The following bug report has been submitted:
Platform: Windows-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open D:\\\2022\\\manuscripts\\\作图\\\1.cxs
Unable to restore "HKL_data_F_phi_float" object
restore_snapshot for "XmapHandler_Static" returned None
restore_snapshot for "FastVolumeSurface" returned None
[Repeated 1 time(s)]Log from Sun Nov 27 18:16:27 2022UCSF ChimeraX version:
1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\\\2022\\\manuscripts\\\chimeraX\\\new figure\\\atp,amppnp比对口袋5.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Redust" returned None
[Repeated 1 time(s)]Log from Fri Sep 9 11:15:24 2022UCSF ChimeraX version: 1.3
(2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\\\2022\\\manuscripts\\\chimeraX\\\2\\\atp,amppnp比对口袋2.cxs
Opened fadd23_atp_omit_superposed.ccp4 as #3, grid size 93,105,99, pixel
0.836,0.884,0.874, shown at level 2.85e+05, step 1, values float32
Opened fadd23_amppnp_omit_superposed.ccp4 as #4, grid size 115,125,123, pixel
0.72,0.736,0.699, shown at level 6.49e+05, step 1, values float32
Log from Fri May 20 11:20:57 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\\\2022\\\manuscripts\\\chimeraX\\\2\\\atp,amppnp比对.cxs
Log from Thu May 5 16:24:59 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\2022\\\manuscripts\\\chimeraX\\\overall atp.cxs"
Log from Sat Feb 26 15:36:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\2022\\\manuscripts\\\chimeraX\\\overall atp.cxs"
Log from Sun Feb 20 01:14:49 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/2022/manuscripts/chimeraX/4配色.cxs
Log from Sat Feb 19 23:16:45 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/2022/manuscripts/chimeraX/4配色.cxs
Log from Sat Feb 19 23:09:29 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/2022/manuscripts/chimeraX/1配色.cxs
Log from Sat Feb 19 22:01:08 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:\2022\manuscripts\source\fadD23_ATP_refine_11-coot-0final.pdb format
> pdb
Summary of feedback from opening
E:\2022\manuscripts\source\fadD23_ATP_refine_11-coot-0final.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2021-02-13 Time 17:24:04 CST +0800 (1613208244.50 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/liux/Desktop/fadsovle/fadD23_ATP2/data/A3P6122_2
31 messages similar to the above omitted
Chain information for fadD23_ATP_refine_11-coot-0final.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select
> /A:21-27,35-40,64-68,88-91,115-118,141-143,165-170,180-184,211-215,238-241,263-268,295-299,325-328,349-352,371-374,383-387,402-406,446-451,454-460,465-467,470-472,489-496,499-507,540-544
943 atoms, 937 bonds, 123 residues, 1 model selected
> select clear
> select /A:470
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:3-470
3374 atoms, 3454 bonds, 4 pseudobonds, 443 residues, 2 models selected
> select clear
> select /A:3-470
3374 atoms, 3454 bonds, 4 pseudobonds, 443 residues, 2 models selected
> select clear
> select /A:460
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:3-460
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> name frozen ndomain1 sel
> select clear
> select /A:461-462
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:461-576
845 atoms, 853 bonds, 2 pseudobonds, 110 residues, 2 models selected
> name frozen cdomain1 sel
> select clear
> select /A:601@N28
1 atom, 1 residue, 1 model selected
> select up
84 atoms, 86 bonds, 1 residue, 1 model selected
> name frozen ligand1 sel
> select clear
> select /A:576
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:3-576
4136 atoms, 4224 bonds, 6 pseudobonds, 543 residues, 2 models selected
> cartoon (#!1 & sel)
> show sel cartoons
> hide sel atoms
> select clear
> open E:/2022/manuscripts/MS/MS/final/fadD23_ATP_refine_11.mtz
Install the Clipper bundle to open "MTZ" format files.
Opener for format 'MTZ' is not installed; see log for more info
> toolshed show
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #7e6da2ff
> color (#!1 & sel) #aa55ffff
> color (#!1 & sel) #0055ffff
> color (#!1 & sel) #555500ff
> color (#!1 & sel) #ff0000ff
> color (#!1 & sel) #aa00ffff
> color sel cadet blue
> color sel light slate gray
> select clear
> select cdomain1
845 atoms, 853 bonds, 2 pseudobonds, 110 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark salmon
> color sel salmon
> color sel dark khaki
> color sel peru
> color sel dark khaki
> color sel hot pink
> color sel dark violet
> color sel orchid
> color sel medium violet red
> color sel medium orchid
> color sel dark magenta
> color sel purple
> color sel medium purple
> color sel pale violet red
> color sel dark slate gray
> color sel midnight blue
> color sel dim gray
> color sel gray
> color sel dark sea green
> color sel light green
> color sel dark gray
> select clear
> select cdomain1
845 atoms, 853 bonds, 2 pseudobonds, 110 residues, 2 models selected
> color sel rosy brown
> select clear
> set bgColor white
> lighting simple
> lighting soft
> lighting simple
[Repeated 2 time(s)]
> lighting full
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel purple
> color sel brown
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
84 atoms, 86 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> ui tool show "Side View"
> save E:/2022/manuscripts/chimeraX/1配色.cxs
——— End of log from Sat Feb 19 22:01:08 2022 ———
opened ChimeraX session
> lighting simple
> lighting soft
> lighting simple
[Repeated 2 time(s)]
> lighting soft
> lighting full
> lighting simple
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel crimson
[Repeated 1 time(s)]
> color sel red
> color sel tomato
> select clear
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> color sel sienna
> select clear
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> color sel medium violet red
> color sel byhetero
> select clear
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> color sel light sea green
> color sel medium turquoise
> select clear
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> color sel medium turquoise
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
> select /A:267
5 atoms, 4 bonds, 1 residue, 1 model selected
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> color sel purple
> color sel dark slate blue
> color sel slate blue
> select clear
> select cdomain1
845 atoms, 853 bonds, 2 pseudobonds, 110 residues, 2 models selected
> color sel hot pink
> select clear
> select cdomain1
845 atoms, 853 bonds, 2 pseudobonds, 110 residues, 2 models selected
> color sel orchid
> color sel magenta
> color sel deep pink
> color sel dark violet
> color sel hot pink
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting simple
> save E:/2022/manuscripts/chimeraX/2配色.cxs
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel turquoise
> select clear
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> color sel light sea green
> select clear
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> color sel cornflower blue
> select clear
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> color sel aquamarine
> select clear
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> color sel royal blue
> color sel steel blue
> color sel teal
> color sel cadet blue
> color sel light slate gray
> color sel slate gray
> color sel blue
> color sel light slate gray
> color sel steel blue
> select clear
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> color sel dark cyan
> color sel cornflower blue
> color sel light sea green
> color sel medium turquoise
> select clear
> lighting simple
> lighting soft
> select cdomain1
845 atoms, 853 bonds, 2 pseudobonds, 110 residues, 2 models selected
> color sel salmon
> color sel dark salmon
> select clear
> lighting simple
> lighting soft
> save E:/2022/manuscripts/chimeraX/4配色.cxs
——— End of log from Sat Feb 19 23:09:29 2022 ———
opened ChimeraX session
> lighting simple
> save E:/2022/manuscripts/chimeraX/4配色.cxs
——— End of log from Sat Feb 19 23:16:45 2022 ———
opened ChimeraX session
> select clear
> select /S:3@O
1 atom, 1 residue, 1 model selected
> hide sel target a
> save "E:/2022/manuscripts/chimeraX/overall atp.cxs"
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save "E:/2022/manuscripts/chimeraX/overall atp.cxs"
——— End of log from Sun Feb 20 01:14:49 2022 ———
opened ChimeraX session
> select /A:461-468
68 atoms, 68 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #48d1ccff
> select clear
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ffff00 interModel false intraModel false intraMol false
> intraRes false select true
0 hydrogen bonds found
> select ligand1
84 atoms, 86 bonds, 1 residue, 1 model selected
> ui tool show Clashes
> clashes
10 clashes
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> close #1.3
> select clear
> save "E:/2022/manuscripts/chimeraX/overall atp.cxs"
——— End of log from Sat Feb 26 15:36:18 2022 ———
opened ChimeraX session
> open E:/2022/manuscripts/MS/MS/final/fadZ5_23_refine_53-coot-0.pdb
Summary of feedback from opening
E:/2022/manuscripts/MS/MS/final/fadZ5_23_refine_53-coot-0.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2021-02-16 Time 18:24:31 CST +0800 (1613471071.06 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/liux/Desktop/fadsovle/Z5_2/data/p61221320201218.
28 messages similar to the above omitted
Chain information for fadZ5_23_refine_53-coot-0.pdb #2
---
Chain | Description
A | No description available
> toolshed show
[Repeated 1 time(s)]
> Matchmaker
Unknown command: Matchmaker
> Matchmaker
Unknown command: Matchmaker
> ui mousemode right "mark maximum"
[Repeated 1 time(s)]
> ui mousemode right "link markers"
> ui tool show "Crystal Contacts"
> hide #!2 models
> crystalcontacts #1
4 pairs of asymmetric units of fadD23_ATP_refine_11-coot-0final.pdb contact at
distance 3.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
13 0 9 2 2 0 0 1
2 0 7 1 1 1 0 1
2 0 7 0 1 1 0 1
2 0 7 0 0 1 0 1
> crystalcontacts #1
4 pairs of asymmetric units of fadD23_ATP_refine_11-coot-0final.pdb contact at
distance 3.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
13 0 9 2 2 0 0 1
2 0 7 1 1 1 0 1
2 0 7 0 1 1 0 1
2 0 7 0 0 1 0 1
> hide #!3 target m
> close #3
> show #!2 models
> 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 fadD23_ATP_refine_11-coot-0final.pdb, chain A (#1) with
fadZ5_23_refine_53-coot-0.pdb, chain A (#2), sequence alignment score = 2679.1
RMSD between 542 pruned atom pairs is 0.314 angstroms; (across all 542 pairs:
0.314)
Alignment identifier is 1/A
Alignment identifier is 2/A
Alignment identifier is 1/A
Alignment identifier is 2/A
> select #2/A:460-461
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/A:317-461
1098 atoms, 1132 bonds, 145 residues, 1 model selected
> select #2/A:460-461
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/A:455-461
61 atoms, 62 bonds, 7 residues, 1 model selected
> select #2/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:3-460
3301 atoms, 3380 bonds, 4 pseudobonds, 434 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel light slate gray
[Repeated 1 time(s)]
> color sel slate gray
> color sel light slate gray
> color sel medium aquamarine
> color sel light sea green
> color sel dark turquoise
> color sel dodger blue
> select #2/A:468
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:468-576
808 atoms, 817 bonds, 1 pseudobond, 106 residues, 2 models selected
> color sel coral
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> select ::name="C16"
49 atoms, 48 bonds, 1 residue, 1 model selected
> color sel dark violet
> color sel medium violet red
> color sel dark slate blue
> color sel rebecca purple
> color sel dark violet
> color sel hot pink
> color sel blue violet
> color sel hot pink
> color sel blue violet
> color sel orchid
> color sel medium violet red
> color sel byhetero
> select ::name="AMP"
84 atoms, 86 bonds, 1 residue, 1 model selected
> select ::name="LIG"
44 atoms, 46 bonds, 1 residue, 1 model selected
> color sel medium violet red
> color sel byhetero
> select clear
Drag select of 207 atoms, 547 residues, 4 pseudobonds, 182 bonds
> hide (#!2 & sel) target a
> select clear
> select ::name="AMP"
84 atoms, 86 bonds, 1 residue, 1 model selected
> select ::name="LIG"
44 atoms, 46 bonds, 1 residue, 1 model selected
> show sel target ab
> select ::name="C16"
49 atoms, 48 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> show (#2 & sidechain) target ab
> hide (#2 & (protein|nucleic)) target a
> cartoon hide #2
> show (#2 & backbone) target ab
> cartoon #2
> select ::name="AMP"
84 atoms, 86 bonds, 1 residue, 1 model selected
> select ::name="C16"
49 atoms, 48 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
Drag select of 1 atoms, 2 residues
> select clear
> select H
89 atoms, 3 residues, 2 models selected
> hide (#!2 & sel) target a
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> ui mousemode right translate
> select #2/A:461
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:461-463
25 atoms, 24 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dodger blue
> select clear
> select add #2/A:464
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:465
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #2/A:466
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #2/A:467
31 atoms, 27 bonds, 4 residues, 1 model selected
> select add #2/A:468
43 atoms, 39 bonds, 5 residues, 1 model selected
> select add #2/A:469
47 atoms, 42 bonds, 6 residues, 1 model selected
> select add #2/A:470
58 atoms, 52 bonds, 7 residues, 1 model selected
> select add #2/A:471
66 atoms, 59 bonds, 8 residues, 1 model selected
> select add #2/A:472
76 atoms, 69 bonds, 9 residues, 1 model selected
> select add #2/A:473
82 atoms, 74 bonds, 10 residues, 1 model selected
> color sel crimson
> color sel dark red
> color sel maroon
> color sel dark red
> color sel crimson
> color sel orange red
> color sel red
> color sel maroon
> color sel fire brick
> color sel tomato
[Repeated 1 time(s)]
> color sel brown
> color sel chocolate
> color sel saddle brown
> color sel sienna
> color sel indian red
> color sel yellow
> color sel gold
> color sel dark orange
> color sel green yellow
> color sel sandy brown
> select clear
> show #!1 models
> hide #!2 models
> select #1/A:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:464
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:465
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:466
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:467
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:468
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:469
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select add #1/A:462
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:463
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/A:464
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #1/A:466
33 atoms, 29 bonds, 4 residues, 1 model selected
> select add #1/A:465
41 atoms, 36 bonds, 5 residues, 1 model selected
> select add #1/A:467
48 atoms, 42 bonds, 6 residues, 1 model selected
> select add #1/A:468
60 atoms, 54 bonds, 7 residues, 1 model selected
> select add #1/A:469
64 atoms, 57 bonds, 8 residues, 1 model selected
> select add #1/A:470
75 atoms, 67 bonds, 9 residues, 1 model selected
> select add #1/A:471
83 atoms, 74 bonds, 10 residues, 1 model selected
> select add #1/A:472
93 atoms, 84 bonds, 11 residues, 1 model selected
> select add #1/A:473
99 atoms, 89 bonds, 12 residues, 1 model selected
> select add #1/A:461
107 atoms, 96 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light salmon
> color sel salmon
> color sel magenta
> color sel dark salmon
> color sel salmon
> color sel indian red
> color sel sienna
> color sel indian red
> color sel tomato
> select clear
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> save E:/2022/manuscripts/chimeraX/2/atp,amppnp比对.cxs
——— End of log from Thu May 5 16:24:59 2022 ———
opened ChimeraX session
> open "E:/2021/data/fadd23_N/fadd23
> 0702本机/SuperposeMaps_23/fadd23_atp_omit_superposed.ccp4"
Opened fadd23_atp_omit_superposed.ccp4 as #3, grid size 93,105,99, pixel
0.836,0.884,0.874, shown at level 2.85e+05, step 1, values float32
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\YMR\Desktop\movie1.mp4
C:\Program Files\ChimeraX 1.3\bin\ffmpeg.exe -r 25 -i
C:\Users\YMR\AppData\Local\Temp\chimovie_qGtW-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\YMR\Desktop\movie1.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 6.3.0 (GCC)
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib
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
'C:\Users\YMR\AppData\Local\Temp\chimovie_qGtW-%05d.ppm':
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 787x566, 25 fps, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0000000000620fe0] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0000000000620fe0] profile High, level 3.1
[libx264 @ 0000000000620fe0] 264 - core 148 r2762 90a61ec - 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=6 lookahead_threads=1
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'C:\Users\YMR\Desktop\movie1.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 786x566,
q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 53 fps=0.0 q=25.0 size= 199kB time=00:00:00.00
bitrate=20904615.4kbits/s speed=0.000135x frame= 66 fps= 57 q=25.0 size= 879kB
time=00:00:00.52 bitrate=13849.9kbits/s speed=0.447x frame= 76 fps= 44 q=25.0
size= 1428kB time=00:00:00.92 bitrate=12716.1kbits/s speed=0.531x frame= 85
fps= 36 q=25.0 size= 1933kB time=00:00:01.28 bitrate=12373.6kbits/s
speed=0.54x frame= 99 fps= 34 q=25.0 size= 2688kB time=00:00:01.84
bitrate=11965.9kbits/s speed=0.639x frame= 110 fps= 32 q=25.0 size= 3297kB
time=00:00:02.28 bitrate=11846.6kbits/s speed=0.662x frame= 123 fps= 22 q=-1.0
Lsize= 6813kB time=00:00:04.80 bitrate=11627.9kbits/s speed=0.849x
video:6811kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.034196%
[libx264 @ 0000000000620fe0] frame I:1 Avg QP:25.38 size: 75988
[libx264 @ 0000000000620fe0] frame P:31 Avg QP:26.89 size: 72828
[libx264 @ 0000000000620fe0] frame B:91 Avg QP:28.78 size: 50990
[libx264 @ 0000000000620fe0] consecutive B-frames: 0.8% 1.6% 0.0% 97.6%
[libx264 @ 0000000000620fe0] mb I I16..4: 6.5% 20.3% 73.2%
[libx264 @ 0000000000620fe0] mb P I16..4: 2.5% 9.8% 50.2% P16..4: 6.7% 9.7%
10.9% 0.0% 0.0% skip:10.2%
[libx264 @ 0000000000620fe0] mb B I16..4: 0.7% 1.8% 13.8% B16..8: 20.0% 22.7%
27.0% direct: 3.1% skip:10.9% L0:43.7% L1:40.1% BI:16.2%
[libx264 @ 0000000000620fe0] 8x8 transform intra:13.8% inter:6.1%
[libx264 @ 0000000000620fe0] coded y,uvDC,uvAC intra: 69.9% 46.8% 45.0% inter:
42.5% 25.3% 23.3%
[libx264 @ 0000000000620fe0] i16 v,h,dc,p: 46% 31% 19% 3%
[libx264 @ 0000000000620fe0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 27% 13% 49% 2% 1%
1% 2% 2% 2%
[libx264 @ 0000000000620fe0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 21% 15% 20% 7% 7%
8% 8% 8% 7%
[libx264 @ 0000000000620fe0] i8c dc,h,v,p: 75% 9% 10% 5%
[libx264 @ 0000000000620fe0] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0000000000620fe0] ref P L0: 46.5% 16.9% 22.7% 13.9%
[libx264 @ 0000000000620fe0] ref B L0: 84.5% 12.1% 3.3%
[libx264 @ 0000000000620fe0] ref B L1: 94.4% 5.6%
[libx264 @ 0000000000620fe0] kb/s:11339.50
Exiting normally, received signal 15.
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 255
Error message:
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 6.3.0 (GCC)
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib
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
'C:\Users\YMR\AppData\Local\Temp\chimovie_qGtW-%05d.ppm':
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 787x566, 25 fps, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0000000000620fe0] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0000000000620fe0] profile High, level 3.1
[libx264 @ 0000000000620fe0] 264 - core 148 r2762 90a61ec - 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=6 lookahead_threads=1
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'C:\Users\YMR\Desktop\movie1.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 786x566,
q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 53 fps=0.0 q=25.0 size= 199kB time=00:00:00.00
bitrate=20904615.4kbits/s speed=0.000135x frame= 66 fps= 57 q=25.0 size= 879kB
time=00:00:00.52 bitrate=13849.9kbits/s speed=0.447x frame= 76 fps= 44 q=25.0
size= 1428kB time=00:00:00.92 bitrate=12716.1kbits/s speed=0.531x frame= 85
fps= 36 q=25.0 size= 1933kB time=00:00:01.28 bitrate=12373.6kbits/s
speed=0.54x frame= 99 fps= 34 q=25.0 size= 2688kB time=00:00:01.84
bitrate=11965.9kbits/s speed=0.639x frame= 110 fps= 32 q=25.0 size= 3297kB
time=00:00:02.28 bitrate=11846.6kbits/s speed=0.662x frame= 123 fps= 22 q=-1.0
Lsize= 6813kB time=00:00:04.80 bitrate=11627.9kbits/s speed=0.849x
video:6811kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.034196%
[libx264 @ 0000000000620fe0] frame I:1 Avg QP:25.38 size: 75988
[libx264 @ 0000000000620fe0] frame P:31 Avg QP:26.89 size: 72828
[libx264 @ 0000000000620fe0] frame B:91 Avg QP:28.78 size: 50990
[libx264 @ 0000000000620fe0] consecutive B-frames: 0.8% 1.6% 0.0% 97.6%
[libx264 @ 0000000000620fe0] mb I I16..4: 6.5% 20.3% 73.2%
[libx264 @ 0000000000620fe0] mb P I16..4: 2.5% 9.8% 50.2% P16..4: 6.7% 9.7%
10.9% 0.0% 0.0% skip:10.2%
[libx264 @ 0000000000620fe0] mb B I16..4: 0.7% 1.8% 13.8% B16..8: 20.0% 22.7%
27.0% direct: 3.1% skip:10.9% L0:43.7% L1:40.1% BI:16.2%
[libx264 @ 0000000000620fe0] 8x8 transform intra:13.8% inter:6.1%
[libx264 @ 0000000000620fe0] coded y,uvDC,uvAC intra: 69.9% 46.8% 45.0% inter:
42.5% 25.3% 23.3%
[libx264 @ 0000000000620fe0] i16 v,h,dc,p: 46% 31% 19% 3%
[libx264 @ 0000000000620fe0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 27% 13% 49% 2% 1%
1% 2% 2% 2%
[libx264 @ 0000000000620fe0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 21% 15% 20% 7% 7%
8% 8% 8% 7%
[libx264 @ 0000000000620fe0] i8c dc,h,v,p: 75% 9% 10% 5%
[libx264 @ 0000000000620fe0] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0000000000620fe0] ref P L0: 46.5% 16.9% 22.7% 13.9%
[libx264 @ 0000000000620fe0] ref B L0: 84.5% 12.1% 3.3%
[libx264 @ 0000000000620fe0] ref B L1: 94.4% 5.6%
[libx264 @ 0000000000620fe0] kb/s:11339.50
Exiting normally, received signal 15.
\-----------------------------
> surface dust #3 size 8.84
> volume #3 style mesh
> open "E:/2021/data/fadd23_N/fadd23
> 0702本机/SuperposeMaps_23/fadd23_amppnp_omit_superposed.ccp4"
Opened fadd23_amppnp_omit_superposed.ccp4 as #4, grid size 115,125,123, pixel
0.72,0.736,0.699, shown at level 6.49e+05, step 1, values float32
> surface dust #3 size 8.84
> surface dust #4 size 7.36
> volume #4 style mesh
> ui tool show "Side View"
> volume #3 color #aa55ff
> volume #4 color magenta
> volume #3 color #aaaaff
> volume #4 color #55ff00
> save E:/2022/manuscripts/chimeraX/2/atp,amppnp比对口袋2.cxs
——— End of log from Fri May 20 11:20:57 2022 ———
opened ChimeraX session
> hide #1.2 models
> ~select #1.2
Nothing selected
> hide #1.1 models
> show #1.1 models
> select #3
2 models selected
> select #4
2 models selected
> select #3
2 models selected
> select #4
2 models selected
> select clear
> select #3
2 models selected
> select #3
2 models selected
> select #4
2 models selected
> select clear
> ~select #1.2
Nothing selected
> select clear
[Repeated 1 time(s)]
> ui tool show "Side View"
> view orient
[Repeated 1 time(s)]
> ui tool show "Side View"
> select ndomain1
3291 atoms, 3370 bonds, 4 pseudobonds, 433 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #48d1ccff
> select clear
Alignment identifier is 1/A
Alignment identifier is 2/A
> select #2/A
4258 atoms, 4348 bonds, 5 pseudobonds, 549 residues, 2 models selected
> select subtract ::name="AMP"
4258 atoms, 4348 bonds, 5 pseudobonds, 549 residues, 2 models selected
> select subtract ::name="C16"
4209 atoms, 4300 bonds, 5 pseudobonds, 548 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!2 & sel) #84d2d6ff
> color (#!2 & sel) #48d1ccff
> select H
89 atoms, 3 residues, 2 models selected
> hide sel target a
> select ::name="AMP"
84 atoms, 86 bonds, 1 residue, 1 model selected
> select ::name="LIG"
44 atoms, 46 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel deep pink
> color sel byhetero
> select clear
> select add #1/A:473
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:472
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #2/A:461
24 atoms, 22 bonds, 3 residues, 2 models selected
> select add #2/A:462
33 atoms, 30 bonds, 4 residues, 2 models selected
> select add #1/A:463
41 atoms, 37 bonds, 5 residues, 2 models selected
> select subtract #1/A:463
33 atoms, 30 bonds, 4 residues, 2 models selected
> select add #1/A:463
41 atoms, 37 bonds, 5 residues, 2 models selected
> ui tool show "Color Actions"
> color sel #84d2d6ff
> color sel #48d1ccff
> select clear
> select add #1/A:461
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:462
17 atoms, 15 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #84d2d6ff
> color sel #48d1ccff
> save E:/2022/manuscripts/chimeraX/2/atp,amppnp比对口袋5.cxs
——— End of log from Fri Sep 9 11:15:24 2022 ———
opened ChimeraX session
> open "D:/2022/fadd23_data/CompositeOmit/AMPPNP
> CompositeOmit_24/fadd23-0702_composite_omit_24.mtz"
Opened (STATIC) (dataset) FOFCWT, PHFOFCWT as #2.1.1.2, grid size 72,54,46,
pixel 0.552,0.552,0.53, shown at level -0.338,0.338, step 1, values float32
Opened crystallographic dataset from D:/2022/fadd23_data/CompositeOmit/AMPPNP
CompositeOmit_24/fadd23-0702_composite_omit_24.mtz
Generated maps:
Reflection Data
(STATIC) (dataset) FOFCWT, PHFOFCWT
Any unwanted maps may be safely closed via the Model panel.
> hide #!1 models
> preset cartoons/nucleotides licorice/ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show "Fit in Map"
> select clear
> select ::name="AMP"
84 atoms, 86 bonds, 1 residue, 1 model selected
> select ::name="C16"
49 atoms, 48 bonds, 1 residue, 1 model selected
> select add ::name="AMP"
133 atoms, 134 bonds, 2 residues, 2 models selected
> select add #2.2/A:1001@N01
134 atoms, 134 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@C02
135 atoms, 135 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@N03
136 atoms, 137 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@C04
137 atoms, 138 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@N05
138 atoms, 139 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@C10
139 atoms, 141 bonds, 3 residues, 2 models selected
> select subtract #2.2/A:1001@C10
138 atoms, 141 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@N09
139 atoms, 142 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@N07
140 atoms, 145 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@C11
141 atoms, 146 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@C30
142 atoms, 146 bonds, 3 residues, 2 models selected
> select subtract #2.2/A:1001@C30
141 atoms, 146 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@C30
142 atoms, 146 bonds, 3 residues, 2 models selected
> select subtract #2.2/A:1001@C30
141 atoms, 147 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O12
142 atoms, 149 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O18
143 atoms, 157 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O17
144 atoms, 158 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O19
145 atoms, 159 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@P20
146 atoms, 160 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O21
147 atoms, 161 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@N23
148 atoms, 163 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@P24
149 atoms, 164 bonds, 3 residues, 2 models selected
> select subtract #2.2/A:1001@P24
148 atoms, 164 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O25
149 atoms, 165 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O27
150 atoms, 166 bonds, 3 residues, 2 models selected
> select add #2.2/A:1001@O26
151 atoms, 167 bonds, 3 residues, 2 models selected
Fit molecules fadD23_ATP_refine_11-coot-0final.pdb (#1),
fadZ5_23_refine_53-coot-0.pdb (#2.2) to map (STATIC) (dataset) FOFCWT,
PHFOFCWT (#2.1.1.2) using 151 atoms
average map value = 0.5889, steps = 92
shifted from previous position = 2.56
rotated from previous position = 0.765 degrees
atoms outside contour = 0, contour level = -0.33766
Position of fadD23_ATP_refine_11-coot-0final.pdb (#1) relative to (STATIC)
(dataset) FOFCWT, PHFOFCWT (#2.1.1.2) coordinates:
Matrix rotation and translation
0.99994588 0.01038809 0.00056365 -1.19711038
-0.01038301 0.99991103 -0.00837394 1.91705276
-0.00065059 0.00836763 0.99996478 -2.72541306
Axis 0.62689184 0.04546760 -0.77777845
Axis point 176.50718406 204.05217128 0.00000000
Rotation angle (degrees) 0.76508423
Shift along axis 1.45647261
Position of fadZ5_23_refine_53-coot-0.pdb (#2.2) relative to (STATIC)
(dataset) FOFCWT, PHFOFCWT (#2.1.1.2) coordinates:
Matrix rotation and translation
0.99994588 0.01038809 0.00056365 -1.19711038
-0.01038301 0.99991103 -0.00837394 1.91705276
-0.00065059 0.00836763 0.99996478 -2.72541306
Axis 0.62689184 0.04546760 -0.77777845
Axis point 176.50718406 204.05217128 0.00000000
Rotation angle (degrees) 0.76508423
Shift along axis 1.45647261
> select clear
> ui tool show "Side View"
> ui tool show "Segment Map"
> hide #!2.1.1.2 models
> show #!2.1.1.2 models
> hide #2.1.1.2.1 models
> hide #2.3 models
> color #2.2 mediumturquoise transparency 0
> select ::name="AMP"
84 atoms, 86 bonds, 1 residue, 1 model selected
> color #2.2#2.1.1.1#2.1.1.2.2#!2#!2.1#!2.1.1#!2.1.1.2 byhetero
> ui tool show "Volume Viewer"
> volume #2.1.1.2 level -0.3715 level 0.3377
> volume #2.1.1.2 level -0.3715 level 0.3038
> save D:/2022/manuscripts/作图/1.cxs includeMaps true
Unable to save 'tools' -> <chimerax.core.tools.Tools object at
0x0000015A2C4B4640> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x0000015A0C6882E0> 'segment map' ->
<chimerax.clipper.maps.xmapset.XmapHandler_Static object at
0x0000015A4C539430> '(STATIC) (dataset) FOFCWT, PHFOFCWT' ->
<chimerax.clipper.clipper_python.data32.HKL_data_F_phi_float object at
0x0000015A4C536230>". Session might not restore properly.
——— End of log from Sun Nov 27 18:16:27 2022 ———
opened ChimeraX session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\y\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 692, in
_recalculate_maps_if_needed
if self._recalc_needed and not xm.thread_running:
AttributeError: 'NoneType' object has no attribute 'thread_running'
Error processing trigger "new frame":
AttributeError: 'NoneType' object has no attribute 'thread_running'
File "C:\Users\y\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\clipper\maps\xmapset.py", line 692, in
_recalculate_maps_if_needed
if self._recalc_needed and not xm.thread_running:
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 472.19
OpenGL renderer: NVIDIA GeForce MX450/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82NC
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 16,952,647,680
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-11300H @ 3.10GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
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: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
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: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
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
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
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: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
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: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
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: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
The last error reported is some Clipper error after opening a session. There was an unrelated earlier error (in the log of a previously saved session) about ffmpeg failing, where it says it received SIGTERM (15), as if the user killed the movie recording.