![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Last modified 5 months ago
#17722 assigned defect
Linux: Could not find ffmpeg executable
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | Tom Goddard, Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-59-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.10rc202505160006 (2025-05-16 00:06:03 UTC)
Description
An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: -1 Error message: Could not find ffmpeg executable at ffmpeg -----------------------------
Log:
UCSF ChimeraX version: 1.10rc202505160006 (2025-05-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /home/csylab/Desktop/etest.cxs format session
Log from Mon May 19 14:17:51 2025UCSF ChimeraX version: 1.10rc202505150242
(2025-05-15)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /home/csylab/Desktop/etest.cxs
Log from Mon May 19 13:21:17 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\aden6\Desktop\conformationalIIIIII.cxs format session
Log from Sun May 18 13:44:33 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5ftj
Summary of feedback from opening 5ftj fetched from pdb
---
notes | Fetching compressed mmCIF 5ftj from http://files.rcsb.org/download/5ftj.cif
Fetching CCD OJA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/OJA/OJA.cif
5ftj title:
Cryo-EM structure of human p97 bound to UPCDC30245 inhibitor [more info...]
Chain information for 5ftj #1
---
Chain | Description | UniProt
A B C D E F | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | TERA_HUMAN 1-806
Non-standard residues in 5ftj #1
---
ADP — adenosine-5'-diphosphate
OJA — 1-(3-(5-fluoro-1H-indol-2-yl)phenyl)piperidin-4-yl)(2-(4-isopropyl-
PIPERAZIN1-yl)ethyl)-carbamate
> select :OJA
204 atoms, 228 bonds, 6 residues, 1 model selected
> select :ADP
324 atoms, 348 bonds, 12 residues, 1 model selected
> select all
34602 atoms, 35082 bonds, 6 pseudobonds, 4476 residues, 2 models selected
> show sel cartoons
> style sel sphere
Changed 34602 atom styles
> style sel sphere
Changed 34602 atom styles
> style sel stick
Changed 34602 atom styles
> show sel cartoons
> hide sel atoms
> ~select
Nothing selected
> select :adp
324 atoms, 348 bonds, 12 residues, 1 model selected
> select :adp,oja
528 atoms, 576 bonds, 18 residues, 1 model selected
> style sel sphere
Changed 528 atom styles
> show sel atoms
> ~select
Nothing selected
> select :mg
Nothing selected
> style sphere
Changed 34602 atom styles
> show atoms
> undo
> select all
34602 atoms, 35082 bonds, 6 pseudobonds, 4476 residues, 2 models selected
> color
> close
> open 5FTL
Summary of feedback from opening 5FTL fetched from pdb
---
note | Fetching compressed mmCIF 5ftl from http://files.rcsb.org/download/5ftl.cif
5ftl title:
Cryo-EM structure of human p97 bound to ATPgS (Conformation I) [more info...]
Chain information for 5ftl #1
---
Chain | Description | UniProt
A B C D E F | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | TERA_HUMAN 1-806
Non-standard residues in 5ftl #1
---
ADP — adenosine-5'-diphosphate
> open 5FTm
Summary of feedback from opening 5FTm fetched from pdb
---
notes | Fetching compressed mmCIF 5ftm from http://files.rcsb.org/download/5ftm.cif
Fetching CCD AGS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/AGS/AGS.cif
5ftm title:
Cryo-EM structure of human p97 bound to ATPgS (Conformation II) [more info...]
Chain information for 5ftm #2
---
Chain | Description | UniProt
A B C D E F | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | TERA_HUMAN 1-806
Non-standard residues in 5ftm #2
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> open 5FTn
Summary of feedback from opening 5FTn fetched from pdb
---
note | Fetching compressed mmCIF 5ftn from http://files.rcsb.org/download/5ftn.cif
5ftn title:
Cryo-EM structure of human p97 bound to ATPgS (Conformation III) [more
info...]
Chain information for 5ftn #3
---
Chain | Description | UniProt
A B C D E F | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | TERA_HUMAN 1-806
Non-standard residues in 5ftn #3
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> select ~sel
103788 atoms, 105510 bonds, 36 pseudobonds, 13182 residues, 7 models selected
> mmaker #3 to #21
No 'to' model specified
> mmaker #3 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 5ftl, chain A (#1) with 5ftn, chain A (#3), sequence alignment
score = 3595.8
RMSD between 366 pruned atom pairs is 1.144 angstroms; (across all 723 pairs:
12.663)
> mmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 5ftl, chain A (#1) with 5ftm, chain A (#2), sequence alignment
score = 3668.4
RMSD between 516 pruned atom pairs is 1.022 angstroms; (across all 723 pairs:
1.884)
> select all
103788 atoms, 105510 bonds, 36 pseudobonds, 13182 residues, 7 models selected
> hide sel atoms
> hide sel cartoons
> select /a
17298 atoms, 17585 bonds, 6 pseudobonds, 2197 residues, 7 models selected
> show sel atoms
> show sel cartoons
> style sel sphere
Changed 17298 atom styles
> style sel stick
Changed 17298 atom styles
> hide sel atoms
> show sel cartoons
> select :Adp
486 atoms, 522 bonds, 18 residues, 2 models selected
> style sel sphere
Changed 486 atom styles
> show sel atoms
> hide sel atoms
> select /a:Adp
81 atoms, 87 bonds, 3 residues, 2 models selected
> show sel atoms
> select :MG
18 atoms, 18 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select /a:Adp, mg, ags
177 atoms, 186 bonds, 2 pseudobonds, 9 residues, 4 models selected
> show sel atoms
> select ~sel & ##selected
103611 atoms, 105324 bonds, 34 pseudobonds, 13173 residues, 7 models selected
> select /a:Adp, mg, ags,oja
177 atoms, 186 bonds, 2 pseudobonds, 9 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 177 atom styles
> style sel sphere
Changed 177 atom styles
> select :oja
Nothing selected
> select :OJA
Nothing selected
> show atoms
> undo
> select :AGS
558 atoms, 594 bonds, 18 residues, 2 models selected
> select :ADP
486 atoms, 522 bonds, 18 residues, 2 models selected
> select :AGS
558 atoms, 594 bonds, 18 residues, 2 models selected
> select :OJA
Nothing selected
> select :OJA
Nothing selected
> select :OJA
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select /a:2-187
4052 atoms, 4115 bonds, 510 residues, 3 models selected
> color cyna
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color blue
> color sel blue
[Repeated 2 time(s)]
> select /a:209-462
5895 atoms, 5985 bonds, 762 residues, 3 models selected
> select /a:483-763
6132 atoms, 6234 bonds, 3 pseudobonds, 783 residues, 6 models selected
> color sel purple
> ~select
Nothing selected
> mohpy
Unknown command: mohpy
> mohp
Unknown command: mohp
> morph
Missing or invalid "structures" argument: empty atom specifier
> morph #1/a to #2/a to #3/q
Expected a keyword
> morph #1/a to #2/a to #3/a
Expected a keyword
> morph #1,2,3 frames 30
Computed 61 frame morph #4
> coordset #4 1,61
> show #!4 atoms
> show #!4 cartoons
> hide #!4 cartoons
> show #!4 cartoons
> hide #!4 atoms
> select 2-187
Expected an objects specifier or a keyword
> select :2-187
32250 atoms, 32754 bonds, 4062 residues, 4 models selected
> color sel cyna
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel cyan
> ~select
Nothing selected
> spilt
Unknown command: spilt
> spilt
Unknown command: spilt
> split
Split 5ftl (#1) into 6 models
Split 5ftm (#2) into 6 models
Split 5ftn (#3) into 6 models
Split Morph - 5ftl (#4) into 6 models
Chain information for 5ftl A #1.1
---
Chain | Description
A | No description available
Chain information for 5ftl B #1.2
---
Chain | Description
B | No description available
Chain information for 5ftl C #1.3
---
Chain | Description
C | No description available
Chain information for 5ftl D #1.4
---
Chain | Description
D | No description available
Chain information for 5ftl E #1.5
---
Chain | Description
E | No description available
Chain information for 5ftl F #1.6
---
Chain | Description
F | No description available
Chain information for 5ftm A #2.1
---
Chain | Description
A | No description available
Chain information for 5ftm B #2.2
---
Chain | Description
B | No description available
Chain information for 5ftm C #2.3
---
Chain | Description
C | No description available
Chain information for 5ftm D #2.4
---
Chain | Description
D | No description available
Chain information for 5ftm E #2.5
---
Chain | Description
E | No description available
Chain information for 5ftm F #2.6
---
Chain | Description
F | No description available
Chain information for 5ftn A #3.1
---
Chain | Description
A | No description available
Chain information for 5ftn B #3.2
---
Chain | Description
B | No description available
Chain information for 5ftn C #3.3
---
Chain | Description
C | No description available
Chain information for 5ftn D #3.4
---
Chain | Description
D | No description available
Chain information for 5ftn E #3.5
---
Chain | Description
E | No description available
Chain information for 5ftn F #3.6
---
Chain | Description
F | No description available
Chain information for Morph - 5ftl A #4.1
---
Chain | Description
A | No description available
Chain information for Morph - 5ftl B #4.2
---
Chain | Description
B | No description available
Chain information for Morph - 5ftl C #4.3
---
Chain | Description
C | No description available
Chain information for Morph - 5ftl D #4.4
---
Chain | Description
D | No description available
Chain information for Morph - 5ftl E #4.5
---
Chain | Description
E | No description available
Chain information for Morph - 5ftl F #4.6
---
Chain | Description
F | No description available
> select :209-462
47160 atoms, 47880 bonds, 6096 residues, 24 models selected
> color sel light grey
> color sel grey
> color #1.2 #a1a1a1ff
> color #1.2 #868686ff
> color #1.2 #888888ff
> color sel #888888
> color sel :481-763
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select :481-763
49344 atoms, 50160 bonds, 24 pseudobonds, 6312 residues, 48 models selected
> color #1.1 #80006fff
> color #1.1 #ef00cfff
> color sel #ef00cf
> select :188-208, 463-480
7392 atoms, 7464 bonds, 936 residues, 24 models selected
> color sel light gray
> ~select
Nothing selected
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!4.1 models
> show #!4.1 models
> ui windowfill toggle
[Repeated 1 time(s)]
> hide #!4 models
> hide #!3 models
> show #!3 models
> select #1,2,3
103788 atoms, 105510 bonds, 36 pseudobonds, 13182 residues, 45 models selected
> show #!4 models
> select add #4
137700 atoms, 139974 bonds, 42 pseudobonds, 17520 residues, 58 models selected
> show sel & #!4.1-6 atoms
> show sel & #!4.1-6 cartoons
> view
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> delete #4
> hide #4 models
> show #4 models
> hide #!3 models
> show #!3 models
> show #!3.1 models
> show #!3.2 models
> show #!3.3 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.5 models
> show #!3.4 models
> show sel & #!3.1-5 atoms
> select all
103788 atoms, 105510 bonds, 36 pseudobonds, 13182 residues, 46 models selected
> show sel & #!3.1-5 atoms
> show sel & #!3.1-5 cartoons
> style sel & #!3.1-5 sphere
Changed 29130 atom styles
> show #!3.6 models
> show sel & #!3.1-6 atoms
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!1.6 models
> show #!2 models
> show #!3 models
> style sel & #!1.1-6#!3.1-6 sphere
Changed 69234 atom styles
> show sel & #!1.1-6#!3.1-6 cartoons
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.1 models
> show #!2.3 models
> show #!2.4 models
> show #!2.5 models
> show #!2.6 models
> show #!3 models
> hide #!3 models
> show sel & #!2.1-6 atoms
> style sel & #!2.1-6 sphere
Changed 34554 atom styles
> select all
103788 atoms, 105510 bonds, 36 pseudobonds, 13182 residues, 46 models selected
> show sel & #!2.1-6 atoms
> hide sel & #!2.1-6 atoms
> show sel & #!2.1-6 atoms
> style sel & #!2.1-6 sphere
Changed 34554 atom styles
> hide sel & #!2.1-6 atoms
> show sel & #!2.1-6 atoms
> ~select
Nothing selected
> morph #1 to #2
Expected a keyword
> morph #1 #2
Computed 551 frame morph #5
> coordset #5 1,551
> show #!1 models
> show #!2.1 models
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> show #!2.5 models
> delete all
> show #3 models
> hide atoms
> color
> close
> open 5ftl 5ftm 5ftn
5ftl title:
Cryo-EM structure of human p97 bound to ATPgS (Conformation I) [more info...]
Chain information for 5ftl #1
---
Chain | Description | UniProt
A B C D E F | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | TERA_HUMAN 1-806
Non-standard residues in 5ftl #1
---
ADP — adenosine-5'-diphosphate
5ftm title:
Cryo-EM structure of human p97 bound to ATPgS (Conformation II) [more info...]
Chain information for 5ftm #2
---
Chain | Description | UniProt
A B C D E F | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | TERA_HUMAN 1-806
Non-standard residues in 5ftm #2
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
5ftn title:
Cryo-EM structure of human p97 bound to ATPgS (Conformation III) [more
info...]
Chain information for 5ftn #3
---
Chain | Description | UniProt
A B C D E F | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | TERA_HUMAN 1-806
Non-standard residues in 5ftn #3
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> mmaker #3 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 5ftl, chain A (#1) with 5ftn, chain A (#3), sequence alignment
score = 3595.8
RMSD between 366 pruned atom pairs is 1.144 angstroms; (across all 723 pairs:
12.663)
> mmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 5ftl, chain A (#1) with 5ftm, chain A (#2), sequence alignment
score = 3668.4
RMSD between 516 pruned atom pairs is 1.022 angstroms; (across all 723 pairs:
1.884)
> select #2 -187
Expected a keyword
> select 2 -187
Expected an objects specifier or a keyword
> select :2-187
24312 atoms, 24690 bonds, 3060 residues, 3 models selected
> color sel cyan
> save C:/Users/aden6/Desktop/conformationalIIIIII.cxs
——— End of log from Sun May 18 13:44:33 2025 ———
opened ChimeraX session
> toolshed show
> ui tool show "Task Manager"
> present "molecular surfaces" "atomic coloring (transparent)")
Unknown command: present "molecular surfaces" "atomic coloring (transparent)")
> present "molecular surfaces" "atomic coloring (transparent)"
Unknown command: present "molecular surfaces" "atomic coloring (transparent)"
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 102726 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> show sel cartoons
> hide sel atoms
> select all
103788 atoms, 105510 bonds, 36 pseudobonds, 13182 residues, 7 models selected
> hide sel atoms
> show sel cartoons
> select :209-462
35370 atoms, 35910 bonds, 4572 residues, 3 models selected
> ui tool show "Color Actions"
> color sel light green
> color sel dark gray
> color sel gray
> color sel dim gray
> color sel aquamarine
> color sel slate gray
> select :481-763
37008 atoms, 37620 bonds, 18 pseudobonds, 4734 residues, 6 models selected
> ui tool show "Color Actions"
> color sel gray
> color sel gainsboro
> color sel plum
> ~select
Nothing selected
> select :188-208, 463-480, 764-806
6036 atoms, 6090 bonds, 762 residues, 3 models selected
> color (#!1-3 & sel) light sea green
> color (#!1-3 & sel) gray
> color (#!1-3 & sel) light gray
> ~select
Nothing selected
> select :ADP, AGS, MG
1062 atoms, 1116 bonds, 12 pseudobonds, 54 residues, 4 models selected
> style sel sphere
Changed 1062 atom styles
> show sel atoms
> color byatoms
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color byatom
> color sel byatom
> ~select
Nothing selected
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> morph
Missing or invalid "structures" argument: empty atom specifier
> morph #1,2,3 frames 30
Computed 61 frame morph #4
> coordset #4 1,61
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> preset #4 "molecular surfaces" "atomic coloring (transparent)"
No preset name matches '#4 molecular surfaces" "atomic coloring (transparent)'
> preset "#4 molecular surfaces" "atomic coloring (transparent)"
No preset name matches '#4 molecular surfaces atomic coloring (transparent)'
> preset "molecular surfaces" #4 "atomic coloring (transparent)"
No preset name in category 'Molecular Surfaces' matches '#4 "atomic coloring
(transparent)"'
> preset "#4 molecular surfaces" "atomic coloring (transparent)"
No preset name matches '#4 molecular surfaces atomic coloring (transparent)'
> hide #!1 models
> morph #1,2
Computed 51 frame morph #5
> coordset #5 1,51
> hide #!4 models
> set bgColor white
> movie record
> movie encode C:\Users\aden6\Desktop\movie1.mp4 framerate 25.0
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> preset apply #4 molecular surfaces "atomic coloring (transparent)"
No preset name matches 'apply #4 molecular surfaces "atomic coloring
(transparent)"'
> preset apply #4 "molecular surfaces" "atomic coloring (transparent)"
No preset name matches 'apply #4 "molecular surfaces" "atomic coloring
(transparent)"'
> preset #4 "molecular surfaces" "atomic coloring (transparent)"
No preset name matches '#4 molecular surfaces" "atomic coloring (transparent)'
> preset "molecular surfaces" "atomic coloring (transparent)" #4
No preset name in category 'Molecular Surfaces' matches '"atomic coloring
(transparent)" #4'
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 12 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> save C:/Users/aden6/Desktop/etest.cxs
——— End of log from Mon May 19 13:21:17 2025 ———
> view name session-start
opened ChimeraX session
> show #!1 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> view
> view orient
[Repeated 1 time(s)]
> view
[Repeated 1 time(s)]
> view orient
[Repeated 1 time(s)]
> view
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting soft
> view
> turn x 90
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> select add #4
33912 atoms, 34464 bonds, 6 pseudobonds, 4338 residues, 2 models selected
> select add #5
67866 atoms, 68970 bonds, 12 pseudobonds, 8676 residues, 10 models selected
> hide #!1 models
> select #4,5
67866 atoms, 68970 bonds, 12 pseudobonds, 8676 residues, 4 models selected
> show #!4 models
> show #!5 models
> delete sel
> show #!1 models
> view name p1
> turn x 90
> view name p2
> select :2-187
24312 atoms, 24690 bonds, 3060 residues, 3 models selected
> hide
> hide sel
> select :2-187
24312 atoms, 24690 bonds, 3060 residues, 3 models selected
> hide sel
> select #1:2-187
7980 atoms, 8106 bonds, 1002 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> undo
[Repeated 3 time(s)]
> show sel & #!1 surfaces
> ~select
Nothing selected
> turn z 180
> turn y 180
> view name p3
> select #1:2-187
7980 atoms, 8106 bonds, 1002 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> turn y 180
> view name p4
> turn x 90
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> select #1:2-187
7980 atoms, 8106 bonds, 1002 residues, 1 model selected
> hide #!1 models
> hide #!2 models
> show #!1 models
> view name p5
> fly p1 p2
> show sel cartoons
> show sel surfaces
> ~select
Nothing selected
> fly p2 p3
> fly p3 p4
> fly p1
> movie record
> fly p1 p2
> fly p2 p3
> crossfade
> hide #1:2-187
> crossfade
> hide ~#1:2-187
> hide #1:2-187
> select #1:2-187
7980 atoms, 8106 bonds, 1002 residues, 1 model selected
> hide sel surfacce cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel surfacce, cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel surfaces, cartoons
> fly p3 p4
> fly p4 p5
> show sel cartoons
> show sel surfaces
> movie encode test.mp4
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: -1
Error message:
Could not find ffmpeg executable at ffmpeg
\-----------------------------
> movie encode /home/csylab/Desktop/test.mp4
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: -1
Error message:
Could not find ffmpeg executable at ffmpeg
\-----------------------------
> movie encode /home/csylab/Desktop/test.mpge
Unrecognized movie file suffix test.mpge, use *.mp4, *.mov, *.wmv, *.ogv,
*.png, *.webm, *.avi
> movie encode /home/csylab/Desktop/test.mp4
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: -1
Error message:
Could not find ffmpeg executable at ffmpeg
\-----------------------------
> movie encode /home/csylab/home/csylab/Desktop/test.mp4
Output directory does not exist: /home/csylab/home/csylab/Desktop
> movie encode
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: -1
Error message:
Could not find ffmpeg executable at ffmpeg
\-----------------------------
> movie encode
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: -1
Error message:
Could not find ffmpeg executable at ffmpeg
\-----------------------------
> save /home/csylab/Desktop/etest.cxs
——— End of log from Mon May 19 14:17:51 2025 ———
> view name session-start
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /home/csylab/Desktop/movie1.mp4
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: -1
Error message:
Could not find ffmpeg executable at ffmpeg
\-----------------------------
OpenGL version: 3.3.0 NVIDIA 535.230.02
OpenGL renderer: NVIDIA GeForce RTX 4060 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 Intel(R) Core(TM) i9-10900 CPU @ 2.80GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 6.4Gi 41Gi 208Mi 14Gi 55Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2805] (rev a1)
Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:5174]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.3
build: 1.2.2.post1
certifi: 2025.4.26
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.6
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505160006
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (3)
comment:1 by , 5 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Linux: Could not find ffmpeg executable |
comment:2 by , 5 months ago
I'll look into why ffmpeg is missing. You can solve the problem immediately with "apt install ffpmeg" as root.
comment:3 by , 5 months ago
How did you install ChimeraX? If you used "apt install", it should have installed ffpmeg as well.
Note:
See TracTickets
for help on using tickets.
Reported by Li guan-Yi