 1 model selected
> color sel gold
> select #2/B
877 atoms, 800 bonds, 198 residues, 1 model selected
> color sel sienna
> select #1//chain_id='YoaA_2'
4940 atoms, 5028 bonds, 636 residues, 1 model selected
> color sel dark blue
> select #2/C
35 atoms, 36 bonds, 4 residues, 1 model selected
> color sel blue violet
> select #2/A
1356 atoms, 1192 bonds, 336 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> open "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/DinG_6fwr.ent"
DinG_6fwr.ent title:
Structure of ding In complex with ssDNA [more info...]
Chain information for DinG_6fwr.ent #3
---
Chain | Description
A | atp-dependent DNA helicase ding
B | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Non-standard residues in DinG_6fwr.ent #3
---
SF4 — iron/sulfur cluster
> ui tool show Matchmaker
> matchmaker #1 to #3
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 DinG_6fwr.ent, chain A (#3) with best_model.pdb, chain YoaA_2 (#1),
sequence alignment score = 1059.5
RMSD between 310 pruned atom pairs is 1.176 angstroms; (across all 616 pairs:
7.955)
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best_model.pdb, chain Chi_2 (#1) with Chi-Psi_pdb3sxu.ent, chain A
(#2), sequence alignment score = 746
RMSD between 141 pruned atom pairs is 0.621 angstroms; (across all 146 pairs:
1.148)
> select #3/B
225 atoms, 237 bonds, 20 residues, 1 model selected
> color sel gray
> select #3/A
5669 atoms, 5675 bonds, 4 pseudobonds, 809 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select #3/A:205@CB
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select add #3/A:199@CA
1 atom, 1 residue, 1 model selected
Drag select of 6 atoms, 5 bonds
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
Drag select of 1 residues, 6 atoms, 5 bonds
> select clear
> select #3/A
5669 atoms, 5675 bonds, 4 pseudobonds, 809 residues, 3 models selected
> cartoon (#!3 & sel)
> select #3/A:199
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:199
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:194
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:194
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:194
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:194
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:194
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:194
6 atoms, 5 bonds, 1 residue, 1 model selected
> select subtract #3/A:194
Nothing selected
> select clear
> select #3/A:156-157
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/A:156-157
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/A:156
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:208-209
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/A:208-626
3315 atoms, 3378 bonds, 1 pseudobond, 415 residues, 2 models selected
> select #3/A
5669 atoms, 5675 bonds, 4 pseudobonds, 809 residues, 3 models selected
> hide (#!3 & sel) target a
> show (#!3 & sel) target ab
> hide (#!3 & sel) target a
> select S
67 atoms, 64 residues, 3 models selected
> select ::name="SF4"
8 atoms, 12 bonds, 1 residue, 1 model selected
> hide #* target a
> show sel target ab
> select #3/A
5669 atoms, 5675 bonds, 4 pseudobonds, 809 residues, 3 models selected
> cartoon hide (#!3 & sel)
Alignment identifier is 3/A
> select #1//chain_id='YoaA_2'
4940 atoms, 5028 bonds, 636 residues, 1 model selected
> select #3/A:664
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:661-664
34 atoms, 36 bonds, 4 residues, 1 model selected
> select #3/A:259-260
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/A:259-520
2078 atoms, 2118 bonds, 1 pseudobond, 258 residues, 2 models selected
> select #1//chain_id='YoaA_2'
4940 atoms, 5028 bonds, 636 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark blue
[Repeated 1 time(s)]
> select #1//chain_id='Chi_2'
1174 atoms, 1200 bonds, 147 residues, 1 model selected
> color sel gold
> color sel goldenrod
> select #2/A
1356 atoms, 1192 bonds, 336 residues, 1 model selected
> color sel khaki
> select #2/B
877 atoms, 800 bonds, 198 residues, 1 model selected
> color sel brown
[Repeated 1 time(s)]
> select #2/A
1356 atoms, 1192 bonds, 336 residues, 1 model selected
> cartoon sel
> select #3/B
225 atoms, 237 bonds, 20 residues, 1 model selected
> show sel target ab
> hide #* target a
> show sel target ab
[Repeated 1 time(s)]
> style sel ball
Changed 225 atom styles
> style sel stick
Changed 225 atom styles
> style sel sphere
Changed 225 atom styles
> style sel ringFill thick
Changed 20 residue ring styles
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
> hide sel target a
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 225 atom styles
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> nucleotides sel ladder
> nucleotides sel stubs
> show (sel-residues & sidechain) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel tube/slab
> nucleotides sel slab
> nucleotides sel fill
> nucleotides sel atoms
> nucleotides sel fill
> cartoon sel
> select #3/A
5669 atoms, 5675 bonds, 4 pseudobonds, 809 residues, 3 models selected
> select ::name="SF4"
8 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1//chain_id='YoaA_2'
4940 atoms, 5028 bonds, 636 residues, 1 model selected
Alignment identifier is 1/YoaA_2
> select #1/YoaA_2:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/YoaA_2:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/YoaA_2:107-108
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/YoaA_2:107-108
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/YoaA_2:108
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:108
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/YoaA_2:168
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:168
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/YoaA_2:173-174
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/YoaA_2:173-174
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/YoaA_2:168
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:168
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #1/YoaA_2:108
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:108
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/YoaA_2:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:168
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:168
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> cartoon hide sel
> cartoon sel
> hide sel target a
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction 020524/Kaylie_021224/YoaA_Chi_Psi_DinG.cxs"
> select #1/YoaA_2:438
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:438
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/YoaA_2:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/YoaA_2:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1//chain_id='Chi_2'
1174 atoms, 1200 bonds, 147 residues, 1 model selected
Alignment identifier is 1/Chi_2
> select #1/Chi_2:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
[Repeated 1 time(s)]
> color sel byhetero
> select #1/Chi_2:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Chi_2:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/Chi_2:72
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Chi_2:72
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> ui tool show Distances
> select #1//chain_id='Chi_2':72
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:599
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:72
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Chi_2:72
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance style color black
[Repeated 2 time(s)]Exactly two atoms must be selected!
> select clear
> select add #1//chain_id='YoaA_2':599@ND2
1 atom, 1 residue, 1 model selected
> select add #1//chain_id='Chi_2':72@OE1
2 atoms, 2 residues, 1 model selected
> select clear
> select #1//chain_id='Chi_2':72@OE1
1 atom, 1 residue, 1 model selected
> ui mousemode right "tape measure"
Drag select of 1 atoms
> ui mousemode right "tape measure"
> ui mousemode right select
> ui mousemode right distance
> select clear
[Repeated 1 time(s)]
> distance #1//chain_id='Chi_2':72@OE1 #1//chain_id='YoaA_2':599@ND2
Distance between best_model.pdb #1//chain_id='Chi_2' GLU 72 OE1 and /YoaA_2
ASN 599 ND2: 2.662Å
> select #1//chain_id='Chi_2':72@OE2
1 atom, 1 residue, 1 model selected
> distance #1//chain_id='Chi_2':72@OE2 #1//chain_id='YoaA_2':621@NH2
Distance between best_model.pdb #1//chain_id='Chi_2' GLU 72 OE2 and /YoaA_2
ARG 621 NH2: 3.245Å
> distance #1//chain_id='Chi_2':54@OE1 #1//chain_id='YoaA_2':438@NH2
Distance between best_model.pdb #1//chain_id='Chi_2' GLU 54 OE1 and /YoaA_2
ARG 438 NH2: 2.911Å
> distance #1//chain_id='Chi_2':53@OD2 #1//chain_id='YoaA_2':438@NE
Distance between best_model.pdb #1//chain_id='Chi_2' ASP 53 OD2 and /YoaA_2
ARG 438 NE: 2.806Å
> ui mousemode right select
Drag select of 6 residues
> select clear
Drag select of 3 residues
> help help:user/preferences.html#startup
> bgColor
Unknown command: bgColor
> bgColor white
Unknown command: bgColor white
> set bgColor white
> select clear
> select #1//chain_id='Chi_2':34
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:34
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:34
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B
877 atoms, 800 bonds, 198 residues, 1 model selected
Alignment identifier is 2/B
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/B:51-52
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/B:51-62
90 atoms, 90 bonds, 12 residues, 1 model selected
> show sel target ab
> hide sel target a
> select #2/B:52
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:53-54
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/B:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #2/B:59-60
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/B:59-60
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/B:59
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:59
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/Chi_2:33
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/Chi_2:33
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/Chi_2:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/Chi_2:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/Chi_2:61
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Chi_2:61-64
31 atoms, 31 bonds, 4 residues, 1 model selected
> show sel target ab
> hide sel target a
> select #2/B:59
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:59
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:36
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Chi_2:36
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/Chi_2:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Chi_2:73-77
30 atoms, 30 bonds, 5 residues, 1 model selected
> show sel target ab
> select #1/Chi_2:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Chi_2:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel target a
> select #1/Chi_2:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:75-79
31 atoms, 31 bonds, 5 residues, 1 model selected
> hide sel target a
> select #1/Chi_2:74
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:74
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #2/B:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:127-128
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #2/B:127-133
68 atoms, 71 bonds, 7 residues, 1 model selected
> show sel target ab
> hide sel target a
> select #2/B:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/Chi_2:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/Chi_2:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:74-75
18 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel target a
> select #2/A
1356 atoms, 1192 bonds, 336 residues, 1 model selected
Alignment identifier is 2/A
> select #2/A:74
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:74-75
18 atoms, 18 bonds, 2 residues, 1 model selected
> show sel target ab
> color sel byhetero
> select #2/B:130
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:130
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> ui mousemode right distance
> select #2/B:129@OE1
1 atom, 1 residue, 1 model selected
> select #2/A:75@NH1
1 atom, 1 residue, 1 model selected
> distance #2/B:129@OE1 #2/A:75@NH1
Distance between Chi-Psi_pdb3sxu.ent #2/B GLU 129 OE1 and /A ARG 75 NH1:
3.877Å
> ui mousemode right select
Drag select of 2 residues
Drag select of 3 residues
[Repeated 1 time(s)]Drag select of 7 residues
> select clear
> select #1/YoaA_2:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:619-620
18 atoms, 17 bonds, 2 residues, 1 model selected
> show sel target ab
> color sel byhetero
Drag select of 3 residues
> select clear
Drag select of 1 residues
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> ~label sel residues
> select #1/YoaA_2:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:619-620
18 atoms, 17 bonds, 2 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select #1//chain_id='YoaA_2':621
11 atoms, 10 bonds, 1 residue, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select #1//chain_id='YoaA_2':621
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1//chain_id='YoaA_2':621
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right label
> select #1//chain_id='YoaA_2':621@CB
1 atom, 1 residue, 1 model selected
> select #1//chain_id='YoaA_2':621
11 atoms, 10 bonds, 1 residue, 1 model selected
> label #1/YoaA_2:621
> label #1/YoaA_2:438
> label #1/YoaA_2:599
> label #1/Chi_2:54
> label #1/Chi_2:53
> label #1/Chi_2:72
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.9782,-0.085224,-0.18938,13.935,0.0010008,-0.90997,0.41468,13.286,-0.20767,-0.40583,-0.89004,20.232
> undo
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right select
> select clear
[Repeated 1 time(s)]Drag select of 1 bonds, 2 residues
> select #2/B:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel target a
> ui mousemode right distance
> select #2/B:56@OD1
1 atom, 1 residue, 1 model selected
> select #2/B:56@OD1
1 atom, 1 residue, 1 model selected
> select #1//chain_id='Chi_2':34@NE
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms, 2 residues
> select #2/B:56@OD1
1 atom, 1 residue, 1 model selected
> distance #1//chain_id='Chi_2':34@NE #2/B:59@NH1
Distance between best_model.pdb #1//chain_id='Chi_2' ARG 34 NE and Chi-
Psi_pdb3sxu.ent #2/B ARG 59 NH1: 4.577Å
> distance #1//chain_id='Chi_2':34@NE #2/B:56@OD1
Distance between best_model.pdb #1//chain_id='Chi_2' ARG 34 NE and Chi-
Psi_pdb3sxu.ent #2/B ASP 56 OD1: 3.498Å
> ui mousemode right label
> label #2/B:56
> label #2/B:59
> label #1/Chi_2:34
> select #2/B:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:60
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:60
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select clear
[Repeated 1 time(s)]
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions.cxs"
——— End of log from Mon Feb 12 10:40:44 2024 ———
opened ChimeraX session
> select #2/A:57-58
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/A:57-58
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/A:57
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:57
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/Chi_2:57
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/Chi_2:57
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> ui mousemode right label
> select #1//chain_id='Chi_2':57@CB
1 atom, 1 residue, 1 model selected
> label #1/Chi_2:57
> ui mousemode right label
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select #2/A:57
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:57
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/B
877 atoms, 800 bonds, 198 residues, 1 model selected
> ui tool show "Color Actions"
> color sel brown
> undo
> ui tool show "Color Actions"
> color sel sienna
> color sel saddle brown
> select #2/B:130
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #2/B:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #2/B:59
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
Drag select of 4 residues
> select clear
[Repeated 1 time(s)]
> select #2/C
35 atoms, 36 bonds, 4 residues, 1 model selected
> cartoon sel
> show sel target ab
> select #2/A:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/A:63-64
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:63-65
24 atoms, 24 bonds, 3 residues, 1 model selected
> show sel target ab
> select #2/A:64
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:64-65
18 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel target a
> select #2/A:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #1/Chi_2:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/Chi_2:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui mousemode right label
> label #2/A:75
> ui mousemode right select
> ui tool show Distances
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions.cxs"
> ui mousemode right distance
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions.cxs"
> ui mousemode right label
> ui mousemode right distance
> distance #2/B:130@NE2 #2/A:75@NH2
Distance between Chi-Psi_pdb3sxu.ent #2/B HIS 130 NE2 and /A ARG 75 NH2: 3.1Å
> ui mousemode right distance
> ui mousemode right select
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions.cxs"
[Repeated 1 time(s)]
——— End of log from Mon Feb 12 13:28:33 2024 ———
opened ChimeraX session
> label defaultHeight 0.69
[Repeated 1 time(s)]
> label defaultHeight 0.6799999999999999
> label defaultHeight 0.68
[Repeated 1 time(s)]
> label defaultHeight 0.67
[Repeated 1 time(s)]
> label defaultHeight 0.68
[Repeated 1 time(s)]
> label defaultHeight 0.6900000000000001
> label defaultHeight 0.69
[Repeated 1 time(s)]
> label defaultHeight 0.7
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting simple
> mlp sel
Map values for surface "best_model.pdb_Chi_2 SES surface": minimum -28.76,
mean -4.915, maximum 22.17
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "best_model.pdb_Chi_2 SES surface": minimum -28.76,
mean -4.915, maximum 22.17
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "best_model.pdb_Chi_2 SES surface": minimum -28.76,
mean -4.915, maximum 22.17
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select #3/B
225 atoms, 237 bonds, 20 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 216 atom styles
> nucleotides sel tube/slab shape box
[Repeated 1 time(s)]
> nucleotides sel ladder
> nucleotides sel atoms
> style nucleic & sel stick
Changed 216 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 216 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 216 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape muffler
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel tube/slab shape box
> nucleotides sel slab
> style nucleic & sel stick
Changed 216 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 216 atom styles
> color sel byelement
> color sel byhetero
> color sel dim gray
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs"
> ui mousemode right distance
> distance #2/B:56@OD2 #2/A:63@OG
Distance between Chi-Psi_pdb3sxu.ent #2/B ASP 56 OD2 and /A SER 63 OG: 4.246Å
> select #1/Chi_2:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/Chi_2:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> ui mousemode right select
> select #1/Chi_2:33-34
25 atoms, 26 bonds, 2 residues, 1 model selected
> select #1/Chi_2:33-34
25 atoms, 26 bonds, 2 residues, 1 model selected
> select #1/Chi_2:33
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/Chi_2:33
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide (#!1 & sel) target a
> select #1/Chi_2:126
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:126
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/B:125-127
21 atoms, 20 bonds, 3 residues, 1 model selected
> show sel target ab
> select #2/B:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:125-127
21 atoms, 20 bonds, 3 residues, 1 model selected
> hide sel target a
> select #2/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select #1/Chi_2:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Chi_2:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> show (#!1 & sel) target ab
[Repeated 1 time(s)]
> select #2/A:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> ui mousemode right distance
> select #2/A:74@CD
1 atom, 1 residue, 1 model selected
> select #2/B:126@SG
1 atom, 1 residue, 1 model selected
> select #2/A:74@CD
1 atom, 1 residue, 1 model selected
> distance #2/A:74@CG #2/B:126@SG
Distance between Chi-Psi_pdb3sxu.ent #2/A PRO 74 CG and /B CYS 126 SG: 4.240Å
> ui tool show Distances
> ~distance #2/A:74@CG #2/B:126@SG
> select #2/A:74@CD
1 atom, 1 residue, 1 model selected
> select #2/B:126@SG
1 atom, 1 residue, 1 model selected
> distance #2/B:126@SG #2/A:74@CD
Distance between Chi-Psi_pdb3sxu.ent #2/B CYS 126 SG and /A PRO 74 CD: 3.681Å
> ui mousemode right label
> label #2/A:74
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs"
——— End of log from Mon Feb 12 13:43:19 2024 ———
opened ChimeraX session
> select #1/YoaA_2:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/YoaA_2:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> ui mousemode right distance
> distance #1//chain_id='Chi_2':54@OE2 #1//chain_id='YoaA_2':620@OG1
Distance between best_model.pdb #1//chain_id='Chi_2' GLU 54 OE2 and /YoaA_2
THR 620 OG1: 3.393Å
> ui mousemode right distance
> ui mousemode right select
> select clear
> select #1/Chi_2:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Chi_2:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Chi_2:75-76
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/Chi_2:75-76
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/Chi_2:58
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Chi_2:58-59
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/Chi_2:59
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Chi_2:58-59
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/Chi_2:58-59
16 atoms, 15 bonds, 2 residues, 1 model selected
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs"
——— End of log from Thu Feb 15 15:26:57 2024 ———
opened ChimeraX session
> ui tool show Distances
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> save "/Users/kapadgett/Dropbox (UFL)/Kaylie/Protein Models/Craig
> YoaAChi_AF/Updated AF prediction
> 020524/Kaylie_021224/YoaA_Chi_Psi_DinG_Interactions_021224.cxs"
——— End of log from Fri Feb 16 09:15:12 2024 ———
opened ChimeraX session
> cd "/Users/kaylie/Dropbox (UFL)/Kaylie/NB290/NB290pg65"
Current working directory is: /Users/kaylie/Dropbox
(UFL)/Kaylie/NB290/NB290pg65
> save "/Users/kaylie/Dropbox
> (UFL)/Kaylie/NB290/NB290pg65/050324_InteractingResidues.cxs"
——— End of log from Fri May 3 12:11:38 2024 ———
opened ChimeraX session
> view name p2
> select add #1
6114 atoms, 6228 bonds, 5 pseudobonds, 783 residues, 3 models selected
> select subtract #1
1 model selected
> hide #1.1 models
> hide #2.1 models
> hide #4.1 models
> hide #!4 models
> set view p1
Expected a keyword
> view set p1
Expected an objects specifier or a view name or a keyword
> set p1
Expected a keyword
> view name p1
> hide ~/YoaA_2
> undo
> view p1
> zoom 2
> y 90
Unknown command: y 90
> zoom 1.5
> x20
Unknown command: x20
> x 20
Unknown command: x 20
> move x 20
> move x -5
> move y 20
> move y -10
> turn x 45
> turn x -45
> turn y 45
> turn y -45
> turn x 10
> turn x -10
> turn y 10
[Repeated 2 time(s)]
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> show #!4 models
> turn y 10
> turn y -10
> move x 5
> move y 5
> zoom 1.1
[Repeated 2 time(s)]
> hide #!4 models
> hide #2.1 models
> show #2.1 models
> show #!4 models
> show #4.1 models
> hide #4.1 models
> view name p2
> show #4.1 models
> turn x 10
> turn x -10
> turn y 10
> turn y 50
[Repeated 2 time(s)]
> move x 20
> turn y 20
[Repeated 3 time(s)]
> show #1.1 models
> turn y 20
[Repeated 2 time(s)]
> view p2
> rotate y 20
Unknown command: rotate y 20
> turn y 20
[Repeated 1 time(s)]
> move x 20
> turn y 20
[Repeated 4 time(s)]
> move x 20
> move x -10
> zoom 1.1
[Repeated 1 time(s)]
> move y 5
> move y -5
> move x -5
> move x 5
> move y 5
> move x -2
> view set p3
Expected an objects specifier or a view name or a keyword
> view p1
> view p2
> view p3
Expected an objects specifier or a view name or a keyword
> view p3
Expected an objects specifier or a view name or a keyword
> turn y 50
> move x 50
> move x -50
[Repeated 1 time(s)]
> move x 50
> move y 2-
Expected a number or a keyword
> move y 20
> move y -20
> move x 20
[Repeated 1 time(s)]
> move x -20
> move x 10
> turn y 30
[Repeated 4 time(s)]
> zoom 1.1
> move y 5
> set view p3
Expected a keyword
> view set p3
Expected an objects specifier or a view name or a keyword
> view name p3
> view p1
> view p2
> view p3
> view p1
> move y 10
> move x 10
[Repeated 1 time(s)]
> zoom 2
[Repeated 1 time(s)]
> move y -5
> move y 5
> move x -5
> turn x -5
> turn x 5
> turn y -5
> turn y 5
[Repeated 5 time(s)]
> turn y -5
[Repeated 1 time(s)]
> turn x -5
[Repeated 3 time(s)]
> turn x 5
[Repeated 11 time(s)]
> turn x -5
[Repeated 5 time(s)]
> turn y 5
[Repeated 1 time(s)]
> turn y -5
[Repeated 12 time(s)]
> turn y 5
[Repeated 11 time(s)]
> turn x 5
> turn x -5
[Repeated 2 time(s)]
> move y 10
> view name p4
> turn x 5
> turn x -5
> turn y 5
> turn y -5
[Repeated 11 time(s)]
> turn y 5
[Repeated 2 time(s)]
> move x -5
[Repeated 1 time(s)]
> turn y 5
[Repeated 5 time(s)]
> turn y -5
[Repeated 6 time(s)]
> move x -5
> turn x -5
[Repeated 3 time(s)]
> turn x 5
[Repeated 5 time(s)]
> view name p5
> select #1/Chi_2:66
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:66
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:74
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:74
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Chi_2:64
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/Chi_2:64
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (#!1 & sel) target ab
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select add #1
6114 atoms, 6228 bonds, 5 pseudobonds, 783 residues, 4 models selected
> select subtract #1
1 model selected
> view name p6
> view p5
> view p4
> fly p1 p2
> cd "/Users/kaylie/Dropbox (UFL)/Kaylie/NB290/NB290pg65"
Current working directory is: /Users/kaylie/Dropbox
(UFL)/Kaylie/NB290/NB290pg65
> save "/Users/kaylie/Dropbox
> (UFL)/Kaylie/NB290/NB290pg65/050824_InteractingResidues.cxs"
——— End of log from Wed May 8 12:41:32 2024 ———
opened ChimeraX session
> view p1
> fly p1 p2 1000
> view p1
> fly p1 p2
> view p1
> fly p2 wait 1000 fly p3
fly: Unknown position name "wait"
> fly p2
> wait 1000
> fly p3
> view p1
> fly p2
> wait 1000
> fly p3
> view p1
> fly p1 1000 p2
> fly p1 100 p2
> fly p1 150 p2
> view p1
> select protein
13648 atoms, 13919 bonds, 12 pseudobonds, 1734 residues, 5 models selected
> select add #1
13648 atoms, 13919 bonds, 12 pseudobonds, 1734 residues, 7 models selected
> select add #2
13934 atoms, 13919 bonds, 12 pseudobonds, 2020 residues, 8 models selected
> select subtract #1
7820 atoms, 7691 bonds, 5 pseudobonds, 1237 residues, 6 models selected
> select subtract #2
5552 atoms, 5663 bonds, 1 pseudobond, 699 residues, 2 models selected
> select add #3
5894 atoms, 5912 bonds, 4 pseudobonds, 829 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #1
6114 atoms, 6228 bonds, 5 pseudobonds, 783 residues, 3 models selected
> select subtract #1
1 model selected
> select add #1
6114 atoms, 6228 bonds, 5 pseudobonds, 783 residues, 3 models selected
> hide 1/Chi_2
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Change Chain IDs"
> changechains sel Chi_2 C
Chain IDs of 147 residues changed
> changechains sel YoaA_2 D
Chain IDs of 636 residues changed
Must select one or more chain IDs from the list on the left
> hide C
> undo
> hide D
> undo
> hide atoms
> undo
> hide Chain A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/a
> undo
> hide models best_model.pdb
Expected ',' or a keyword
> hide best_model.pdb
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /best_model.pdb
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /b-c cartoons
> undo
> hide cartoons cartoon
Expected ',' or a keyword
> hide cartoons cartoons
Expected ',' or a keyword
> view p1
> select subtract #1
1 model selected
> select add #1
6114 atoms, 6228 bonds, 5 pseudobonds, 783 residues, 3 models selected
> select subtract #1
1 model selected
> view p1
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> hide /#!1 models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> undo
> show #!1models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #!1 models
> Fly p1 200 p2 ; wait ; Crossfade 60 ; hide #!1 models ; hide #!3 models ;
> wait
Unknown command: Fly p1 200 p2 ; wait ; Crossfade 60 ; hide #!1 models ; hide
#!3 models ; wait
> Fly p1 200 p2 ; wait
Unknown command: Fly p1 200 p2 ; wait
> Fly p1 200 p2
Unknown command: Fly p1 200 p2
> fly p1 200 p2
> wait
> undo
[Repeated 1 time(s)]
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 60
> show #!1 models
> show #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 60
> show #!1 models
> show #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> view p1
> fly p1 200 p2
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
> crossfade 60
> show #!1 models
> show #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> view p1
> fly p1 200 p2
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
> crossfade 60
> show #!1 models
> show #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> view p1
[Repeated 1 time(s)]
> fly p1 200 p2 crossfade 60 hide #!1 models hide #!3 models
fly: Unknown position name "crossfade"
> view p1
> fly p1 200 p2
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
> crossfade 60
> show #!1 models
> show #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 60
> show #!1 models
> show #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 30
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> fly p2 200 p3
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200 show #!1 models ; show #!3 models ; wait 30
Expected a keyword
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> rotate
Unknown command: rotate
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn 360
Expected an axis vector or a keyword
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn y 360
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn x 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll 50 ; show #!1 models ; show #!3 models ; wait 30 ;
Expected an axis vector or a keyword
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn y 360
> wait
wait requires a frame count argument unless motion is in progress
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn y 360
> wait 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn y 360
> wait 360
> freeze ; show #!1 models ; show #!3 models ; wait 30 ;
Unknown command: freeze ; show #!1 models ; show #!3 models ; wait 30 ;
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn y 360
> wait 360 freeze ; show #!1 models ; show #!3 models ; wait 30 ;
Expected a keyword
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> wait 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360 stop ; wait 360 ; show #!1 models ; show #!3 models ; wait 30 ;
Expected 'forever' or an integer >= 1 or a keyword
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360 stop 20 ; wait 360 ; show #!1 models ; show #!3 models ; wait 30
> ;
Expected 'forever' or an integer >= 1 or a keyword
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> stop
> wait 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> stop
> wait 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> wait
wait requires a frame count argument unless motion is in progress
> stop
> wait 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> wait
wait requires a frame count argument unless motion is in progress
> stop
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> wait
wait requires a frame count argument unless motion is in progress
> stop
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> wait 20
> stop
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> wait
wait requires a frame count argument unless motion is in progress
> stop
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn y 360
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> turn x 360
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 200
> roll y 360 100
> view p1
> fly p1 200 p2
> roll y 360 100
> view p1
> fly p1 200 p2
> roll y
> view p1
> fly p1 200 p2
> roll y 360 100
> view p1
> fly p1 200 p2
> roll y 360 100
> stop
> view p1
> fly p1 200 p2
> roll y 360 100
> stop
> view p1
> fly p1 200 p2
> turn y 360 100
> view p1
> fly p1 200 p2
> turn y 360 100
> view p1
> fly p1 200 p2
> turn
> view p1
> fly p1 200 p2
> turn y 360 200
> view p1
> fly p1 200 p2
> turn y 1 360 200
Expected a keyword
> view p1
> fly p1 200 p2
> turn y 1 360
> view p1
> fly p1 200 p2
> turn y 1 720
> view p1
> fly p1 200 p2
> turn y 1 480
> view p1
> fly p1 200 p2
> turn y 1 540
> view p1
> fly p1 200 p2
> turn y 1 540
> view p1
> fly p1 200 p2
> turn y 1 540
> fly p2
> view p1
> fly p1 200 p2
> turn y 1 540
> fly p2
> view p1
> fly p1 200 p2
> turn y 1 560
> view p1
> fly p1 200 p2
> turn y 1 580
> view p1
> fly p1 200 p2
> turn y 1 570
> view p1
> fly p1 200 p2
> turn y 1 570
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait 200
> show #!1 models
> show #!3 models
> wait 30
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait
> show #!1 models
> show #!3 models
> wait 30
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait 570
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait 20
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait 570
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 570
> wait 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 360
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfase 60 ; show #!1 models ; show #!3 models ; wait 30 ;
Unknown command: crossfase 60 ; show #!1 models ; show #!3 models ; wait 30 ;
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> crossfade 60
> hide #!1 models
> hide #!3 models
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait
wait requires a frame count argument unless motion is in progress
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 30
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 30
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> crossfade 60
> show #!1 models
> show #!3 models
> wait 30
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> fly p3 200 p4
> wait
> fly p3 200 p4
> wait
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> view p1
> select add #1
6114 atoms, 6228 bonds, 5 pseudobonds, 783 residues, 3 models selected
> select subtract #1
1 model selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> crossfade 60
> hide #!2 models
> wait 100
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
fly: Nothing displayed to calculate center of rotation
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> crossfade 60
> hide #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!2 models
> wait 100
> fly p4 200 p5
> wait
> turn y 1 360
> wait 400
> show #!2 models
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> crossfade 60
> hide #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!2 models
> wait 100
> fly p4 200 p5
> wait
> turn y 1 360
> wait 400
> view p5
> view p4
> view p5
> fly p4 p5
> fly p4 p5 p6
> fly p5
> transparency #1,3-4 70
> transparency #1,3-4 0
> view p4
[Repeated 1 time(s)]
> name view p5
"p5": invalid atom specifier
> view name p5
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
fly: Nothing displayed to calculate center of rotation
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> crossfade 60
> hide #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!2 models
> wait 100
> fly p4 200 p5
> wait
> turn y 1 360
> wait 400
> view p1
> show #!2 models
> save "/Users/kaylie/UFL Dropbox/Kaylie Padgett-
> Pagliai/Kaylie/NB290/NB290pg65/051724_InteractingResidues.cxs"
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> crossfade 60
> hide #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!2 models
> wait 100
> fly p4 200 p5
> wait
> turn y 1 360
> wait 400
> view p1
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
fly: Nothing displayed to calculate center of rotation
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> crossfade 60
> hide #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!2 models
> wait 100
> fly p4 200 p5
> wait
> turn y 1 360
> wait 400
> fly p5 200 p1
> wait
> fly p5 200 p1
> wait stop
Expected an integer >= 1 or a keyword
> show #!2 models
> view p1
> movie record
> stop
> movie encode
Movie saved to /Users/kaylie/Desktop/movie.mp4
> view p1
[Repeated 2 time(s)]
> movie record
> fly p1 200 p2
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/movie/movie.py", line 172, in capture_image
i.save(save_path, self.img_fmt)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/Image.py", line 2320, in save
save_handler(self, fp, filename)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/PpmImagePlugin.py", line 324, in _save
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 524, in _save
s = encoder.encode_to_file(fh, bufsize)
OSError: [Errno 28] No space left on device
Error processing trigger "frame drawn":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 524, in _save
s = encoder.encode_to_file(fh, bufsize)
See log for complete Python traceback.
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> fly p2 200 p3
> wait
> crossfade 60
> hide #!1 models
> hide #!3 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!1 models
> show #!3 models
> wait 100
> turn y 1 360
> wait 400
> fly p3 200 p4
> wait
> crossfade 60
> hide #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> show #!2 models
> wait 100
> turn y 1 360
> wait 400
> crossfade 60
> hide #!2 models
> wait 100
> fly p4 200 p5
> wait
> turn y 1 360
> wait 400
> fly p5 200 p1
> wait
> Movie encode /Users/kaylie/UFL Dropbox/Kaylie Padgett-
> Pagliai/Kaylie/NB290/NB290pg65/051724_InteractingResidues.mp4 quality
> highest framerate 50
Unknown command: Movie encode /Users/kaylie/UFL Dropbox/Kaylie Padgett-
Pagliai/Kaylie/NB290/NB290pg65/051724_InteractingResidues.mp4 quality highest
framerate 50
> Movie encode quality highest framerate 50
Unknown command: Movie encode quality highest framerate 50
> Movie encode
Unknown command: Movie encode
> movie encode quality highest framerate 50
/Applications/ChimeraX-1.5.app/Contents/bin/ffmpeg -r 50.0 -i
/var/folders/tn/3k8t61997ll8938j3vq_s55w0000gn/T/chimovie_pavH-%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 15 /Users/kaylie/Desktop/movie.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/tn/3k8t61997ll8938j3vq_s55w0000gn/T/chimovie_pavH-%05d.ppm':
Duration: 00:00:43.24, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1240x1464, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7fa6f800de00] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7fa6f800de00] profile High, level 4.2
[libx264 @ 0x7fa6f800de00] 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=15.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/kaylie/Desktop/movie.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1240x1464, q=-1--1, 50 fps, 12800 tbn, 50 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= 41 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 78 fps= 77 q=23.0 size= 598kB time=00:00:00.26 bitrate=18841.1kbits/s
speed=0.256x frame= 122 fps= 80 q=23.0 size= 2261kB time=00:00:01.14
bitrate=16249.3kbits/s speed=0.747x frame= 164 fps= 81 q=23.0 size= 4186kB
time=00:00:01.98 bitrate=17318.7kbits/s speed=0.976x frame= 200 fps= 79 q=23.0
size= 6041kB time=00:00:02.70 bitrate=18326.9kbits/s speed=1.07x frame= 232
fps= 76 q=23.0 size= 7963kB time=00:00:03.34 bitrate=19529.4kbits/s speed=
1.1x frame= 261 fps= 74 q=23.0 size= 9968kB time=00:00:03.92
bitrate=20831.3kbits/s speed=1.11x frame= 295 fps= 73 q=23.0 size= 10786kB
time=00:00:04.60 bitrate=19207.7kbits/s speed=1.14x frame= 338 fps= 74 q=23.0
size= 11741kB time=00:00:05.46 bitrate=17615.8kbits/s speed= 1.2x frame= 380
fps= 75 q=23.0 size= 12237kB time=00:00:06.30 bitrate=15912.4kbits/s
speed=1.25x frame= 421 fps= 76 q=23.0 size= 13466kB time=00:00:07.12
bitrate=15492.8kbits/s speed=1.28x frame= 467 fps= 77 q=23.0 size= 14269kB
time=00:00:08.04 bitrate=14538.7kbits/s speed=1.33x frame= 509 fps= 77 q=23.0
size= 15011kB time=00:00:08.88 bitrate=13847.5kbits/s speed=1.35x frame= 543
fps= 77 q=23.0 size= 15985kB time=00:00:09.56 bitrate=13697.7kbits/s
speed=1.35x frame= 577 fps= 76 q=23.0 size= 17187kB time=00:00:10.24
bitrate=13749.8kbits/s speed=1.35x frame= 618 fps= 76 q=23.0 size= 18035kB
time=00:00:11.06 bitrate=13358.1kbits/s speed=1.37x frame= 659 fps= 77 q=23.0
size= 18732kB time=00:00:11.88 bitrate=12916.9kbits/s speed=1.38x frame= 697
fps= 76 q=23.0 size= 19664kB time=00:00:12.64 bitrate=12743.9kbits/s
speed=1.39x av_interleaved_write_frame(): No space left on device
frame= 720 fps= 74 q=23.0 size= 20428kB time=00:00:13.10
bitrate=12774.6kbits/s speed=1.35x Error writing trailer of
/Users/kaylie/Desktop/movie.mp4: No space left on deviceframe= 720 fps= 72
q=23.0 Lsize= 20428kB time=00:00:13.10 bitrate=12774.6kbits/s speed=1.32x
video:20458kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x7fa6f800de00] frame I:3 Avg QP: 9.27 size:167556
[libx264 @ 0x7fa6f800de00] frame P:267 Avg QP:19.56 size: 43600
[libx264 @ 0x7fa6f800de00] frame B:450 Avg QP:22.43 size: 20771
[libx264 @ 0x7fa6f800de00] consecutive B-frames: 12.5% 11.4% 3.3% 72.8%
[libx264 @ 0x7fa6f800de00] mb I I16..4: 55.5% 13.0% 31.5%
[libx264 @ 0x7fa6f800de00] mb P I16..4: 2.1% 3.3% 1.5% P16..4: 14.3% 8.5% 8.0%
0.0% 0.0% skip:62.3%
[libx264 @ 0x7fa6f800de00] mb B I16..4: 0.3% 0.3% 0.1% B16..8: 10.9% 7.6% 5.1%
direct: 1.8% skip:74.0% L0:43.0% L1:45.0% BI:11.9%
[libx264 @ 0x7fa6f800de00] 8x8 transform intra:42.9% inter:28.8%
[libx264 @ 0x7fa6f800de00] coded y,uvDC,uvAC intra: 20.6% 44.7% 34.8% inter:
8.2% 11.4% 7.1%
[libx264 @ 0x7fa6f800de00] i16 v,h,dc,p: 65% 17% 8% 9%
[libx264 @ 0x7fa6f800de00] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 11% 11% 66% 2% 1% 2%
1% 3% 1%
[libx264 @ 0x7fa6f800de00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 26% 17% 26% 5% 6% 6%
5% 5% 3%
[libx264 @ 0x7fa6f800de00] i8c dc,h,v,p: 61% 16% 16% 7%
[libx264 @ 0x7fa6f800de00] Weighted P-Frames: Y:10.9% UV:6.7%
[libx264 @ 0x7fa6f800de00] ref P L0: 61.5% 11.3% 20.2% 6.8% 0.2%
[libx264 @ 0x7fa6f800de00] ref B L0: 81.5% 15.6% 2.9%
[libx264 @ 0x7fa6f800de00] ref B L1: 92.4% 7.6%
[libx264 @ 0x7fa6f800de00] kb/s:11939.42
Conversion failed!
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 1
Error message:
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/tn/3k8t61997ll8938j3vq_s55w0000gn/T/chimovie_pavH-%05d.ppm':
Duration: 00:00:43.24, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1240x1464, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7fa6f800de00] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7fa6f800de00] profile High, level 4.2
[libx264 @ 0x7fa6f800de00] 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=15.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/kaylie/Desktop/movie.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1240x1464, q=-1--1, 50 fps, 12800 tbn, 50 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= 41 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 78 fps= 77 q=23.0 size= 598kB time=00:00:00.26 bitrate=18841.1kbits/s
speed=0.256x frame= 122 fps= 80 q=23.0 size= 2261kB time=00:00:01.14
bitrate=16249.3kbits/s speed=0.747x frame= 164 fps= 81 q=23.0 size= 4186kB
time=00:00:01.98 bitrate=17318.7kbits/s speed=0.976x frame= 200 fps= 79 q=23.0
size= 6041kB time=00:00:02.70 bitrate=18326.9kbits/s speed=1.07x frame= 232
fps= 76 q=23.0 size= 7963kB time=00:00:03.34 bitrate=19529.4kbits/s speed=
1.1x frame= 261 fps= 74 q=23.0 size= 9968kB time=00:00:03.92
bitrate=20831.3kbits/s speed=1.11x frame= 295 fps= 73 q=23.0 size= 10786kB
time=00:00:04.60 bitrate=19207.7kbits/s speed=1.14x frame= 338 fps= 74 q=23.0
size= 11741kB time=00:00:05.46 bitrate=17615.8kbits/s speed= 1.2x frame= 380
fps= 75 q=23.0 size= 12237kB time=00:00:06.30 bitrate=15912.4kbits/s
speed=1.25x frame= 421 fps= 76 q=23.0 size= 13466kB time=00:00:07.12
bitrate=15492.8kbits/s speed=1.28x frame= 467 fps= 77 q=23.0 size= 14269kB
time=00:00:08.04 bitrate=14538.7kbits/s speed=1.33x frame= 509 fps= 77 q=23.0
size= 15011kB time=00:00:08.88 bitrate=13847.5kbits/s speed=1.35x frame= 543
fps= 77 q=23.0 size= 15985kB time=00:00:09.56 bitrate=13697.7kbits/s
speed=1.35x frame= 577 fps= 76 q=23.0 size= 17187kB time=00:00:10.24
bitrate=13749.8kbits/s speed=1.35x frame= 618 fps= 76 q=23.0 size= 18035kB
time=00:00:11.06 bitrate=13358.1kbits/s speed=1.37x frame= 659 fps= 77 q=23.0
size= 18732kB time=00:00:11.88 bitrate=12916.9kbits/s speed=1.38x frame= 697
fps= 76 q=23.0 size= 19664kB time=00:00:12.64 bitrate=12743.9kbits/s
speed=1.39x av_interleaved_write_frame(): No space left on device
frame= 720 fps= 74 q=23.0 size= 20428kB time=00:00:13.10
bitrate=12774.6kbits/s speed=1.35x Error writing trailer of
/Users/kaylie/Desktop/movie.mp4: No space left on deviceframe= 720 fps= 72
q=23.0 Lsize= 20428kB time=00:00:13.10 bitrate=12774.6kbits/s speed=1.32x
video:20458kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x7fa6f800de00] frame I:3 Avg QP: 9.27 size:167556
[libx264 @ 0x7fa6f800de00] frame P:267 Avg QP:19.56 size: 43600
[libx264 @ 0x7fa6f800de00] frame B:450 Avg QP:22.43 size: 20771
[libx264 @ 0x7fa6f800de00] consecutive B-frames: 12.5% 11.4% 3.3% 72.8%
[libx264 @ 0x7fa6f800de00] mb I I16..4: 55.5% 13.0% 31.5%
[libx264 @ 0x7fa6f800de00] mb P I16..4: 2.1% 3.3% 1.5% P16..4: 14.3% 8.5% 8.0%
0.0% 0.0% skip:62.3%
[libx264 @ 0x7fa6f800de00] mb B I16..4: 0.3% 0.3% 0.1% B16..8: 10.9% 7.6% 5.1%
direct: 1.8% skip:74.0% L0:43.0% L1:45.0% BI:11.9%
[libx264 @ 0x7fa6f800de00] 8x8 transform intra:42.9% inter:28.8%
[libx264 @ 0x7fa6f800de00] coded y,uvDC,uvAC intra: 20.6% 44.7% 34.8% inter:
8.2% 11.4% 7.1%
[libx264 @ 0x7fa6f800de00] i16 v,h,dc,p: 65% 17% 8% 9%
[libx264 @ 0x7fa6f800de00] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 11% 11% 66% 2% 1% 2%
1% 3% 1%
[libx264 @ 0x7fa6f800de00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 26% 17% 26% 5% 6% 6%
5% 5% 3%
[libx264 @ 0x7fa6f800de00] i8c dc,h,v,p: 61% 16% 16% 7%
[libx264 @ 0x7fa6f800de00] Weighted P-Frames: Y:10.9% UV:6.7%
[libx264 @ 0x7fa6f800de00] ref P L0: 61.5% 11.3% 20.2% 6.8% 0.2%
[libx264 @ 0x7fa6f800de00] ref B L0: 81.5% 15.6% 2.9%
[libx264 @ 0x7fa6f800de00] ref B L1: 92.4% 7.6%
[libx264 @ 0x7fa6f800de00] kb/s:11939.42
Conversion failed!
\-----------------------------
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 25 days, 3 hours, 42 minutes
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 Support: Metal 3
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 Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 17 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → movie encode failure |
comment:2 by , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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ffmpeg reports "conversion failed". ChimeraX 1.5.