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Opened 4 years ago
Closed 4 years ago
#5750 closed defect (not a bug)
Out of space writing file history
| 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: Linux-5.11.0-41-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3rc202111230539 (2021-11-23 05:39:18 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3rc202111230539 (2021-11-23)
© 2016-2021 Regents of the University of California. All rights reserved.
> open 6nj9_interactions.cxs
Log from Wed Dec 8 23:04:13 2021UCSF ChimeraX version: 1.3rc202111230539
(2021-11-23)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6nj9
6nj9 title:
Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex
[more info...]
Chain information for 6nj9 #1
---
Chain | Description | UniProt
A E | Histone H3.2 | H32_XENLA
B F | Histone H4 | H4_XENLA
C G | Histone H2A type 1 | H2A1_XENLA
D H | Histone H2B 1.1 | H2B11_XENLA
I | 601 DNA Strand 1 |
J | 601 DNA Strand 2 |
K M | Histone-lysine N-methyltransferase, H3 lysine-79 specific | DOT1L_HUMAN
L N | Ubiquitin | UBB_HUMAN
Non-standard residues in 6nj9 #1
---
SAM — S-adenosylmethionine
> show cartoons
> hide atoms
> select :sam
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select /K:196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
198 atoms, 205 bonds, 22 residues, 1 model selected
> select up
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> rainbow sel
> select clear
> select /K:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /K:305
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /K:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /K:243
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 32 atom styles
> color sel byhetero
> select clear
> select /K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> style sel ball
Changed 27 atom styles
> select clear
> select /K:500@CE
1 atom, 1 residue, 1 model selected
> cofr sel
> select /K:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
198 atoms, 205 bonds, 22 residues, 1 model selected
> select up
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> save
> /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dot1L.pdb
> selectedOnly true relModel #1
> open
> /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dot1L.pdb
Summary of feedback from opening
/home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dot1L.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 44
LYS A 56 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG A 63 ALA A 75 1
13
Start residue of secondary structure not found: HELIX 3 3 GLN A 76 PHE A 78 1
3
Start residue of secondary structure not found: HELIX 4 4 GLN A 85 ALA A 114 1
30
Start residue of secondary structure not found: HELIX 5 5 NLE A 120 ARG A 131
1 12
82 messages similar to the above omitted
Chain information for 6nj9_dot1L.pdb #2
---
Chain | Description
K | No description available
> hide #!1 models
> select #2
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> rainbow sel
> select clear
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> style sel ball
Changed 27 atom styles
> select clear
> show #2 surfaces
> hide #!2 surfaces
> select #2
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> color (#!2 & sel) orange
> select clear
> show #!2 surfaces
> lighting soft
> select #2/K:500@N6
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 27 atom styles
> color sel byhetero
> color sel byatom
> select clear
> lighting simple
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> hide #!2 surfaces
> select clear
> select #2/K:130
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light coral
> select #2
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> ~select #2
1 model selected
> select #2
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> color sel yellow
> color sel khaki
> select clear
> select #2/K:130
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> color sel light coral
> select clear
> select #2/K:243
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 2 models selected
> color sel teal
> select clear
[Repeated 1 time(s)]
> select #2/K:308
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
148 atoms, 153 bonds, 19 residues, 2 models selected
> color sel fire brick
> select clear
> show #!2 surfaces
> transparency 20
> transparency 30
> hide #!2 surfaces
> show #!2 surfaces
> transparency 0
> surface #2 gridSpacing 0.3
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> select up
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> select down
27 atoms, 29 bonds, 1 residue, 2 models selected
> color sel byatom
> select clear
> hide #!2 surfaces
> select #2/K:245
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel teal
> show sel surfaces
> select clear
> show #!2 surfaces
> hide #!2 surfaces
> select #2/K:245
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel khaki
> select clear
> show #!2 surfaces
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting simple
> lighting soft
> lighting gentle
> lighting soft
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select clear
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select clear
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting soft
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> clip front 0 position #2:sam@ce
> clip front -1 position #2:sam@ce
> clip front 1 position #2:sam@ce
> clip model #2:sam false
> select clear
> ~clip
> transparency 20
> lighting soft
> hide #!2 surfaces
> clip front 1 position #2:sam@ce
> show #!2 surfaces
> transparency 0
> clip front 0 position #2:sam@ce
> clip front -1 position #2:sam@ce
> clip front -2 position #2:sam@ce
> ~clip
> hide #!2 surfaces
> select clear
> select #2/K:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> color sel blue
> select clear
[Repeated 1 time(s)]
> select #2/K:243
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 2 models selected
> color sel tomato
> color sel cornflower blue
> select add #2/K:136
44 atoms, 44 bonds, 5 residues, 2 models selected
> select up
132 atoms, 136 bonds, 16 residues, 2 models selected
> select add #2/K:295
141 atoms, 144 bonds, 17 residues, 2 models selected
> select up
280 atoms, 289 bonds, 35 residues, 2 models selected
> show sel surfaces
> select clear
> show #!2 surfaces
> select #2/K:243@CE2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
32 atoms, 32 bonds, 4 residues, 2 models selected
> color sel chartreuse
> color sel green
> color sel spring green
> select #2/K:306@OG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
148 atoms, 153 bonds, 19 residues, 2 models selected
> color sel deep pink
> color sel dark violet
> color sel hot pink
> color sel burly wood
> color sel pale goldenrod
> color sel violet
> color sel light green
> color sel dark sea green
> color sel gray
> color sel orchid
> color sel blue violet
> color sel deep pink
> color sel magenta
> color sel tomato
> lighting simple
> select clear
> select add #2/K:136@N
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> select add #2/K:243@CE2
101 atoms, 104 bonds, 13 residues, 2 models selected
> select up
111 atoms, 115 bonds, 13 residues, 2 models selected
> select up
132 atoms, 136 bonds, 16 residues, 2 models selected
> lighting soft
> set bgColor white
> select clear
> select #2.1
2680 atoms, 329 residues, 1 model selected
> ~select #2.1
1 model selected
> select #2
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> color sel yellow
> color sel gold
> color sel orange
> color sel sandy brown
> color sel goldenrod
> color sel orange
> color sel gold
> color sel green yellow
> color sel goldenrod
[Repeated 1 time(s)]
> color sel sandy brown
> color sel indian red
> color sel coral
> color sel dark salmon
> color sel salmon
> color sel dark salmon
> color sel light salmon
> color sel wheat
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> color sel goldenrod
[Repeated 2 time(s)]
> color sel sandy brown
> color sel goldenrod
> select clear
> hide #!2 surfaces
> graphics silhouettes false
> select clear
> select #2/K:137
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> color sel green
> color sel chartreuse
> color sel spring green
> color sel lime green
> color sel lime
> color sel medium sea green
> select #2/K:243
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 2 models selected
> color sel fire brick
> select #2/K:306
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
148 atoms, 153 bonds, 19 residues, 2 models selected
> color sel slate blue
> select clear
> show #!2 surfaces
> lighting simple
> lighting soft
> lighting simple
> select #2/K:307@N
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
148 atoms, 153 bonds, 19 residues, 2 models selected
> select add #2/K:243@CE2
149 atoms, 153 bonds, 20 residues, 2 models selected
> select up
159 atoms, 164 bonds, 20 residues, 2 models selected
> select up
180 atoms, 185 bonds, 23 residues, 2 models selected
> select add #2/K:131@CZ
181 atoms, 185 bonds, 24 residues, 2 models selected
> select up
191 atoms, 196 bonds, 24 residues, 2 models selected
> select up
280 atoms, 289 bonds, 35 residues, 2 models selected
> transparency sel 20
> transparency sel 30
> transparency sel 50
> select clear
> transparency 50
> select clear
[Repeated 2 time(s)]
> hide #!2 surfaces
> select clear
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byatom
> select clear
> lighting soft
> show #!2 surfaces
> transparency 0
> select clear
[Repeated 1 time(s)]
> hide #!2 surfaces
> select #2/K:135
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> select add #2/K:312
112 atoms, 116 bonds, 13 residues, 2 models selected
> select up
248 atoms, 257 bonds, 31 residues, 2 models selected
> select add #2/K:243
259 atoms, 268 bonds, 32 residues, 2 models selected
> select up
280 atoms, 289 bonds, 35 residues, 2 models selected
> show sel surfaces
> select clear
[Repeated 1 time(s)]
> surface #2 probeRadius 1.2 gridSpacing 0.3
> select clear
[Repeated 1 time(s)]
> hide #!2 surfaces
> select #2/K:273
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
138 atoms, 141 bonds, 17 residues, 2 models selected
> show sel surfaces
> color sel light coral
> select clear
> show #!2 surfaces
> select #2/K:274@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
138 atoms, 141 bonds, 17 residues, 2 models selected
> color sel violet
> color sel deep pink
> color sel magenta
> color sel blue violet
> color sel hot pink
> color sel dark salmon
> color sel medium turquoise
> select clear
> show #!1 models
> select #1
18814 atoms, 19780 bonds, 371 pseudobonds, 1884 residues, 2 models selected
> surface #1 probRadius 1.2 gridSpacing 0.3
Expected a keyword
> surface #1 probeRadius 1.2 gridSpacing 0.3
> select clear
> hide #!2 models
> select #1/K:150@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
95 atoms, 95 bonds, 12 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> hide sel surfaces
> select clear
[Repeated 1 time(s)]
> select #1/K:273
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
138 atoms, 141 bonds, 17 residues, 2 models selected
> color sel maroon
> color sel crimson
> color sel red
> show sel surfaces
> select clear
> select #1/K:294
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/K:293
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!1 cartoons
[Repeated 1 time(s)]
> show #!1 cartoons
> hide #!1 surfaces
> color #1 bychain
> select clear
[Repeated 1 time(s)]
> select #1/M:181
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
43 atoms, 45 bonds, 5 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> select add #1/N:32
2715 atoms, 2786 bonds, 331 residues, 2 models selected
> select up
2816 atoms, 2887 bonds, 344 residues, 3 models selected
> select up
3304 atoms, 3382 bonds, 405 residues, 3 models selected
> delete sel
> save
> /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9.pdb
> models #1
> hide #!1 atoms
> select #1:sam
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 27 atom styles
> color sel byatom
> select clear
> select #1/E:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
6nj9 #1/E NLE 79: phi -56.8, psi -32.8 trans
Changed 438 bond radii
> swapaa #1/E:79 LYS criteria 2 rotLib Dunbrack
Using Dunbrack library
6nj9 #1/E NLE 79: phi -56.8, psi -32.8 trans
Applying LYS rotamer (chi angles: -175.3 176.1 179.1 180.0) to 6nj9 #1/E LYS
79
> style sel sphere
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> select #1/E:79@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting simple
> select #1/K:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
198 atoms, 202 bonds, 23 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> color (#!1 & sel) orange
> select clear
> set bgColor black
> set bgColor white
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> surface #1
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> hide #!1 surfaces
> graphics silhouettes false
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> select #1/K:500@N6
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byatom
> select clear
> select #1/K:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> style sel ball
Changed 11 atom styles
> select clear
> lighting simple
> select #1/G:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> lighting soft
> view #1
> select #1/E:79@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> style sel ball
Changed 9 atom styles
> select clear
> lighting soft
> lighting full
> graphics silhouettes false
> lighting simple
> open 7k6q
7k6q title:
Active state Dot1 bound to the H4K16ac nucleosome [more info...]
Chain information for 7k6q #3
---
Chain | Description | UniProt
A E | Histone H3.2 | H32_XENLA
B F | Histone H4 | H4_XENLA
C G | Histone H2A type 1 | H2A1_XENLA
D H | Histone H2B 1.1 | H2B11_XENLA
I | DNA (146-mer) |
J | DNA (146-mer) |
K | Histone-lysine N-methyltransferase, H3 lysine-79 specific | DOT1_YEAST
L | Ubiquitin | UBC_HUMAN
Non-standard residues in 7k6q #3
---
SAM — S-adenosylmethionine
> mmaker #3 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 6nj9, chain C (#1) with 7k6q, chain G (#3), sequence alignment
score = 511.2
RMSD between 107 pruned atom pairs is 0.603 angstroms; (across all 107 pairs:
0.603)
> show #!1,3 cartoons
> hide #!1,3 atoms
> select clear
> hide #!3 models
> show #!3 models
> select #3/K:260
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/k:252-264
94 atoms, 96 bonds, 13 residues, 1 model selected
> color sel red
> select clear
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #1/L:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 6 residues, 2 models selected
> select up
597 atoms, 603 bonds, 75 residues, 2 models selected
> mlp sel
Map values for surface "6nj9_L SES surface": minimum -28.06, mean -3.871,
maximum 24.51
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting simple
> select #1/K:324
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
103 atoms, 104 bonds, 12 residues, 2 models selected
> mlp sel
Map values for surface "6nj9_K SES surface": minimum -29.35, mean -3.751,
maximum 26.98
To also show corresponding color key, enter the above mlp command and add key
true
> select add #1/K:332
110 atoms, 111 bonds, 13 residues, 2 models selected
> select up
118 atoms, 120 bonds, 14 residues, 2 models selected
> mlp sel
Map values for surface "6nj9_K SES surface": minimum -29.35, mean -3.751,
maximum 26.98
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
> select #1/L:9@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
35 atoms, 34 bonds, 5 residues, 2 models selected
> select up
597 atoms, 603 bonds, 75 residues, 2 models selected
> hide sel surfaces
> select clear
> select #1/L:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> lighting soft
> select clear
> graphics silhouettes true
> show #!2 models
> hide #!1 models
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> cofr sel
> select clear
> hide #!2 models
> show #!2 models
> hide #2.1 models
Drag select of 46 atoms, 187 residues, 24 bonds
> select clear
Drag select of 2 residues
> select clear
Drag select of 17 atoms, 162 residues, 8 bonds
> show sel surfaces
> select clear
Drag select of 6nj9_dot1L.pdb_K SES surface, 363400 of 891434 triangles, 21
atoms, 161 residues, 15 bonds
> hide sel surfaces
> select clear
Drag select of 6nj9_dot1L.pdb_K SES surface, 264264 of 891434 triangles, 70
atoms, 278 residues, 37 bonds
> hide sel surfaces
> select clear
[Repeated 1 time(s)]
> select #2.1
2680 atoms, 329 residues, 1 model selected
> show sel surfaces
> select clear
> clip back 0 position #2:sam@sd
> transparency #2 50
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes false
> transparency #2 20
> graphics driver
OpenGL version: 3.3.0 NVIDIA 460.91.03
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
> graphics quality
Quality 1, atom triangles 2000, bond triangles 160, ribbon divisions 20
> graphics rate
Maximum framerate 60
> graphics quality 2
> graphics quality 1
> lighting soft
> graphics quality 2
> select #2/K:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> style sel ball
Changed 2 atom styles
> select clear
> graphics silhouettes true
> graphics silhouettes false
> graphics quality 1
> graphics quality 3
> select #2/K:212@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> lighting simple
> catroon style #2
Unknown command: catroon style #2
> graphics quality catroon style #2
Expected a number or a keyword
> cartoon
> cartoon style
6nj9 #1
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
6nj9_dot1L.pdb #2
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
7k6q #3
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> cartoon style #2 width 1
> cartoon style #2 width 2
> cartoon style #2 width 3
> cartoon style #2 width 1.5
> cartoon style #2 width 2
> cartoon style #2 width 1.5
> cartoon style #2 width 1.8
> cartoon style #2 width 2
> cartoon style #2 width 2 thickness 1
> cartoon style #2 width 2 thickness 2
> cartoon style #2 width 2 thickness 0.5
> cartoon style #2 width 2 thickness 0.4
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting simple
> view orient
> lighting
Intensity: 1
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0.5
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 0.4
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01)
> lighting soft
> transparency 0
> ~clip
> lighting
Intensity: 0
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.5
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)
> lighting soft intensity 1
> lighting soft intensity 0
> lighting soft intensity 0 fillIntensity 1
> lighting soft intensity 0 fillIntensity 0
> lighting soft intensity 0 fillIntensity 0.2
> lighting soft intensity 0 fillIntensity 0.3
> lighting soft intensity 0 fillIntensity 0.4
> lighting soft intensity 0 fillIntensity 0
> lighting soft intensity 0 fillIntensity 0 Shadow true
Expected a keyword
> lighting soft intensity 0 fillIntensity 0 shadows true
> lighting soft intensity 0 fillIntensity 0 shadows false
> lighting soft
> lighting gentle
> lighting
Intensity: 0
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.5
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 128, depth bias 0.05)
> graphics silhouettes false
> set subdivision 3
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> color sel white
> select clear
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select clear
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> select up
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> select clear
> select #2/K:500@N7
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> save
> /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/sam.pdb
> selectedOnly true relModel #2
> select clear
> select #2/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> select up
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> select down
27 atoms, 29 bonds, 1 residue, 2 models selected
> hide sel
> select clear
> open sam.pdb
Summary of feedback from opening sam.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 44
LYS A 56 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG A 63 ALA A 75 1
13
Start residue of secondary structure not found: HELIX 3 3 GLN A 76 PHE A 78 1
3
Start residue of secondary structure not found: HELIX 4 4 GLN A 85 ALA A 114 1
30
Start residue of secondary structure not found: HELIX 5 5 NLE A 120 ARG A 131
1 12
74 messages similar to the above omitted
> select #4
27 atoms, 29 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 27 atom styles
> lighting model #4 simple
Expected a keyword
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> hide #!2 models
> select clear
> show #!2 models
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byatom
> color sel white
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> style sel ball
Changed 27 atom styles
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel light gray
> color sel lime
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel white
> select clear
> graphics silhouettes true
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 27 atom styles
> select clear
> select #4/K:500@CE
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> close #2
> close #4
> show #!1 models
> close #3
> view
> show surfaces
> color bychain
> select clear
[Repeated 1 time(s)]
> hide surfaces
> lighting simple
> select /K:118
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
138 atoms, 140 bonds, 17 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> ui tool show "Color Actions"
> color sel goldenrod
> color sel khaki
> color sel pale goldenrod
> color sel peach puff
> color sel navajo white
> color sel yellow
> color sel gold
> color sel orange
> color sel dark orange
> select clear
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> select /L:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 5 residues, 2 models selected
> select up
597 atoms, 603 bonds, 75 residues, 2 models selected
> color sel
> color
> select /E:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /a,e
1633 atoms, 1657 bonds, 198 residues, 1 model selected
> color sel lime green
> color sel spring green
> color sel lawn green
> color sel chartreuse
[Repeated 1 time(s)]
> color sel green
> color sel lime
> color sel green
> color sel chartreuse
> color sel lime green
> color sel forest green
> color sel green
> color sel lawn green
> color sel spring green
> color sel lime green
> select clear
> select /b,f
1416 atoms, 1432 bonds, 176 residues, 1 model selected
> color sel red
> color sel orange red
> color sel crimson
> color sel tomato
> color sel brown
> color sel chocolate
[Repeated 2 time(s)]
> color sel indian red
> color sel dodger blue
> color sel turquoise
> color sel rebecca purple
> color sel medium slate blue
> color sel pale goldenrod
> color sel khaki
> color sel violet
> select /a,e
1633 atoms, 1657 bonds, 198 residues, 1 model selected
> color sel violet
> color sel pale goldenrod
> color sel spring green
> color sel sea green
> color sel royal blue
> color sel dark khaki
> color sel peru
> color sel wheat
> color sel lime green
> color sel spring green
> color sel medium sea green
> color sel magenta
> color sel orchid
> color sel crimson
> select /b,f
1416 atoms, 1432 bonds, 176 residues, 1 model selected
> color sel pale green
> color sel medium spring green
> color sel dark turquoise
[Repeated 1 time(s)]
> color sel medium spring green
> color sel dark turquoise
> color sel dodger blue
> color sel dark turquoise
> select /c,g
1686 atoms, 1706 bonds, 218 residues, 1 model selected
> color sel burly wood
> color sel tan
> color sel silver
> color sel thistle
> color sel salmon
> color sel light coral
[Repeated 1 time(s)]
> color sel wheat
> color sel tan
> color sel rosy brown
> color sel dark gray
> color sel seashell
> color sel lavender blush
> color sel papaya whip
> color sel blanched almond
> color sel misty rose
> color sel bisque
> color sel moccasin
> color sel navajo white
> color sel peach puff
> color sel pink
> color sel thistle
> color sel sandy brown
> color sel dark salmon
[Repeated 1 time(s)]
> color sel peru
> color sel light salmon
> color sel dark khaki
> color sel dark salmon
> color sel wheat
> color sel burly wood
> color sel rosy brown
> color sel tan
> color sel pale violet red
> color sel teal
> color sel lime
> color sel chocolate
> color sel medium sea green
> color sel dark orange
> color sel yellow
> color sel gold
> color sel sandy brown
[Repeated 1 time(s)]
> color sel deep sky blue
> color sel sandy brown
> select /d,h
1486 atoms, 1508 bonds, 190 residues, 1 model selected
> color sel gray
> color sel dim gray
> color sel red
> color sel dark red
> color sel dark cyan
> color sel beige
> color sel black
> color sel dark green
> color sel orchid
> color sel medium orchid
> color sel medium violet red
> color sel medium orchid
> color sel orchid
> color sel blue violet
> color sel hot pink
> color sel dark violet
> color sel deep pink
> color sel magenta
> color sel deep pink
> color sel light sea green
> color sel fire brick
> color sel maroon
> color sel dark olive green
> color sel green
> color sel steel blue
> color sel green
> color sel olive
> select clear
> select /L:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /l
597 atoms, 603 bonds, 75 residues, 1 model selected
> color sel fire brick
> color sel red
> color sel orange red
> color sel crimson
> color sel dark red
> color sel crimson
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel tomato
> color sel brown
> color sel chocolate
> color sel sienna
> color sel saddle brown
> color sel indian red
> color sel yellow
> color sel gold
> color sel aquamarine
> color sel crimson
> color sel dim gray
> color sel dark turquoise
> color sel teal
> select /k
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> color sel sandy brown
> color sel goldenrod
> color sel dark orange
> color sel goldenrod
> color sel crimson
> color sel dark red
> color sel crimson
> color sel orange red
> color sel dark red
> color sel crimson
> color sel sandy brown
> color sel goldenrod
> color sel green yellow
> color sel dark orange
[Repeated 1 time(s)]
> color sel goldenrod
> color sel green yellow
> color sel dark orange
> color sel orange
> color sel indian red
> color sel sienna
> color sel coral
> color sel saddle brown
> color sel chocolate
[Repeated 1 time(s)]
> color sel brown
[Repeated 1 time(s)]
> color sel tomato
> color sel fire brick
> color sel maroon
> color sel dark red
> color sel crimson
> color sel orange red
> color sel red
> select clear
> select /I:126
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
2975 atoms, 3333 bonds, 146 residues, 2 models selected
> select /i,j
5986 atoms, 6714 bonds, 371 pseudobonds, 292 residues, 2 models selected
> color sel gray
> color sel dim gray
> color sel medium slate blue
> color sel slate blue
> color sel dim gray
> color sel gainsboro
> color sel dim gray
> color sel silver
> color sel dim gray
> color sel navy
> color sel slate gray
> show sel surfaces
> color sel slate gray
> color sel dim gray
> hide sel surfaces
> select /k
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> color sel crimson
[Repeated 1 time(s)]
> color sel dark red
> color sel crimson
> select /a,e
1633 atoms, 1657 bonds, 198 residues, 1 model selected
> color sel goldenrod
> color sel green yellow
[Repeated 1 time(s)]
> color sel dark orange
> color sel green yellow
> color sel cyan
> color sel blue
> color sel cyan
> color sel green yellow
> color sel lime
> color sel chartreuse
> color sel lawn green
> color sel green
> color sel lime green
> select /b,f
1416 atoms, 1432 bonds, 176 residues, 1 model selected
> color sel dark orange
> color sel forest green
> color sel green
> color sel saddle brown
> color sel dark violet
> color sel deep pink
> color sel slate blue
> color sel dark sea green
> lighting simple
> lighting soft
> color sel dark cyan
> color sel light slate gray
> color sel slate blue
[Repeated 1 time(s)]
> color sel medium slate blue
> color sel orange red
> color sel tomato
> color sel brown
> color sel chocolate
> color sel dark turquoise
> color sel medium spring green
> color sel dark turquoise
> color sel medium slate blue
> color sel dodger blue
> color sel medium slate blue
> color sel turquoise
> color sel medium aquamarine
> color sel teal
> color sel medium slate blue
> select /l
597 atoms, 603 bonds, 75 residues, 1 model selected
> color sel khaki
[Repeated 1 time(s)]
> color sel wheat
> color sel goldenrod
> color sel sandy brown
> color sel orange
> color sel gold
> color sel orange
> color sel dark orange
> color sel orange red
> color sel gold
> color sel orange
[Repeated 1 time(s)]
> color sel dark orange
> color sel green yellow
> color sel goldenrod
> select clear
> lighting full
> lighting simple
> select /l
597 atoms, 603 bonds, 75 residues, 1 model selected
> lighting soft
> color sel cyan
> color sel teal
> color sel medium aquamarine
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
> color sel cornflower blue
> color sel dark violet
> color sel hot pink
> color sel dark cyan
> color sel cornflower blue
> color sel dark cyan
> color sel cornflower blue
> lighting simple
> lighting soft
> set subdivision 3
> select :sam
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byatom
> select clear
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save 6nj9_soft_1.png transparentBackground true
> view name 1
> save 6nj9_interactions.cxs
> view 1
> view
> select /E:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel ball
Changed 9 atom styles
> color sel byhetero
> select clear
> open 6nog.pdb
6nog.pdb title:
Poised-state DOT1L bound to the H2B-ubiquitinated nucleosome [more info...]
Chain information for 6nog.pdb #2
---
Chain | Description | UniProt
A E | histone H3.2 | H32_XENLA
B | histone H4 | H4_XENLA
C | histone H2A type 1 | H2A1_XENLA
D | H2B1.1 | H2B11_XENLA
F | histone H4 | H4_XENLA
G | histone H2A type 1 | H2A1_XENLA
H | H2B1.1 | H2B11_XENLA
I | 601 DNA strand 1 |
J | 601 DNA strand 2 |
K | histone-lysine N-methyltransferase, H3 lysine-79 specific | DOT1L_HUMAN
L | ubiquitin | J3QS39_HUMAN
> select #2
14929 atoms, 15798 bonds, 3 pseudobonds, 1416 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> mmaker #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 6nj9, chain K (#1) with 6nog.pdb, chain K (#2), sequence alignment
score = 1455
RMSD between 282 pruned atom pairs is 0.889 angstroms; (across all 302 pairs:
1.183)
> hide #!1 models
> select clear
> select #2/K:77
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
211 atoms, 215 bonds, 25 residues, 1 model selected
> select up
2431 atoms, 2486 bonds, 302 residues, 1 model selected
> delete sel
> select #2/L:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
18 atoms, 17 bonds, 2 residues, 1 model selected
> select up
593 atoms, 599 bonds, 74 residues, 1 model selected
> delete sel
> mmaker #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 6nj9, chain C (#1) with 6nog.pdb, chain G (#2), sequence alignment
score = 488.1
RMSD between 105 pruned atom pairs is 0.495 angstroms; (across all 105 pairs:
0.495)
> show #!1 models
> view 1
> select #1/K:500@CE
1 atom, 1 residue, 1 model selected
> cofr sel
> view 1
> select clear
[Repeated 1 time(s)]
> select #1/K:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/K:305
25 atoms, 26 bonds, 2 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 25 atom styles
> style sel ball
Changed 25 atom styles
> color sel byhetero
> style sel sphere
Changed 25 atom styles
> select add #1/E:79@NZ
26 atoms, 26 bonds, 3 residues, 2 models selected
> select up
34 atoms, 34 bonds, 3 residues, 3 models selected
> style sel sphere
Changed 34 atom styles
> select add #1/K:500@SD
35 atoms, 34 bonds, 4 residues, 3 models selected
> select up
61 atoms, 63 bonds, 4 residues, 3 models selected
> style sel sphere
Changed 61 atom styles
> select add #2/A:79
70 atoms, 71 bonds, 5 residues, 4 models selected
> show sel atoms
> style sel ball
Changed 70 atom styles
> select clear
[Repeated 1 time(s)]
> select #2/A:79@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
6nog.pdb #2/A LYS 79: phi -164.6, psi 127.3 trans
Changed 438 bond radii
> swapaa #2/A:79 LYS criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
6nog.pdb #2/A LYS 79: phi -164.6, psi 127.3 trans
Applying LYS rotamer (chi angles: -175.7 175.9 179.5 -180.0) to 6nog.pdb #2/A
LYS 79
> select #2/A:79@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> color #2/a,e lime green
> color byhetero
> color #2/b,f Medium Slate Blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> select #2/b,f
1272 atoms, 1286 bonds, 160 residues, 1 model selected
> color sel medium slate blue
> select #2/c,g
1609 atoms, 1629 bonds, 209 residues, 1 model selected
> color sel sandy brown
> select #2/d,h
1456 atoms, 1478 bonds, 187 residues, 1 model selected
> color sel olive drab
> color sel olive
> select clear
> select #2/i,j
5986 atoms, 6714 bonds, 292 residues, 1 model selected
> color sel dim gray
> select clear
> hide #!2 models
> show #!2 models
> select #1/E:79@NZ
1 atom, 1 residue, 1 model selected
> select add #1/K:500@CE
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between 6nj9 #1/E LYS 79 NZ and /K SAM 500 CE: 2.332Å
> close #3
> select clear
> hide #!2 models
> select add #1/K:131@CE2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select add #1/K:305@CD1
12 atoms, 11 bonds, 2 residues, 2 models selected
> select up
25 atoms, 26 bonds, 2 residues, 2 models selected
> style sel sphere
Changed 25 atom styles
> select clear
> select add #1/E:79@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> style sel sphere
Changed 9 atom styles
> select clear
> show #!2 models
> select add #2/A:79@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 9 atom styles
> hide #!1 models
> select clear
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting simple
> show #!1 models
> lighting soft
> hide #!2 models
> select #1/K:305@CB
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> style sel ball
Changed 14 atom styles
> style sel sphere
Changed 14 atom styles
> select add #1/E:79@CA
15 atoms, 15 bonds, 2 residues, 2 models selected
> select clear
> select add #1/K:305@CB
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select add #1/K:131@CD2
15 atoms, 15 bonds, 2 residues, 2 models selected
> select up
25 atoms, 26 bonds, 2 residues, 2 models selected
> style sel ball
Changed 25 atom styles
> select clear
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> select add #1/K:305@CG
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select add #1/K:131@CD2
15 atoms, 15 bonds, 2 residues, 2 models selected
> select up
25 atoms, 26 bonds, 2 residues, 2 models selected
> style sel sphere
Changed 25 atom styles
> select clear
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting gentle
> graphics silhouettes false
> graphics silhouettes true
> lighting gentle depthCue true
> lighting gentle depthCue true depthCueStart 0.2 depthCueEnd 1.0
> lighting gentle depthCue true depthCueStart 0.5 depthCueEnd 1.0
> lighting gentle depthCue true depthCueStart 0.3 depthCueEnd 1.0
> lighting gentle depthCue true depthCueStart 0.5 depthCueEnd 1.0
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> lighting simple
> save 6nj9_active_simple_1.png transparentBackground ture
Invalid "transparentBackground" argument: Expected true or false (or 1 or 0)
> save 6nj9_active_simple_1.png transparentBackground true
> lighting soft
> lighting simple
> lighting soft
> save 6nj9_active_soft_1.png transparentBackground true
> save view lys79
Cannot determine format for 'view'
> view name lys79
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting gentle
> lighting soft
> lighting gentle
> lighting soft
> lighting gentle
[Repeated 1 time(s)]
> lighting soft
> lighting gentle
> lighting soft
> lighting simple
> view 1
> lighting simple
> show #!2 models
> hide #!1 models
> select #2/J:43
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/J:44
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
3011 atoms, 3381 bonds, 146 residues, 1 model selected
> show sel cartoons
> select clear
> select #2/J:43
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/J:44
42 atoms, 46 bonds, 2 residues, 1 model selected
> select up
3011 atoms, 3381 bonds, 146 residues, 1 model selected
> transparency sel 50
> select clear
> select #2/J:43
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/J:44
42 atoms, 46 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select clear
> show #!1 models
> view 1
> show cartoons
> select clear
> view 1
> view name 2
> hide #!2 models
> select #1/E:79@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> style sel ball
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> select #1/K:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
57 atoms, 57 bonds, 7 residues, 2 models selected
> transparency sel target c
Missing or invalid "percent" argument: Expected a number
> transparency sel 50 target c
> select #1/K:128
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> select down
100 atoms, 104 bonds, 12 residues, 2 models selected
> transparency sel 50 target c
> select #1/K:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> transparency sel 50 target c
> select clear
> lighting simple
> lighting soft
> transparency sel 70 target c
> select clear
> select #1/K:128
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> transparency sel 70 target c
> lighting simple
> select clear
> select #1/K:134
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> transparency sel 0 target c
> select clear
> select #1/K:132
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 12 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium turquoise
> color sel turquoise
> color sel dodger blue
> color sel crimson
> select clear
> select #1/E:79@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> style sel sphere
Changed 9 atom styles
> lighting soft
> select clear
> lighting soft
> lighting full
> lighting simple
[Repeated 1 time(s)]
> select #1/E:79@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> transparency sel 50 target a
> select clear
> select #1/E:79@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> transparency sel 0 target a
> select clear
> select #1/K:305@CB
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> style sel ball
Changed 14 atom styles
> select clear
> view 2
> select #1/K:305@CD1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> style sel sphere
Changed 14 atom styles
> select clear
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting simple
> lighting full
> lighting simple
> lighting
Intensity: 1
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0.5
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 0.4
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01)
> lighting fillIntensity 1
> lighting fillIntensity 0.5
> lighting fillIntensity 0.
> lighting fillIntensity 0.5
> lighting fillIntensity 0.2
> lighting fillIntensity 0.8
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting fillIntensity 0.5
> lighting soft
> select clear
> lighting
Intensity: 0
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.5
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)
> lighting fillIntensity 0.2
> lighting gentle
> lighting
Intensity: 0
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.5
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 128, depth bias 0.05)
> lighting gentle
> lighting soft
> view 2
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> set subdivision 3
> set subdivision 10
> set subdivision 1
> set subdivision 10
> lighting simple
> graphics silhouettes false
> lighting simple
> lighting soft
> save 6nj9_view2_k79_soft1.png transparentBackground true
> view 2
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> view list
Named views: 1, 2, lys79
> view lys79
> view 2
> show #!2 models
> hide #!1 models
> select #2/A:79@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel ball
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel sphere
Changed 9 atom styles
> show #!1 models
> select clear
> hide #!2 models
> view name lys79
> save 6nj9_view2_k79_soft1.png transparentBackground true
> show #!2 models
> hide #!1 models
> save 6nj9_view2_k79_soft2.png transparentBackground true
> view 2
> show #!1 models
> hide #!2 models
> graphics silhouettes true
> save 6nj9_view2.png transparentBackground true
> view name lys79
[Repeated 1 time(s)]
> view 2
> view lys79
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save 6nj9_view2_k79_soft1.png transparentBackground true
> show #!2 models
> hide #!1 models
> save 6nj9_view2_k79_soft2.png transparentBackground true
> select #2/I:113
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:95
40 atoms, 43 bonds, 2 residues, 1 model selected
> distance sel
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
40
> select clear
> ui tool show "Scale Bar"
> scalebar
> scalebar 10
> lighting gentle
> lighting soft
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 61, in _color_changed
self._update_scalebar()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 65, in _update_scalebar
self._show_scalebar()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 70, in _show_scalebar
options = self._changed_options()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 90, in _changed_options
length = self._length.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '10lig'
ValueError: invalid literal for int() with base 10: '10lig'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 61, in _color_changed
self._update_scalebar()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 65, in _update_scalebar
self._show_scalebar()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 70, in _show_scalebar
options = self._changed_options()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 90, in _changed_options
length = self._length.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '10lig'
ValueError: invalid literal for int() with base 10: '10lig'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
See log for complete Python traceback.
> scalebar off
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 65, in _update_scalebar
self._show_scalebar()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 70, in _show_scalebar
options = self._changed_options()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 90, in _changed_options
length = self._length.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '10lig'
ValueError: invalid literal for int() with base 10: '10lig'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 65, in _update_scalebar
self._show_scalebar()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 70, in _show_scalebar
options = self._changed_options()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/label/scalebar_gui.py", line 90, in _changed_options
length = self._length.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '10lig'
ValueError: invalid literal for int() with base 10: '10lig'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value
return self.string_to_value(self._line_edit.text())
See log for complete Python traceback.
> scalebar
> scalebar 10
> save test_N10.png transparentBackground true supersample 10
> save test_N3.png transparentBackground true supersample 10
> save test_N3.png transparentBackground true
> save test_ps01.png transparentBackground true pixelSize 0.1
> save test_ps001.png transparentBackground true pixelSize 0.01
> graphics silhouettes false
> graphics silhouettes true
> save test_ps005.png transparentBackground true pixelSize 0.05
> save test_ps002.png transparentBackground true pixelSize 0.02
> show #!1 models
> hide #!4 models
> view 2
> show #!4 models
> hide #!2 models
> hide #!4 models
> select #1/K:131@CD2
1 atom, 1 residue, 1 model selected
> view 2
> select clear
> view 2
[Repeated 1 time(s)]
> lighting soft
> save 6nj9_view2ps002.png transparentBackground true
> save 6nj9_view2ps002.png transparentBackground true pixelSize 0.02
> save 6nj9_interactions.cxs
——— End of log from Wed Dec 8 23:04:13 2021 ———
opened ChimeraX session
> view 2
> save 6nj9_complex.png transparentBackground true pixelSize 0.1
> save 6nj9_complex.png transparentBackground true pixelSize 0.05
> hide #!1 atoms
> save 6nj9_complex.png transparentBackground true pixelSize 0.05
> select :sam
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save 6nj9_complex.png transparentBackground true pixelSize 0.05
> view 2
> select add #1/K:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/E:79
20 atoms, 19 bonds, 2 residues, 2 models selected
> select add #1/K:305
34 atoms, 34 bonds, 3 residues, 3 models selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select #1/F:19
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> view 2
> save 6nj9_k79_active.png transparentBackground true pixelSize 0.02
> hide #!1 atoms
> select :sam
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/l:36,71,73
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 24 atom styles
> open
> /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dup.pdb
> format pdb
Chain information for 6nj9_dup.pdb #3
---
Chain | Description
A | No description available
B F | No description available
C G | No description available
D H | No description available
E | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> select #3
15511 atoms, 16399 bonds, 1479 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> color #1/a,e lime green
> color #1/b,f medium slate blue
> color #3/c,g sandy brown
> color #3/d,h olive
> hide #!1 models
> select clear
> hide #3 models
> show #!1 models
> color #3/a,e lime green
> color #3/b,f medium slate blue
> show #3 models
> hide #!1 models
> color #3/k crimson
> color #3/l cornflower blue
> color #3/i,j dim gray
> view 2
> show #!1 models
> hide #!1 models
> show #!1 models
> select #3/l:36,71,73
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> show #3/l:36,71,73 atoms
> style #3/l:36,71,73 stick
Changed 24 atom styles
> show #1/l:36,71,73 atoms
> style #3/l:36,71,73 sphere
Changed 24 atom styles
> style #3/l:36,71,73 sphere trans 50 traget a
Expected a keyword
> select #1/l:36,71,73
24 atoms, 21 bonds, 3 residues, 1 model selected
> transparency sel 50 target a
> hide #3 models
> show #3 models
> select #3/l:36,71,73
24 atoms, 21 bonds, 3 residues, 1 model selected
> style sel stick
Changed 24 atom styles
> select clear
> lighting simple
> lighting soft
> show #1/k:284,290,322,326
> transparency #1/k:284,290,322,326 50 target a
> transparency #3/k:284,290,322,326 50 target a
> style #1/k:284,290,322,326 stick
Changed 35 atom styles
> style #1/k:284,290,322,326 sphere
Changed 35 atom styles
> select #3/k:284,290,322,326
35 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 35 atom styles
> transparency sel 0 target a
> select clear
> select #1/K:500@CE
1 atom, 1 residue, 1 model selected
> cofr sel
> select clear
> view 2
> lighting simple
[Repeated 1 time(s)]
> view 2
> lighting soft
> select #1/k:284,290,322,326
35 atoms, 32 bonds, 4 residues, 1 model selected
> transparency sel 0 target a
> select clear
> select #1/L:73@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #1/L:71@CD1
9 atoms, 7 bonds, 2 residues, 2 models selected
> select up
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #1/L:36@CG2
17 atoms, 14 bonds, 3 residues, 2 models selected
> select up
24 atoms, 21 bonds, 3 residues, 2 models selected
> transparency sel 0 target a
> select clear
[Repeated 1 time(s)]
> style #3#!1 stick
Changed 31022 atom styles
> style #3#!1 ball
Changed 31022 atom styles
> style #3#!1 sphere
Changed 31022 atom styles
> select #1/K:500@N1
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> select up
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> select down
27 atoms, 29 bonds, 1 residue, 2 models selected
> style sel stick
Changed 27 atom styles
> style sel ball
Changed 27 atom styles
> select clear
> view 2
> save 6nj9_ub.png transparentBackground true pixelSize 0.02
> hide #3#!1 atoms
> show #3#!1 atoms
> hide #3#!1 atoms
> select #1/k:284,290,322,326
35 atoms, 32 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 35 atom styles
> show sel atoms
> select #1/l:36,71,73
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> view name Ub
> save 6nj9_interactions.cxs
> hide #3#!1 atoms
> show :sam atoms
> select :sam
54 atoms, 58 bonds, 2 residues, 2 models selected
> style sel ball
Changed 54 atom styles
> color sel byatom
> select clear
> view Ub
> select clear
> select #1/I:34
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
2975 atoms, 3333 bonds, 146 residues, 2 models selected
> select up
15511 atoms, 16399 bonds, 1479 residues, 2 models selected
> select down
2975 atoms, 3333 bonds, 146 residues, 13 models selected
> style sel sphere
Changed 2975 atom styles
> show sel atoms
> select clear
> scene dna save
Unknown command: scene dna save
> scene scene_name save
Unknown command: scene scene_name save
> scene
Unknown command: scene
> scene
Unknown command: scene
> scene list
Unknown command: scene list
> scene
Unknown command: scene
> hide #3#!1 atoms
> select clear
> select :sam
54 atoms, 58 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> select #1/K:500@CE
1 atom, 1 residue, 1 model selected
> cofr sel
> view 2
> select #1/K:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/G:21
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
50 atoms, 49 bonds, 7 residues, 2 models selected
> select up
843 atoms, 853 bonds, 109 residues, 2 models selected
> select add #1/H:43
852 atoms, 861 bonds, 110 residues, 2 models selected
> select up
958 atoms, 971 bonds, 122 residues, 3 models selected
> select up
1586 atoms, 1607 bonds, 204 residues, 3 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6nj9_G SES surface #1.8: minimum, -24.56, mean 2.46,
maximum 19.16
Coulombic values for 6nj9_H SES surface #1.9: minimum, -14.09, mean 1.47,
maximum 12.15
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select #1/L:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
22 atoms, 23 bonds, 3 residues, 2 models selected
> select up
597 atoms, 603 bonds, 75 residues, 2 models selected
> hide sel cartoons
> hide #3 models
> hide #!1 models
> show #3 models
> hide #3 models
> show #!1 models
> select #1/G:22@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
50 atoms, 49 bonds, 7 residues, 2 models selected
> select up
843 atoms, 853 bonds, 109 residues, 2 models selected
> select add #1/H:47@NE2
844 atoms, 853 bonds, 110 residues, 2 models selected
> select up
852 atoms, 861 bonds, 110 residues, 3 models selected
> select up
958 atoms, 971 bonds, 122 residues, 3 models selected
> select up
1586 atoms, 1607 bonds, 204 residues, 3 models selected
> transparency sel 50
> transparency sel 70
> transparency sel 30
> select clear
> select #1/g:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> select #1/h:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select clear
> view 2
> transparency 0
> select #1/H:116@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
149 atoms, 151 bonds, 21 residues, 2 models selected
> select up
743 atoms, 754 bonds, 95 residues, 2 models selected
> select add #1/G:22@CA
744 atoms, 754 bonds, 96 residues, 2 models selected
> select up
747 atoms, 757 bonds, 96 residues, 3 models selected
> select up
793 atoms, 803 bonds, 102 residues, 3 models selected
> select up
1586 atoms, 1607 bonds, 204 residues, 3 models selected
> transparency sel 30
> transparency sel 50
> transparency sel 20
> view 2
> select clear
> view name anchor
> save 6nj9_interactions.cxs
> view 2
[Repeated 1 time(s)]
> view name anchor
> cofr #1
> view 2
[Repeated 1 time(s)]
> view name anchor
> save 6nj9_anchor.png transparentBackground true pixelSize 0.02
> view 2
> hide surfaces
> select #1/l
597 atoms, 603 bonds, 75 residues, 1 model selected
> show sel cartoons
> select clear
> view 2
> view name h4
> select clear
> select #1/K:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
198 atoms, 205 bonds, 22 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6nj9_K SES surface #1.12: minimum, -18.74, mean -2.63,
maximum 9.74
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select #1/f:17-19
32 atoms, 32 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 32 atom styles
> select clear
> select #1/K:29@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
230 atoms, 240 bonds, 28 residues, 2 models selected
> select up
2707 atoms, 2779 bonds, 330 residues, 2 models selected
> transparency sel 50
> transparency sel 30
[Repeated 1 time(s)]
> select #1/k:115,138
21 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> color sel green target a
> color sel cyan target a
> color sel byhetero target a
> select clear
> view h4
> select clear
> save 6nj9_h4tail.png transparentBackground true pixelSize 0.02
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> style sel sphere
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> select clear
> select #1/k:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> select clear
> select #1/E:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> view h4
[Repeated 1 time(s)]
> save 6nj9_h4tail.png transparentBackground true pixelSize 0.02
> view h4
> view name h4
> view h4
> view name h4
> view h4
> save 6nj9_h4tail.png transparentBackground true pixelSize 0.02
> view 2
> ~surface
> select clear
> hide #!1 atoms
> select :sam
54 atoms, 58 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> show #!2 models
> select #1/E:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #3 models
> hide #!1 models
> select #3/K:124
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
57 atoms, 57 bonds, 7 residues, 1 model selected
> select up
2707 atoms, 2779 bonds, 330 residues, 1 model selected
> hide sel cartoons
> select #3/K:500@C2'
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/L:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 4 residues, 1 model selected
> select up
597 atoms, 603 bonds, 75 residues, 1 model selected
> hide sel cartoons
> select #3/E:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> view 2
> select clear
> hide #3 models
> show #3 models
> hide #!2 models
> select clear
> show #!2 models
> select #2/A:79@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
54 atoms, 54 bonds, 6 residues, 1 model selected
> select up
791 atoms, 803 bonds, 96 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime
> color sel medium aquamarine
> color sel teal
> color sel steel blue
> color sel medium turquoise
> color sel gold
> color sel orange
> color sel green yellow
> color sel goldenrod
> color sel orange red
> color sel red
> color sel crimson
> color sel maroon
> color sel tomato
> color sel fire brick
> color sel brown
> color sel chocolate
> color sel byhetero
> color sel lime green
> color sel byhetero
> color sel green
> color sel dark cyan
> color sel aquamarine
> color sel lime green
> select clear
> select #2/A:79@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> view 2
[Repeated 1 time(s)]
> select #2/A:79@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel deep pink
> color sel magenta
> color sel violet
> color sel crimson
> color sel orange red
> color sel gold
> color sel yellow
> color sel byhetero
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!1 models
> hide #!1 models
> show #3 models
> select up
54 atoms, 54 bonds, 6 residues, 1 model selected
> select up
791 atoms, 803 bonds, 96 residues, 1 model selected
> color sel gold
> color sel byhetero
> select clear
> view 2
> save 6nj9_6nog_k79.png transparentBackground true pixelSize 0.02
> save 6nj9_6nog_k79_ps005.png transparentBackground true pixelSize 0.05
> show #!1 models
> rename #3 6nj9_dup
> open 6nj9_dup.pdb
Chain information for 6nj9_dup.pdb #5
---
Chain | Description
A | No description available
B F | No description available
C G | No description available
D H | No description available
E | No description available
I | No description available
J | No description available
K | No description available
L | No description available
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/file_history.py", line 93, in file_history_changed_cb
self.update_html()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/file_history.py", line 88, in update_html
fhw.setHtml(html)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 272, in setHtml
tf.write(bytes(html, "utf-8"))
OSError: [Errno 28] No space left on device
Error processing trigger "file history changed":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 272, in setHtml
tf.write(bytes(html, "utf-8"))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 460.91.03
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer:
Model:
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 5.9Gi 4.2Gi 111Mi 5.5Gi 9.3Gi
Swap: 15Gi 3.0Mi 15Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107 [GeForce GTX 1050 Ti] [10de:1c82] (rev a1)
Subsystem: Gigabyte Technology Co., Ltd GP107 [GeForce GTX 1050 Ti] [1458:3764]
Kernel driver in use: nvidia
Locale: ('en_IN', 'ISO8859-1')
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: 2.0.7
ChimeraX-AddCharge: 1.2.1
ChimeraX-AddH: 2.1.10
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: 1.30.2
ChimeraX-AtomicLibrary: 4.1.5
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
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-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: 1.3rc202111230539
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-LinuxSupport: 1.0
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
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
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
line-profiler: 3.3.0
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: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.22
psutil: 5.8.0
ptyprocess: 0.7.0
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
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
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
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Out of space writing file history |
comment:2 by , 4 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
The file history is limited to 200 entries and the thumbnail images are small so the file history can only be may 20 Mbytes in size. If the user has that little disk space there will be lots of places errors occur. I don't think it is worth trying to catch all those. The error message is clear enough
Error processing trigger "file history changed":
OSError: [Errno 28] No space left on device
Note:
See TracTickets
for help on using tickets.
Maybe catch this error and do something nicer?