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Opened 2 years ago
Closed 2 years ago
#9196 closed defect (not a bug)
Movie duplicate: No such file or directory
| 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: Windows-10-10.0.22621
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Work\JHR\new_figure5\ct4_details.cxs format session
Log from Fri Feb 10 16:46:19 2023You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> pwd
Current working directory is: C:\ProgramData\ChimeraX
> cd ~/C:/work
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd C:
Current working directory is: C:\ProgramData\ChimeraX
> cd ../
Current working directory is: C:\ProgramData
> ls
Unknown command: ls
> cd ../
Current working directory is: C:\
> ls
Unknown command: ls
> cd work
Current working directory is: C:\work
> cd JHR
Current working directory is: C:\work\JHR
> cd new_figure5
Current working directory is: C:\work\JHR\new_figure5
> load final.mmcif
Unknown command: load final.mmcif
> open final.mmcif
Summary of feedback from opening final.mmcif
---
warnings | Unknown polymer entity '1' near line 52
Unknown polymer entity '2' near line 1748
Atom H is not in the residue template for GLY /AAA:23
Atom H is not in the residue template for MET /BBB:45
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
note | Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Chain information for final.mmcif #1
---
Chain | Description
AAA | No description available
BBB | No description available
> open WYTG2C4VC93F.pdb
No such file/path: WYTG2C4VC93F.pdb
> open WYTG2C4VC93F3.pdb
Summary of feedback from opening WYTG2C4VC93F3.pdb
---
warnings | Ignored bad PDB record found on line 3295
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 3296
#BEGIN_POSE_ENERGIES_TABLE fixed_WTGFBRIIC4_fixed.pdb
Ignored bad PDB record found on line 3297
label fa_atr fa_rep fa_sol fa_intra_atr_xover4 fa_intra_rep_xover4
fa_intra_sol_xover4 lk_ball lk_ball_iso lk_ball_bridge lk_ball_bridge_uncpl
fa_elec fa_intra_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc
dslf_fa13 omega fa_dun_dev fa_dun_rot fa_dun_semi p_aa_pp hxl_tors ref
rama_prepro total
Ignored bad PDB record found on line 3298
weights 1 0.55 1 1 0.55 1 0.92 -0.38 -0.33 -0.33 1 1 1.25 1 1 1 1 1.25 0.48
0.69 0.76 0.78 0.61 1 1 0.5 NA
Ignored bad PDB record found on line 3299
pose -1202.93 2854.76 898.023 -63.2206 26.7073 41.0703 483.01 -483.268
-1.12393 -7.66925 -343.142 -46.792 14.1019 -102.349 -43.1923 -20.5143 -4.40426
0 31.8132 25.2551 121.602 174.443 -28.1602 64.1792 -55.0514 55.4111 2388.56
209 messages similar to the above omitted
Chain information for WYTG2C4VC93F3.pdb #2
---
Chain | Description
A | No description available
B | No description available
> align #2:/b toAtoms #1:/b
Missing or invalid "atoms" argument: only initial part "#2" of atom specifier
valid
> align #2/b toAtoms #1/b
Unequal number of atoms to pair, 1651 and 0
> close
> open tg2_crystal.pdb
Chain information for tg2_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> load tg2_design.pdb
Unknown command: load tg2_design.pdb
> open tg2_design.pdb
Chain information for tg2_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 81.2,88.6,94.9
> color #2/b 93.7,93.7,93.7
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 70.3,65.23,83.9
> color #2/b 93.7,93.7,93.7
> save tg2_align.tif width 1200 height 1200 supersample 9
> transparentBackground true
> save C:/Work/JHR/new_figure5/tg2_align.cxs
> close
> open ct4_crystal.pdb
Chain information for ct4_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open ct4_design.pdb
Chain information for ct4_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 70.3,65.23,83.9
> color #2/b 93.7,93.7,93.7
> save ct4_align.tif width 1200 height 1200 supersample 9
> transparentBackground true
> save C:/Work/JHR/new_figure5/ct4_align.cxs
> close
> open tg2_crystal.pdb
Chain information for tg2_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open tg2_design.pdb
Chain information for tg2_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 70.3,65.23,83.9
> color #2/b 93.7,93.7,93.7
> hide /b cartoons
> show /b surfaces
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 70.3,65.23,83.9
> color #2/b 93.7,93.7,93.7
> hide /b surfaces
> surface #1/b
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 70.3,65.23,83.9
> color #2/b 93.7,93.7,93.7
> cartoon style helix width 1.5 thickness 0.3
> cartoon style helix width 1 thickness 0.3
> cartoon style helix width 1 thickness 0.5
> cartoon style helix width 0.5 thickness 0.5
> cartoon style helix width 0.5 thickness 0.3
> interfaces ~solvent
6 buried areas: #1/B #2/B 3140, #2/A #1/A 2977, #1/B #2/A 858, #2/B #2/A 853,
#1/B #1/A 821, #2/B #1/A 800
> select
3300 atoms, 3338 bonds, 420 residues, 2 models selected
> select #1/b:<5
2066 atoms, 2073 bonds, 263 residues, 2 models selected
> show sel atoms
> color sel byhetero
> show sel atoms
> hide #2 atoms
> ~surface #2
> close
> color sel byhetero
> show sel atoms
> hide #2 atoms
> open tg2_crystal.pdb
Chain information for tg2_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open tg2_design.pdb
Chain information for tg2_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 70.3,65.23,83.9
> color #2/b 93.7,93.7,93.7
> cartoon style helix width 0.5 thickness 0.3
> select /b:<5 & /a
359 atoms, 333 bonds, 48 residues, 2 models selected
> show sel atoms
> color sel byhetero
> hide cartoons /b
Expected ',' or a keyword
> hide /b cartoons
> surface #1/b
> color #1/b 91.37,86.2,84.31
> ~select
Nothing selected
> select add #2/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:84
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> cartoon style helix width 0.3 thickness 0.3
> atom style sphere
Unknown command: atom style sphere
> styple
Unknown command: styple
> style
> style atom sphere
Expected a keyword
> style sel sphere
Changed 17 atom styles
> style sel ball
Changed 17 atom styles
> style sel ball
Changed 17 atom styles
> style sel ball
Changed 17 atom styles
> style sel ball
Changed 17 atom styles
> style sel sphere
Changed 17 atom styles
> style sel sphere
Changed 17 atom styles
> style sel stick
Changed 17 atom styles
> style sel ball
Changed 17 atom styles
> style sel sphere
Changed 17 atom styles
> style sel stick
Changed 17 atom styles
> setattr b radius 0.25 @n,ca, c,o
Expected a keyword
> setattr b radius 0.25 #1/a@n,ca, c,o
Expected a keyword
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> select add #1/B:81@OE1
18 atoms, 15 bonds, 3 residues, 2 models selected
> select up
26 atoms, 23 bonds, 3 residues, 3 models selected
> select up
193 atoms, 192 bonds, 25 residues, 3 models selected
> select up
1671 atoms, 1691 bonds, 212 residues, 3 models selected
> select down
193 atoms, 192 bonds, 25 residues, 3 models selected
> select down
26 atoms, 23 bonds, 3 residues, 3 models selected
> select down
18 atoms, 15 bonds, 3 residues, 3 models selected
> select up
26 atoms, 23 bonds, 3 residues, 3 models selected
> select up
193 atoms, 192 bonds, 25 residues, 3 models selected
> select add #1/B:89@NH1
194 atoms, 192 bonds, 26 residues, 3 models selected
> select #1/B:109@ND1
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> select up
167 atoms, 172 bonds, 21 residues, 2 models selected
> select up
884 atoms, 902 bonds, 111 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for tg2_crystal.pdb_B SES surface #1.1: minimum, -14.05, mean
-2.38, maximum 11.18
To also show corresponding color key, enter the above coulombic command and
add key true
> close
> open tg2_crystal.pdb
Chain information for tg2_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open tg2_design.pdb
Chain information for tg2_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 21.8,46.1,11.3
> color #1/b 71.5,71.5,71.5
> color #2/a 70.3,65.23,83.9
> color #2/b 93.7,93.7,93.7
> cartoon style helix width 0.5 thickness 0.3
> select #1/b:<5 & /a
340 atoms, 313 bonds, 45 residues, 2 models selected
> select #1/b:<5 & /a
340 atoms, 313 bonds, 45 residues, 2 models selected
> show sel atoms
> color sel byhetero
> coulombic #1/b
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for tg2_crystal.pdb_B SES surface #1.1: minimum, -14.05, mean
-2.38, maximum 11.18
> hide cartoons /b
Expected ',' or a keyword
> hide /b cartoons
> color #1/a 63.92,77.65,48.63
> color #1/b 71.5,71.5,71.5
> color #2/a 43.5,65.9,86.3
> color #2/b 93.7,93.7,93.7
> select #1/b:<5 & /a
340 atoms, 313 bonds, 45 residues, 2 models selected
> show sel atoms
> color sel byhetero
> coulombic #1/b
Coulombic values for tg2_crystal.pdb_B SES surface #1.1: minimum, -14.05, mean
-2.38, maximum 11.18
> hide /b cartoons
> ~select
Nothing selected
> close
> open tg2_crystal.pdb
Chain information for tg2_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open tg2_design.pdb
Chain information for tg2_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 63.92,77.65,48.63
> color #1/b 71.5,71.5,71.5
> color #2/a 43.5,65.9,86.3
> color #2/b 93.7,93.7,93.7
> cartoon style helix width 0.5 thickness 0.3
> select #1/b:<5 & /a
340 atoms, 313 bonds, 45 residues, 2 models selected
> select add #2/A:83
348 atoms, 320 bonds, 46 residues, 2 models selected
> show sel atoms
> color sel byhetero
> coulombic #1/b
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for tg2_crystal.pdb_B SES surface #1.1: minimum, -14.05, mean
-2.38, maximum 11.18
> hide /b cartoons
> ~select
Nothing selected
> save tg2_side_chain.tif width 1200 height 1200 supersample 9
> transparentBackground true
> save C:/Work/JHR/new_figure5/tg2_details.cxs
> close
> open tg2_crystal.pdb
Chain information for tg2_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open tg2_design.pdb
Chain information for tg2_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 63.92,77.65,48.63
> color #1/b 71.5,71.5,71.5
> color #2/a 43.5,65.9,86.3
> color #2/b 93.7,93.7,93.7
> save tg2_align_side_view.tif width 1200 height 1200 supersample 9
> transparentBackground true
> save tg2_align_top_view.tif width 1200 height 1200 supersample 9
> transparentBackground true
> close
> open ct4_crystal.pdb
Chain information for ct4_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open ct4_design.pdb
Chain information for ct4_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 63.92,77.65,48.63
> color #1/b 71.5,71.5,71.5
> color #2/a 43.5,65.9,86.3
> color #2/b 93.7,93.7,93.7
> save ct4_align_top_view.tif width 1200 height 1200 supersample 9
> transparentBackground true
> save ct4_align_side_view.tif width 1200 height 1200 supersample 9
> transparentBackground true
> close
> open ct4_crystal.pdb
Chain information for ct4_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open ct4_design.pdb
Chain information for ct4_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide atoms
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/a 63.92,77.65,48.63
> color #1/b 71.5,71.5,71.5
> color #2/a 43.5,65.9,86.3
> color #2/b 93.7,93.7,93.7
> cartoon style helix width 0.5 thickness 0.3
> select #1/b:<5 & /a
398 atoms, 387 bonds, 46 residues, 2 models selected
> show sel atoms
> color sel byhetero
> coulombic #1/b
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for ct4_crystal.pdb_B SES surface #1.1: minimum, -12.54, mean
-2.24, maximum 8.52
> hide /b cartoons
> ~select
Nothing selected
> select #1/b:<5 & /a
398 atoms, 387 bonds, 46 residues, 2 models selected
> select add #2/A:101
407 atoms, 395 bonds, 47 residues, 2 models selected
> select add #1/A:84
416 atoms, 403 bonds, 48 residues, 2 models selected
> show sel atoms
> color sel byhetero
> coulombic #1/b
Coulombic values for ct4_crystal.pdb_B SES surface #1.1: minimum, -12.54, mean
-2.24, maximum 8.52
> hide /b cartoons
> ~select
Nothing selected
> select add #1/A:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/A:64
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #1/A:46
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #2/A:22
31 atoms, 27 bonds, 4 residues, 2 models selected
> select /a:22-46，64-83
Expected an objects specifier or a keyword
> select /a:22-46，/a:64-83
Expected an objects specifier or a keyword
> select /a:22-46 /a:64-83
774 atoms, 782 bonds, 90 residues, 2 models selected
> hide sel cartoons
> save ct4_side_chain.tif width 1200 height 1200 supersample 9
> transparentBackground true
> save C:/Work/JHR/new_figure5/ct4_details.cxs
——— End of log from Fri Feb 10 16:46:19 2023 ———
opened ChimeraX session
> show cartoons #1/a
Expected ',' or a keyword
> close
> open C:/Work/JHR/new_figure5/ct4_crystal.pdb
Chain information for ct4_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open C:/Work/JHR/new_figure5/ct4_design.pdb
Chain information for ct4_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> color #1/b 91.37,86.2,84.31
> color #2/b 93.7,93.7,93.7
> select H
Nothing selected
> delete atoms sel
> delete bonds sel
> color #2/a 43.5,65.9,86.3
> color #1/a 63.92,77.65,48.63
> select #1/a:89,90,92,93,96
38 atoms, 35 bonds, 5 residues, 1 model selected
> color sel byhetero
> show sel atoms
> color sel 63.92,77.65,48.63 atoms
> color sel byhetero
> name frozen interfaceA sel
> select sel:<6 & #1/b
84 atoms, 77 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel 91.37,86.2,84.31 atoms
> color sel byhetero
> name frozen interfaceB sel
> select #2/a:89,90,92,93,96
38 atoms, 35 bonds, 5 residues, 1 model selected
> color sel byhetero
> show sel atoms
> color sel 43.5,65.9,86.3 atoms
> color sel byhetero
> name frozen interfaceA sel
> select sel:<6 & #2/b
96 atoms, 91 bonds, 12 residues, 1 model selected
> show sel atoms
> color sel 93.7,93.7,93.7 atoms
> color sel byhetero
> name frozen interfaceB sel
> close
> open C:/Work/JHR/new_figure5/ct4_crystal.pdb
Chain information for ct4_crystal.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open C:/Work/JHR/new_figure5/ct4_design.pdb
Chain information for ct4_design.pdb #2
---
Chain | Description
A | No description available
B | No description available
> open ct4_design.pdb
No such file/path: ct4_design.pdb
> lighting gentle
> set bgColor white
> set silhouettes true
> set silhouetteDepthJump 0.02
> pwd
Current working directory is: C:\ProgramData\ChimeraX
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> cd C:/Work
Current working directory is: C:\Work
> cd application
Current working directory is: C:\Work\application
> cd seminar
Current working directory is: C:\Work\application\seminar
> pwd
Current working directory is: C:\Work\application\seminar
> open ct4_design.pdb
No such file/path: ct4_design.pdb
> color #1/b 91.37,86.2,84.31
> color #2/b 93.7,93.7,93.7
> select H
Nothing selected
> delete atoms sel
> delete bonds sel
> color #2/a 43.5,65.9,86.3
> color #1/a 63.92,77.65,48.63
> view name p1
> turn x 90
> view name p2
> select /a:11,15,18,19
72 atoms, 70 bonds, 8 residues, 2 models selected
> name frozen IH1 sel
> size sel stickRadius +0.08
Changed 70 bond radii
> color IH1 byhetero
> select IH1:<6 & /b
230 atoms, 232 bonds, 26 residues, 2 models selected
> name frozen IH1_interface
Missing or invalid "objects" argument: empty atom specifier
> name frozen IH1_interface sel
> size sel stickRadius +0.08
Changed 232 bond radii
> cartoon style width 1.5 thickness 0.3
> ~select
Nothing selected
> view
> view name p1
> turn x 90
> view name p2
> zoom 1.5
> view name p3
> show IH1 atoms
> zoom 2
> zoom 1.5
> turn x 90
> view name p4
> show IH1 atoms
> show IH1_interface atoms
> color IH1_interface atoms byhetero
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color IH1_interface byhetero
> ui tool show H-Bonds
> hbonds IH1 restrict cross IH1_interface reveal t
Expected a keyword
> hbonds IH1 restrict IH1_interface reveal true
13 hydrogen bonds found
> hbonds IH1 restrict IH1_interface reveal true color indigo
13 hydrogen bonds found
> hbonds IH1 restrict IH1_interface reveal true color rebecca purple
13 hydrogen bonds found
> hbonds IH1 restrict IH1_interface reveal true color yellow green
13 hydrogen bonds found
> hbonds IH1 restrict IH1_interface reveal true color medium orchid
13 hydrogen bonds found
> hbonds IH1 restrict IH1_interface reveal true color medium orchid name
> H1hbond
13 hydrogen bonds found
> hide H1hbond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> close H1hbond
Expected a models specifier or a keyword
> ~display H1hbond
> hide H1hbond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3 models
> hide #4 models
> show #4 models
> hide #4
> show #4
> hide atoms
> hide #4
> move record
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> movie record
> fly p1 p2
> fly p2 p3
> crossfade
> show IH1 atoms
> show IH1_interface atoms
> fly p3 p4
> crossfade
> show #4
> movie encode CT4_H1
Unrecognized movie file suffix CT4_H1, use *.ogv, *.mov, *.mp4, *.png, *.webm,
*.avi, *.wmv
> movie encode CT4_H1.mp4
Movie saved to CT4_H1.mp4
> hide IH1
> hide #4
> hide IH1_interface
> select /a:51,54,55,58
62 atoms, 58 bonds, 8 residues, 2 models selected
> color sel byhetero
> style sel stick
Changed 62 atom styles
> size sel stickRadius +0.08
Changed 58 bond radii
> name frozen IH2
Missing or invalid "objects" argument: empty atom specifier
> name frozen IH2 sel
> select sel:<6 & /b
138 atoms, 132 bonds, 14 residues, 2 models selected
> color sel byhetero
> style sel stick
Changed 138 atom styles
> size sel stickRadius +0.08
Changed 132 bond radii
> name frozen IH2_interface
Missing or invalid "objects" argument: empty atom specifier
> name frozen IH2_interface sel
> hbonds IH2 restrict IH2_interface reveal true color medium orchid name
> H2hbond
8 hydrogen bonds found
> show atoms IH2
Expected ',' or a keyword
> show IH2 atoms
> show IH2_interface atoms
> delete #3
> hide #4 models
> hide #5 models
> hide atoms
> ~select
Nothing selected
> select /a:89,93,94,97,101
78 atoms, 70 bonds, 10 residues, 2 models selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 78 atom styles
> size sel stickRadius +0.08
Changed 70 bond radii
> select sel:<6 & /b
249 atoms, 230 bonds, 32 residues, 2 models selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 249 atom styles
> size sel stickRadius +0.08
Changed 230 bond radii
> name frozen IH3_interface
Missing or invalid "objects" argument: empty atom specifier
> name frozen IH3_interface sel
> hide atoms
> show IH3 atom
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show IH2 atoms
> ~select
Nothing selected
> select /a:89,93,94,97,101
78 atoms, 70 bonds, 10 residues, 2 models selected
> name frozon IH3 sel
"IH3 sel": invalid atom specifier
> name frozen IH3 sel
> hbonds IH3 restrict IH3_interface reveal true color medium orchid name
> H3hbond
10 hydrogen bonds found
> hide #6
> hide atoms
> ~select
Nothing selected
> view
> view name p1
> turn x 90
> turn x -90
[Repeated 1 time(s)]
> view name p2
> zoom 1.75
> view name p3
> show IH1 atoms
> show IH1_interface atoms
> view name p4
> hide #6 models
> show #4
> ~hide #4
Unknown command: ~hide #4
> display #4
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show bonds #4
Expected ',' or a keyword
> show #4 bonds
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> show #4 hbond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #4 hbonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #4
> show #4 atoms
> show #4 bonds
> show #4 pbonds
> show #4 pseudobonds
> show #3 pseudobonds
> show #3
> show #4
> show #5
> show #6
> hide #5
> hide #6
> hide atoms #6
Expected ',' or a keyword
> hide hbonds
> hide atoms
> show IH1 atoms
> show IH1_interface atoms
> show #4
> show #4 models
> hide #4 models
> select add #4
13 pseudobonds, 1 model selected
> show #4 models
> select subtract #4
Nothing selected
> hide #4 target m
> show #4 target m
> hide #4 target m
> show #4 target m
> hide atoms
[Repeated 1 time(s)]
> hide #4 target m
> show IH2 atoms
[Repeated 1 time(s)]
> show IH2_interface atoms
> show #5 targete m
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #5 target m
> show #5
> view name p5
> view name p6
> hide atoms
> hide #5
> view name p7
> show IH3 atoms
> show IH3_interface atoms
> view name p8
> show #6
> show #6 target m
> view name p9
> movie record
> fly p1 p2
> hide atoms
> hide #5
> show #4 models
> select clear
[Repeated 3 time(s)]
> delete sel
> select add #4
13 pseudobonds, 1 model selected
> ~select
Nothing selected
> hide #4 target m
> view
> move record p1 50 p2
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> movie record p1 50 p2
Expected a keyword
> movie record
Already recording a movie
> movie reset
> movie record
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> fly p1 50 p2
> fly p2 p3
> crossfade
> show IH1 atoms
> show IH1_interface atoms
> fly p3 p4
> show #4 target m
> crossfade
> hide atoms
> hide #4 target m
> fly p4 p5
> crossfade
> show IH2 atoms
> show IH2_interface atoms
> fly p5 25 p6
> crossfade
> show #5
> crossfade
> hide atoms
> hide #5
> fly p6 20 p7
> crossfade
> show IH3 atoms
> show IH3_interface atoms
> fly p7 p8
> crossfade
> show #6
> crossfade
> hide atoms
> hide #6
> fly p8 p2
> movie encode CT4_test1
Unrecognized movie file suffix CT4_test1, use *.ogv, *.mov, *.mp4, *.png,
*.webm, *.avi, *.wmv
> movie encode CT4_test1.png
Movie saved to CT4_test1.png
> save C:/Work/application/seminar/ct4_movie.cxs
> movie encode CT4_test1.mp4
No frames have been recorded
> view name p1
> view name p2
> hide #5 models
> hide #6 models
> movie record
> fly p1 25 p2
> fly p2 p3
> crossfade
> show IH1 atoms
> show IH1_interface atoms
> fly p3 p4
> show #4 target m
> crossfade
> hide atoms
> hide #4 target m
> fly p4 p5
> crossfade
> show IH2 atoms
> show IH2_interface atoms
> fly p5 25 p6
> crossfade
> show #5
> crossfade
> hide atoms
> hide #5
> fly p6 20 p7
> crossfade
> show IH3 atoms
> show IH3_interface atoms
> fly p7 p8
> crossfade
> show #6
> crossfade
> hide atoms
> hide #6
> fly p8 p2
> movie encode CT4_test1.mp4
Movie encoding failed because no images were recorded.
> movie record
> fly p1 25 p2
> fly p2 p3
> crossfade
> show IH1 atoms
> show IH1_interface atoms
> fly p3 p4
> show #4 target m
> crossfade
> hide atoms
> hide #4 target m
> fly p4 p5
> crossfade
> show IH2 atoms
> show IH2_interface atoms
> fly p5 25 p6
> crossfade
> show #5
> crossfade
> hide atoms
> hide #5
> fly p6 20 p7
> crossfade
> show IH3 atoms
> show IH3_interface atoms
> fly p7 p8
> crossfade
> show #6
> crossfade
> hide atoms
> hide #6
> fly p8 p2
> movie reset
> movie record
> fly p1 20 p2
> movie reset
> fly p1 20 p1 50 p2
> fly p1 p1 p1 50 p2
> movie reset
No movie being recorded.
> movie record
> fly p1 p1 p1 50 p2
> fly p1 p1 50 p2
> movie reset
> movie record
> fly p1 p1 50 p2
> fly p2 p3
> crossfade
> show IH1 atoms
> show IH1_interface atoms
> fly p3 p4
> crossfade
> show #4 target m
> crossfade
> hide atoms
> hide #4 target m
> fly p4 p5
> crossfade
> show IH2 atoms
> show IH2_interface atoms
> fly p5 25 p6
> crossfade
> show #5
> crossfade
> show #5
> crossfade
> show #5 target m
> crossfade
> hide atoms
> hide #5 target m
> fly p6 20 p7
> crossfade
> show IH3 atoms
> show IH3_interface atoms
> fly p7 p8
> fly p7 crossfade
fly: Unknown position name "crossfade"
> crossfade
> show #6
> crossfade
> show #6 target m
> crossfade
> hide atoms
> hide #6 target m
> fly p8 50 p2
> movie encode CT4_test1.mp4
Movie saved to CT4_test1.mp4
> save C:/Work/application/seminar/ct4_movie.cxs
> movie record
> duplicate
Unknown command: duplicate
> movie duplicate
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\moviecmd.py", line 259, in movie_duplicate
session.movie.postprocess('duplicate', frames)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 289, in postprocess
self.capture_image() # Capture all frames right now.
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 179, in capture_image
self.save_duplicate_images()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 218, in save_duplicate_images
image = Image.open(save_path)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\PIL\Image.py", line
2953, in open
fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\prote\\\AppData\\\Local\\\Temp\\\chimovie_CiHN--0001.ppm'
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\prote\\\AppData\\\Local\\\Temp\\\chimovie_CiHN--0001.ppm'
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\PIL\Image.py", line
2953, in open
fp = builtins.open(filename, "rb")
See log for complete Python traceback.
> movie reset
> move reset
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> movie reset
No movie being recorded.
> fly p1
> movie record
> movie duplicate
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\moviecmd.py", line 259, in movie_duplicate
session.movie.postprocess('duplicate', frames)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 289, in postprocess
self.capture_image() # Capture all frames right now.
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 179, in capture_image
self.save_duplicate_images()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 218, in save_duplicate_images
image = Image.open(save_path)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\PIL\Image.py", line
2953, in open
fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\prote\\\AppData\\\Local\\\Temp\\\chimovie_FU2x--0001.ppm'
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\prote\\\AppData\\\Local\\\Temp\\\chimovie_FU2x--0001.ppm'
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\PIL\Image.py", line
2953, in open
fp = builtins.open(filename, "rb")
See log for complete Python traceback.
> movie reset
> fly p1 30 p2
> fly p2 p3
> crossfade
> show IH1 atoms
> show IH1_interface atoms
> fly p3 p4
> movie duplicate 25
No movie being recorded.
> movie record
> movie duplicate 25
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\moviecmd.py", line 259, in movie_duplicate
session.movie.postprocess('duplicate', frames)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 289, in postprocess
self.capture_image() # Capture all frames right now.
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 179, in capture_image
self.save_duplicate_images()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\movie\movie.py", line 218, in save_duplicate_images
image = Image.open(save_path)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\PIL\Image.py", line
2953, in open
fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\prote\\\AppData\\\Local\\\Temp\\\chimovie_eY80--0001.ppm'
FileNotFoundError: [Errno 2] No such file or directory:
'C:\\\Users\\\prote\\\AppData\\\Local\\\Temp\\\chimovie_eY80--0001.ppm'
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\PIL\Image.py", line
2953, in open
fp = builtins.open(filename, "rb")
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 528.79
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: Alienware
Model: Alienware x15 R2
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 34,015,088,640
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i9-12900H
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Movie duplicate: No such file or directory |
comment:2 by , 2 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
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User tried to duplicate a movie frame before any frame was recorded.
This should raise a UserError. It has been reported once before I think. If it is reported again I will improve the error reporting.