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Opened 11 months ago
Closed 11 months ago
#16500 closed defect (fixed)
Could not install pyKVFinder module from PyPi repository
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/avorkas/Desktop/ChR1 strucural images/CHR1.cxs"
Opened J548__localfilter.mrc as #1, grid size 288,288,288, pixel 0.821, shown
at level 1, step 1, values float32
Not registering illegal selector name "/A:92-120"
Log from Sat Sep 7 13:44:36 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open S:\19_CaChR1\final\J548__localfilter.mrc format mrc
Opened J548__localfilter.mrc as #1, grid size 288,288,288, pixel 0.821, shown
at level 0.000141, step 2, values float32
> volume #1 style image maximumIntensityProjection true
> volume #1 maximumIntensityProjection false showOutlineBox true imageMode
> "tilted slab" tiltedSlabAxis 0.7922,-0.6098,-0.02302 tiltedSlabOffset 7.22
> tiltedSlabSpacing 0.821 tiltedSlabPlaneCount 28
> volume #1 region 0,0,0,287,287,287 step 1 colorMode opaque8 imageMode "box
> faces"
> volume #1 orthoplanes xyz positionPlanes 143,143,143 imageMode orthoplanes
> open "S:/19_CaChR1/final/final structure of CR1.pdb"
Chain information for final structure of CR1.pdb #2
---
Chain | Description
A B | No description available
> volume #1 region 0,0,142,287,287,142 step 1 colorMode auto8 imageMode "full
> region"
> volume #1 region 0,0,0,287,287,287 step 2
> volume #1 style mesh region 0,0,0,287,287,287 step 2
> volume showOutlineBox false
> transparency 50
> volume hide
> ui mousemode right select
Drag select of 174 atoms, 337 residues, 172 bonds
> volume show
[Repeated 1 time(s)]Drag select of 1 J548__localfilter.mrc , 174 atoms, 418
residues, 172 bonds
> select clear
Drag select of 1 J548__localfilter.mrc , 174 atoms, 336 residues, 172 bonds
> show #1.2 models
> hide #1.2 models
> select subtract #1.1
2779 atoms, 172 bonds, 338 residues, 2 models selected
> hide #2 models
> show #2 models
> select add #2
4340 atoms, 4468 bonds, 558 residues, 2 models selected
> select subtract #2
1 model selected
> set bgColor white
> color #2 #ff007fff
> volume #1 change image level -0.0006802,0 level 1.028,0.8 level 10.28,1
> volume #1 level 1.592
> select /A
2162 atoms, 2234 bonds, 271 residues, 1 model selected
> show sel surfaces
> transparency sel 50
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> color sel orange
> color sel yellow
> color sel byhetero
> hide sel surfaces
[Repeated 1 time(s)]
> select /A:285@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
66 atoms, 66 bonds, 9 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> hide sel surfaces
> select clear
> hide #1.1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel surfaces
> transparency sel 50
> volume style mesh
[Repeated 1 time(s)]
> volume hide
> select /B:604@C12
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
2160 atoms, 2234 bonds, 269 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select down
20 atoms, 20 bonds, 1 residue, 2 models selected
> show sel surfaces
> transparency sel 50
> select /A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel surfaces
> color sel byhetero
> select clear
Drag select of final structure of CR1.pdb_A SES surface, 497 of 5194
triangles, 3 atoms, 6 residues, 2 bonds
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> view
> lighting simple
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> show surfaces
> hide cartoons
> lighting soft
> quality high
Unknown command: quality high
> quality high
Unknown command: quality high
> surface style #2 mesh
> surface style #2 dot
> surface style #2 solid
> select /A:235@CD2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
245 atoms, 254 bonds, 29 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> hide sel atoms
> select clear
> clip plane
Expected a keyword
> clip surface
Expected a keyword
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.1475
> volume #1 color #82828280
> volume #1 color #00000080
> volume #1 color #9c9c9c80
> volume #1 step 4
> volume #1 step 1
> view
> view orient
> ui tool show "Side View"
> hide #!1 models
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
[Repeated 3 time(s)]
> select clear
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> view sel
> view orient
> ui tool show "Side View"
> select clear
> select #A: 1-50
Expected an objects specifier or a keyword
> select #A: 1,50
Expected an objects specifier or a keyword
> select #A: 1:50
Expected an objects specifier or a keyword
> select #A 1:50
Expected an objects specifier or a keyword
> select #A 1:50
Expected an objects specifier or a keyword
> select #1:20-40.a
Expected an objects specifier or a keyword
> select #1:20-40
Nothing selected
> select #1: 20-40
Nothing selected
> select #2 :1-50
11 atoms, 11 residues, 1 model selected
> select #2 :1-90
498 atoms, 498 bonds, 84 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select /B:233@CB
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
245 atoms, 254 bonds, 29 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 5 models selected
> select /B:208@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
161 atoms, 161 bonds, 22 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> hide sel surfaces
> select /A:191@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
72 atoms, 72 bonds, 10 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> hide sel surfaces
Drag select of 120 atoms, 120 bonds
> hide sel atoms
Drag select of 20 atoms, 20 bonds
> hide sel atoms
> select #2 :1-90
498 atoms, 498 bonds, 84 residues, 1 model selected
> view sel
> ui tool show "Side View"
> view orient
> view
[Repeated 1 time(s)]
> view orient
> show sel cartoons
> select /B:87
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
45 atoms, 46 bonds, 6 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 5 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 7 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 8 models selected
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> select /B:68
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
179 atoms, 183 bonds, 26 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> hide sel cartoons
> select /A:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show "Modeller Comparative"
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select
> /A:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select /A:89
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:89
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:92-93
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> view sel
> view
> view orient
> name frozen TMHA sel
[Repeated 2 time(s)]
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> show #2.2 target m
> view #2.2 clip false
No displayed objects specified.
> select TMHA
2140 atoms, 258 bonds, 268 residues, 1 model selected
> select clear
> select /A:92-93
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> name TMHA a
"a": invalid atom specifier
> name frozen TMHA sel
> select TMHA
2140 atoms, 258 bonds, 268 residues, 1 model selected
> select clear
> select TMHA
2140 atoms, 258 bonds, 268 residues, 1 model selected
> select clear
> ui tool show "Model Panel"
> ui tool show "Altloc Explorer"
> table
Unknown command: modeller table
> select helix
3000 atoms, 3092 bonds, 362 residues, 1 model selected
> select clear
> select /A:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> name /A:92-120 TMHA
Not registering illegal selector name "/A:92-120"
> name TMH'A /A:92-120
"/A:92-120 ": contains extra trailing text
> name TMH-A /A:92-120
"/A:92-120 ": contains extra trailing text
> name TMHA /A:92-120
"/A:92-120 ": contains extra trailing text
> name /A:92-120
"/A:92-120" is not defined
> name a, /A:92-120
"/A:92-120 ": contains extra trailing text
> label TMHA
> DELETE LABEL
Unknown command: DELETE LABEL
> delete label
Missing or invalid "atoms" argument: invalid atoms specifier
> ~label
> hide sel cartoons
> show sel cartoons
> select /A:127
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:127-145
167 atoms, 172 bonds, 19 residues, 1 model selected
> name frozen TMHB sel
> select /A:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> name frozen TMHC sel
> select /A:193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:193-214
161 atoms, 161 bonds, 22 residues, 1 model selected
> name frozen TMHD sel
> select /A:218
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:218-246
245 atoms, 254 bonds, 29 residues, 1 model selected
> name frozen TMHE sel
> select /A:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> name frozen TMHF sel
> select /A:288-289
19 atoms, 20 bonds, 2 residues, 1 model selected
> select /A:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> name frozen TMHG sel
> select clear
> select /A:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> name frozen N-Terminus sel
> select /A:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:121-126
45 atoms, 46 bonds, 6 residues, 1 model selected
> name frozen PL1 sel
> select /A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:147-161
115 atoms, 117 bonds, 15 residues, 1 model selected
> select /A:146
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:146-163
140 atoms, 143 bonds, 18 residues, 1 model selected
> name frozen PL2 sel
> select /A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:183-192
72 atoms, 72 bonds, 10 residues, 1 model selected
> name frozen PL3 sel
> select /A:215
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:215-217
21 atoms, 20 bonds, 3 residues, 1 model selected
> name frozen PL4 sel
> select /A:247
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:247-252
46 atoms, 47 bonds, 6 residues, 1 model selected
> name frozen PL5 sel
> select /A:279
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> name frozen PL6 sel
> select clear
> color BLUE PL1-PL5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color PL1-PL5 BLUE
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color PL1-PL5 blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color PL1 blue
> color PL2 blue
> color PL3 blue
> color PL4 blue
> color PL5 blue
> color PL1 blue
> color N-Terminus blue
Drag select of 1 residues
> select clear
[Repeated 3 time(s)]
> select
> /A:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select clear
> select /A:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> select /A:186
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:186-189
26 atoms, 25 bonds, 4 residues, 1 model selected
> select /A:279
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:279-286
60 atoms, 60 bonds, 8 residues, 1 model selected
> select /A:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> color PL5 blue
> color PL4 blue
> color PL3 blue
> color PL2 blue
> color PL6 blue
> select clear
[Repeated 2 time(s)]
> select /A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel cartoons
> show sel atoms
> color sel byhetero
> show #!1 models
> volume #1 level 4.574
> volume #1 level 1.277
Drag select of 1 J548__localfilter.mrc , 128 residues
> select clear
> select #1
3 models selected
> select clear
> volume #1 style surface
> select /A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> view sel
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> transparency sel 0
> volume hide
> volume show
> volume style mesh
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/e136 density map and
> point out.png" width 1101 height 789 supersample 3 transparentBackground
> true
> select #1
3 models selected
> select #1
3 models selected
> select clear
> select #1
3 models selected
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> volume style surface
> volume style mesh
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/e136 density map and
> point out.png" width 1101 height 789 supersample 3 transparentBackground
> true
> view orient
> ui tool show "Side View"
> hide #!1 models
> ~label
> hide atoms
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
[Repeated 2 time(s)]
> select /A:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> /A:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select /A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 3 atoms, 25 residues, 2 bonds
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select clear
Drag select of 143 atoms, 67 residues, 125 bonds
> hide sel atoms
> select clear
> hide atoms
> select /A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
Drag select of 20 atoms, 20 bonds
> hide sel atoms
> show #!1 models
> select /A:302
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select /A:302
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> view
> view orient
> select clear
> hide #!1 models
> show #2.3 models
> show #2.4 models
> show surfaces
> hide cartoons
> hide atoms
Drag select of final structure of CR1.pdb_A SES surface, final structure of
CR1.pdb_A SES surface, final structure of CR1.pdb_B SES surface, final
structure of CR1.pdb_B SES surface
> select /A:277@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
64 atoms, 67 bonds, 7 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> color #2 #ff007fff
> transparency 80 surfaces
> select clear
> select /A:259@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
141 atoms, 145 bonds, 17 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select /B:169@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
164 atoms, 170 bonds, 19 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select ~sel & ##selected
2180 atoms, 2234 bonds, 289 residues, 1 model selected
> select ~sel & ##selected
2160 atoms, 2234 bonds, 269 residues, 1 model selected
> transparency 0 surfaces
> show sel surfaces
[Repeated 1 time(s)]
> select clear
> show surfaces
> select /A:242@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
245 atoms, 254 bonds, 29 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select transaprency 80 s
Expected an objects specifier or a keyword
> select transarency 80 s
Expected an objects specifier or a keyword
> select transparency 80 s
Expected an objects specifier or a keyword
> surface style #2.1-2 mesh
> transparency (#!2 & sel) 80
> surface style #2.1-2 solid
> select clear
> color bychain
> color byhetero
> color bychain
> color bypolymer
> rainbow
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for final structure of CR1.pdb_A SES surface #2.1: minimum,
-14.89, mean -1.30, maximum 13.83
Coulombic values for final structure of CR1.pdb_B SES surface #2.3: minimum,
-14.88, mean -1.31, maximum 14.39
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "final structure of CR1.pdb_A SES surface": minimum
-26.34, mean 1.187, maximum 23.89
Map values for surface "final structure of CR1.pdb_B SES surface": minimum
-25.89, mean 1.19, maximum 23.82
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor
4340 atoms, 558 residues, 4 surfaces, atom bfactor range 10.5 to 96.3
> color bychain
> view
> color #2 #ff007fff
> view
[Repeated 1 time(s)]
> view orient
> view
> select /B:120@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
247 atoms, 258 bonds, 29 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> color (#!2 & sel) hot pink
> select clear
> select /B:324@CE1
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> select up
179 atoms, 184 bonds, 21 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> transparency (#!2 & sel) 80
> show sel cartoons
> select clear
> color N-Terminus blue
> select ~sel & ##selected
Nothing selected
> select down
Nothing selected
> color N-Terminus magenta
> color N-Terminus pink
> select n-terminus
Expected an objects specifier or a keyword
> select N-Terminus
2140 atoms, 255 bonds, 268 residues, 1 model selected
> color (#!2 & sel) hot pink
> color #2 #ff007fff
> select /B:247@NE2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> select up
46 atoms, 47 bonds, 6 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> color (#!2 & sel) hot pink
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 1.png"
> width 861 height 640 supersample 3 transparentBackground true
> select /B:235@CD2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
245 atoms, 254 bonds, 29 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> view sel
> transparency (#!2 & sel) 50
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 2.png"
> width 861 height 640 supersample 3 transparentBackground true
> show #!1 models
> hide #!2 models
> volume #1 level 0.8497
> volume #1 style surface
> volume #1 color #9c7474
> volume #1 color #ff007f
> volume #1 color #ffb8bd
> volume #1 color #ffb9be
> volume #1 color black
> volume #1 color white
> volume #1 color #7d7d7d
> volume #1 color white
> volume #1 color #868686
> view
> view orient
> view
> volume #1 level 0.6665
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #1 level 1.155
> volume #1 level 1.002
> hide #!1 models
> show #!1 models
> hide #!2 models
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/cryoEM map density.png"
> width 861 height 640 supersample 3 transparentBackground true
> volume #1 style image
> volume #1 maximumIntensityProjection true
> volume #1 color #aaaaff color white color white
> volume #1 style surface maximumIntensityProjection false
> volume #1 style mesh
> hide #!1 models
> show #!2 models
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> color (#!2 & sel) yellow
> transparency (#!2 & sel) 70
> transparency (#!2 & sel) 30
> select clear
> select /A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /A:302-303
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:302-311
76 atoms, 77 bonds, 10 residues, 1 model selected
> select /A:297
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:263-297
286 atoms, 298 bonds, 35 residues, 1 model selected
> select
> /A:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select clear
> ui tool show "Modeller Comparative"
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 2/B
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 2.png"
> width 861 height 640 supersample 3
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 2.png"
> width 861 height 640 supersample 3 transparentBackground true
> select /A:144@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
167 atoms, 172 bonds, 19 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 3.png"
> width 861 height 640 supersample 3 transparentBackground true
> select /A:294
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
109 atoms, 111 bonds, 15 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> view
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/chr1 monomer.png" width
> 861 height 640 supersample 3
> view orient
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/top view full.png"
> width 861 height 640 supersample 3 transparentBackground true
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/top view half.png"
> width 861 height 640 supersample 3 transparentBackground true
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/top view full.png"
> width 861 height 640 supersample 3 transparentBackground true
> tilt 90
Unknown command: tilt 90
> tilt
Unknown command: tilt
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/btm view.png" width 861
> height 640 supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/chr1 monomer.png" width
> 861 height 640 supersample 3 transparentBackground true
> set raytrace true
Expected a keyword
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/chr1 monomer.png" width
> 40359 height 30000 supersample 4 transparentBackground true
Image size 40359 x 30000 too large, exceeds maximum OpenGL render buffer size
16384
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/chr1 monomer.png" width
> 2000 height 1487 supersample 4 transparentBackground true
> select clear
> select /B:199
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
161 atoms, 161 bonds, 22 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel surfaces
> transparency (#!2 & sel) 70
> select clear
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel surfaces
> hide sel surfaces
> select clear
> select /A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 3.png"
> width 2000 height 1487 supersample 4 transparentBackground true
> select clear
[Repeated 1 time(s)]
> select /B:222
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
245 atoms, 254 bonds, 29 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> show sel surfaces
> select /A:87
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
45 atoms, 46 bonds, 6 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> show sel surfaces
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 2.png"
> width 2000 height 1487 supersample 4 transparentBackground true
> select /B:84@N
1 atom, 1 residue, 1 model selected
> select /B:84@N
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
23 atoms, 24 bonds, 3 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> transparency (#!2 & sel) 0
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHr1 surface 1.png"
> width 2000 height 1487 supersample 4 transparentBackground true
> show #!1 models
> hide #!2 models
> volume #1 style surface
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/cryoEM map density.png"
> width 2000 height 1487 supersample 4 transparentBackground true
> volume #1 style mesh
> show #!2 models
> volume #1 level -0.005148
> volume #1 level 0.05591
> volume #1 step 2
> volume #1 step 4
> volume #1 step 8
> volume #1 step 1
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/EMMAP AND FIT SURFACE
> MODEL.png" width 2000 height 1487 supersample 4 transparentBackground true
> volume #1 style surface
> volume #1 style mesh
> select /B:70@N
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
179 atoms, 183 bonds, 26 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 5 models selected
> hide sel surfaces
> select clear
> volume #1 level 1.002
> hide #!1 models
> select clear
> select /A:65
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:59
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
179 atoms, 183 bonds, 26 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select clear
> view orient
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/top view full.png"
> width 2000 height 1487 supersample 4 transparentBackground true
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/top view half.png"
> width 2000 height 1487 supersample 4 transparentBackground true
> select clear
[Repeated 1 time(s)]
> turn z 180
[Repeated 1 time(s)]
> turn y 180
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/btm view.png" width
> 2000 height 1487 supersample 4 transparentBackground true
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> show sel surfaces
> select up
20 atoms, 20 bonds, 1 residue, 2 models selected
> show sel surfaces
> transparency (#!2 & sel) 80
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/chr1 monomer.png" width
> 2000 height 1487 supersample 4 transparentBackground true
[Repeated 1 time(s)]
> hide all
> select clear
> select /B:219
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
245 atoms, 254 bonds, 29 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> hide all
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select N-Terminus
2140 atoms, 255 bonds, 268 residues, 1 model selected
> show sel cartoons
> Select TMHA
Unknown command: Select TMHA
> select TMHA
2140 atoms, 258 bonds, 268 residues, 1 model selected
> show sel cartoons
[Repeated 2 time(s)]
> hide sel cartoons
> select clear
> select N-Terminus
2140 atoms, 255 bonds, 268 residues, 1 model selected
> select clear
> select TMHA
2140 atoms, 258 bonds, 268 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select /B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> show sel cartoons
> select clear
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-324
1893 atoms, 1957 bonds, 233 residues, 1 model selected
> select /A:324
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:147-324
1424 atoms, 1467 bonds, 178 residues, 1 model selected
> select /B:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
179 atoms, 183 bonds, 26 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 5 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 7 models selected
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> select /A:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
179 atoms, 183 bonds, 26 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> hide sel cartoons
> select clear
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel surfaces
> select clear
Drag select of final structure of CR1.pdb_A SES surface, 5166 of 5194
triangles, 20 atoms, 20 bonds
> hide sel surfaces
> hide sel atoms
> select /B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> color (#!2 & sel) cornflower blue
> select clear
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> color #2.3 magenta
> color #2.3 #ff007fff
> color #2.3 #ff72c3ff
> undo
[Repeated 1 time(s)]
> select clear
> undo
[Repeated 2 time(s)]
> color #2.3 #ff55ffff
> color #2.3 #55557fff
> color #2.3 #ff007fff
> color #2.3 magenta
> color (#!2 & sel) magenta
> color (#!2 & sel) hot pink
> select clear
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-324
1893 atoms, 1957 bonds, 233 residues, 1 model selected
> transparency 80 cartoons
> select transparency 80 c
Expected an objects specifier or a keyword
> transparency 0 cartoons
> transparency sel 0 cartoons
> transparency sel 0
> transparency select 0 c
Missing or invalid "percent" argument: Expected a number
> transparency select 0
Missing or invalid "percent" argument: Expected a number
> transparency select 80
Missing or invalid "percent" argument: Expected a number
> transparency sel 80
> transparency sel 100
> transparency sel 100c
Missing or invalid "percent" argument: Expected a number
> transparency sel 100 cartoons
> transparency sel 80 cartoons
> transparency sel 80 a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency sel 80 surfaces
> transparency sel 80 a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!2 & sel) yellow
> color sel byhetero
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/Nterminus.png" width
> 2000 height 1487 supersample 4 transparentBackground true
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-324
1893 atoms, 1957 bonds, 233 residues, 1 model selected
> transparency sel 60 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/Nterminus 2.png" width
> 2000 height 1487 supersample 4 transparentBackground true
> select clear
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-324
1893 atoms, 1957 bonds, 233 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
[Repeated 1 time(s)]
> select /B:88-118
252 atoms, 263 bonds, 31 residues, 1 model selected
> select /B:88-118
252 atoms, 263 bonds, 31 residues, 1 model selected
> select /B:181-211
229 atoms, 230 bonds, 31 residues, 1 model selected
> select /B:181-211
229 atoms, 230 bonds, 31 residues, 1 model selected
> select
> /B:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select clear
> select /B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> transparency sel 60 cartoons
> select clear
> select
> /B:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select clear
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select
> /B:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> transparency sel 0 cartoons
> select /B:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:122-161
323 atoms, 332 bonds, 40 residues, 1 model selected
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> transparency sel 60 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHA.png" width 2000
> height 1487 supersample 3 transparentBackground true
> transparency sel 0 cartoons
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:151
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:151
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:124
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:124
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 6 residues
Drag select of 9 residues
Drag select of 17 residues
> transparency sel 60 cartoons
> select clear
> select /B:121-122
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> transparency sel 60 cartoons
> select clear
Drag select of 2 residues
> select clear
[Repeated 1 time(s)]
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:269
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:269
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select clear
[Repeated 3 time(s)]
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /B:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:120-121
26 atoms, 28 bonds, 2 residues, 1 model selected
> select /B:120
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:120
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:90-120
257 atoms, 268 bonds, 31 residues, 1 model selected
> select /B:89-120
267 atoms, 279 bonds, 32 residues, 1 model selected
> select /B:89
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:89
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:60
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:60-61
15 atoms, 14 bonds, 2 residues, 1 model selected
> select clear
> select /B:89
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:89-120
267 atoms, 279 bonds, 32 residues, 1 model selected
> select /B:120-150
268 atoms, 278 bonds, 31 residues, 1 model selected
> select /B:120-150
268 atoms, 278 bonds, 31 residues, 1 model selected
> select /B:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:181-213
239 atoms, 240 bonds, 33 residues, 1 model selected
> select /B:219
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:219
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:237
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:237-266
238 atoms, 243 bonds, 30 residues, 1 model selected
> select clear
> select /B:156
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:156
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:285
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:285-286
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /B:286-316
239 atoms, 244 bonds, 31 residues, 1 model selected
> select /B:286-316
239 atoms, 244 bonds, 31 residues, 1 model selected
> select /B:134
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:133-134
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /B:101-102
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:101-102
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-124
35 atoms, 36 bonds, 4 residues, 1 model selected
> select /B:125
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:125-127
24 atoms, 25 bonds, 3 residues, 1 model selected
> select /B:126
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:125-126
10 atoms, 9 bonds, 2 residues, 1 model selected
> select clear
> select /A:147-324
1424 atoms, 1467 bonds, 178 residues, 1 model selected
> select /A:179
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:179-302
974 atoms, 1002 bonds, 124 residues, 1 model selected
> select /A:117-146
262 atoms, 273 bonds, 30 residues, 1 model selected
> select /A:91-146
475 atoms, 495 bonds, 56 residues, 1 model selected
> select /A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:65
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:65-94
220 atoms, 228 bonds, 30 residues, 1 model selected
> select /A:90-91
10 atoms, 9 bonds, 2 residues, 1 model selected
> select /A:87-91
33 atoms, 33 bonds, 5 residues, 1 model selected
> select /A:57-86
214 atoms, 221 bonds, 30 residues, 1 model selected
> select /A:57-86
214 atoms, 221 bonds, 30 residues, 1 model selected
> select /A:57-58
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /A:57-65
60 atoms, 60 bonds, 9 residues, 1 model selected
> select /A:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:63-301
1907 atoms, 1973 bonds, 239 residues, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select clear
> REFRESH
Unknown command: REFRESH
> refresh
Unknown command: refresh
> select
> /B:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:131
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:131
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select clear
[Repeated 2 time(s)]Drag select of 6 residues
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select clear
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-126
45 atoms, 46 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> transparency sel 60 cartoons
> select
> /B:83-85,92-120,127-145,164-182,193-214,218-246,253-269,272-278,288-302,304-324
1500 atoms, 1546 bonds, 181 residues, 1 model selected
> select clear
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> show sel atoms
> color sel byhetero
> label sel
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> transparency sel 100 cartoons
> transparency sel 100 surfaces
> select /B:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> transparency sel 100 cartoons
> select clear
Drag select of final structure of CR1.pdb_B SES surface, 4505 of 5220
triangles, 23 atoms, 59 residues, 25 bonds
> hide sel atoms
> hide sel surfaces
Drag select of final structure of CR1.pdb_B SES surface, 908 of 5220
triangles, 3 atoms, 26 residues, 1 bonds
> hide sel surfaces
> select clear
Drag select of 3 atoms, 26 residues, 1 bonds
> hide sel atoms
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHA 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select down
Nothing selected
> label sel del
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> delete sel label
Expected a keyword
> delete label
Missing or invalid "atoms" argument: invalid atoms specifier
> delete lab
Missing or invalid "atoms" argument: invalid atoms specifier
> delete la
Missing or invalid "atoms" argument: invalid atoms specifier
> delete l
Missing or invalid "atoms" argument: invalid atoms specifier
> delete
Missing or invalid "atoms" argument: empty atom specifier
> select /B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> delete label
Missing or invalid "atoms" argument: invalid atoms specifier
> delete sel label
Expected a keyword
> ui tool show "Selection Inspector"
> ~label (#!2 & sel) residues
> select clear
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> hide sel atoms
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> show sel cartoons
> transparency sel 0 cartoons
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> transparency sel 100 cartoons
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> show sel atoms
> color sel byhetero
> label sel
> view sel
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/Nterminus 3.png" width
> 2000 height 1487 supersample 4 transparentBackground true
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/Nterminus 3.png" width
> 2000 height 1487 supersample 4 transparentBackground true
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> ~label (#!2 & sel) residues
> hide sel atoms
> select /B:91-120
253 atoms, 264 bonds, 30 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> transparency sel 60 cartoons
Drag select of 212 residues
> transparency sel 100 cartoons
> select /B:209
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:209
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-125
41 atoms, 42 bonds, 5 residues, 1 model selected
> select /B:126
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:126-127
18 atoms, 19 bonds, 2 residues, 1 model selected
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select /B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:57-324
2140 atoms, 2213 bonds, 268 residues, 1 model selected
> transparency sel 600 cartoons
> transparency sel 60 cartoons
> view sel
> select clear
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel surfaces
Drag select of final structure of CR1.pdb_A SES surface, 20 atoms, 20 bonds
> hide sel surfaces
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-126
45 atoms, 46 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL1 .png" width 2000
> height 1487 supersample 4 transparentBackground true
> transparency sel 60 cartoons
> select /B:121-126
45 atoms, 46 bonds, 6 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:127-128
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /B:127-128
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /B:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:127-128
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /B:127-145
167 atoms, 172 bonds, 19 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHB.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:127-145
167 atoms, 172 bonds, 19 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:146
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:146-163
140 atoms, 143 bonds, 18 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:146-163
140 atoms, 143 bonds, 18 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
[Repeated 1 time(s)]
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHC.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:183-192
72 atoms, 72 bonds, 10 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL3.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:183-192
72 atoms, 72 bonds, 10 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:193-246
427 atoms, 437 bonds, 54 residues, 1 model selected
> select /B:193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:193-214
161 atoms, 161 bonds, 22 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHD.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:193-214
161 atoms, 161 bonds, 22 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:215
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:215-217
21 atoms, 20 bonds, 3 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL4.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:215-217
21 atoms, 20 bonds, 3 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:218
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:218-246
245 atoms, 254 bonds, 29 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHE.png" width 861
> height 640 supersample 3
> select /B:218-246
245 atoms, 254 bonds, 29 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:247-248
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B:247-252
46 atoms, 47 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL5.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:247-252
46 atoms, 47 bonds, 6 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHF.png" width 861
> height 640 supersample 3
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:279-280
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /B:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL6.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:288
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHG.png" width 861
> height 640 supersample 3
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/Nterminus 2.png" width
> 2000 height 1487 supersample 4 transparentBackground true
> select /B:57-91
247 atoms, 255 bonds, 35 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> transparency sel 0 cartoons
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHA.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHA.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:92-120
247 atoms, 258 bonds, 29 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-126
45 atoms, 46 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
[Repeated 1 time(s)]
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL1 .png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:218
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:218-246
245 atoms, 254 bonds, 29 residues, 1 model selected
> transparency sel 0 cartoons
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-126
45 atoms, 46 bonds, 6 residues, 1 model selected
> transparency sel 60 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHE.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select /B:218
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:218-246
245 atoms, 254 bonds, 29 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHF.png" width 2000
> height 1487 supersample 3 transparentBackground true
> select /B:121-324
1646 atoms, 1698 bonds, 204 residues, 1 model selected
> select clear
> select /B:254
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:254-281
233 atoms, 242 bonds, 28 residues, 1 model selected
> select /B:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> transparency sel 60 cartoons
> select clear
> select /B:288
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHG.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> transparency sel 60 cartoons
> select /B:57-58
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /B:57-324
2140 atoms, 2213 bonds, 268 residues, 1 model selected
> transparency sel 100 cartoons
> transparency sel 100 surfaces
Drag select of final structure of CR1.pdb_B SES surface, 26 atoms, 169
residues, 26 bonds
> hide sel atoms
> hide sel surfaces
> select clear
> select /B:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:121-126
45 atoms, 46 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> show sel atoms
> color sel byhetero
> LABEL
Unknown command: LABEL
> label
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL1_a.png" width 2000
> height 1487 supersample 3 transparentBackground true
Drag select of 26 atoms, 36 residues, 23 bonds
> hide sel surfaces
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select /B:182
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:182
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:256
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /B:127-128
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /B:127-145
167 atoms, 172 bonds, 19 residues, 1 model selected
> view sel
> show sel atoms
> color sel byhetero
> show sel cartoons
> transparency 0 cartoons
> transparency 100 cartoons
> transparency sel 100 cartoons
> transparency sel 0 cartoons
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> view sel
> select clear
[Repeated 1 time(s)]
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHB 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
Drag select of 110 atoms, 96 residues, 97 bonds
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select clear
> select /B:146
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:146-160
117 atoms, 120 bonds, 15 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL2 A.png" width 2000
> height 1487 supersample 4 transparentBackground true
Drag select of 73 atoms, 70 residues, 62 bonds
> hide sel cartoons
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select /B:146-160
117 atoms, 120 bonds, 15 residues, 1 model selected
> transparency sel 100 cartoons
> select /B:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:161-163
23 atoms, 22 bonds, 3 residues, 1 model selected
> select /B:146
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:146-163
140 atoms, 143 bonds, 18 residues, 1 model selected
> select /A:132
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:132-252
965 atoms, 992 bonds, 121 residues, 1 model selected
> select /B:146
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:146-164
154 atoms, 159 bonds, 19 residues, 1 model selected
> select /A:132-252
965 atoms, 992 bonds, 121 residues, 1 model selected
> select /A:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /B:146
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:146-164
154 atoms, 159 bonds, 19 residues, 1 model selected
> select /B:146
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:146-163
140 atoms, 143 bonds, 18 residues, 1 model selected
> transparency sel 0 cartoons
> show sel cartoons
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL2 A.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:146-163
140 atoms, 143 bonds, 18 residues, 1 model selected
> transparency sel 100 cartoons
> hide sel atoms
> ~label (#!2 & sel) residues
> select clear
> select /B:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHB A.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> transparency sel 100 cartoons
> hide sel atoms
> ~label (#!2 & sel) residues
> select /B:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> transparency sel 0 cartoons
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHC 2.png" width 861
> height 640 supersample 3
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> transparency sel 100 cartoons
> select /B:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:183-192
72 atoms, 72 bonds, 10 residues, 1 model selected
> view sel
> transparency sel 0 cartoons
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL3 A.png" width 861
> height 640 supersample 3
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL3 A.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:183-192
72 atoms, 72 bonds, 10 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:193-194
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /B:193-215
169 atoms, 169 bonds, 23 residues, 1 model selected
> view sel
> show sel cartoons
> show sel atoms
> color sel byhetero
> transparency sel 0 cartoons
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /B:300
8 atoms, 7 bonds, 1 residue, 1 model selected
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHD 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:193-215
169 atoms, 169 bonds, 23 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select clear
> select /B:193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:193-214
161 atoms, 161 bonds, 22 residues, 1 model selected
> transparency sel 0 cartoons
> show sel atoms
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHD 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:193-214
161 atoms, 161 bonds, 22 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:215
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:215-217
21 atoms, 20 bonds, 3 residues, 1 model selected
> view sel
> show sel atoms
> color sel byhetero
> transparency sel 0 cartoons
> view orient
> view sel
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL4 A.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:215-217
21 atoms, 20 bonds, 3 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:218
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:218-246
245 atoms, 254 bonds, 29 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHE 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:218-246
245 atoms, 254 bonds, 29 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:247
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:247-252
46 atoms, 47 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> view sel
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL5 A.png" width 2000
> height 1487 supersample 4 transparentBackground true
> transparency sel 100 cartoons
> hide sel atoms
> ~label (#!2 & sel) residues
> select /B:253-254
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHF 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:279
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> select /B:279
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
No displayed objects specified.
> show sel atoms
> transparency sel 0 cartoons
> show sel cartoons
[Repeated 1 time(s)]
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/PL6 A.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:279-287
66 atoms, 66 bonds, 9 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:288
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> view sel
> show sel cartoons
> transparency sel 0 cartoons
> show sel atoms
> color sel byhetero
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHG 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
Drag select of 20 atoms, 20 bonds
> hide sel atoms
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 2 models selected
> label (#!2 & sel) attribute name
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHG 3.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
Drag select of 20 atoms, 39 residues, 20 bonds
> hide sel atoms
> select clear
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> transparency sel 100 cartoons
> select /B:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
No displayed objects specified.
> show sel cartoons
> show sel atoms
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHC 2.png" width 2000
> height 1487 supersample 3 transparentBackground true
> select /B:254
6 atoms, 5 bonds, 1 residue, 1 model selected
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHC 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:164-182
164 atoms, 170 bonds, 19 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:57-58
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /B:57-324
2140 atoms, 2213 bonds, 268 residues, 1 model selected
> transparency sel 0 cartoons
> view sel
> view orient
> transparency sel 0 cartoons
> show sel cartoons
> select clear
> select /B:57-324
2140 atoms, 2213 bonds, 268 residues, 1 model selected
> transparency sel 100 cartoons
> ~label (#!2 & sel) residues
> select /B:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> transparency sel 0 cartoons
> show sel atoms
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHF 2.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:253-278
222 atoms, 231 bonds, 26 residues, 1 model selected
> hide sel atoms
> ~label (#!2 & sel) residues
> transparency sel 100 cartoons
> select /B:288
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> transparency sel 0 cartoons
> show sel atoms
> label (#!2 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select ::name="RET"
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 20 atoms, 18 residues, 20 bonds
> hide sel atoms
> select /B:216
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/TMHG 3.png" width 2000
> height 1487 supersample 4 transparentBackground true
> select /B:288-324
297 atoms, 305 bonds, 37 residues, 1 model selected
> select /B:57-58
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /B:57-324
2140 atoms, 2213 bonds, 268 residues, 1 model selected
> transparency sel 0 cartoons
> hide sel atoms
> ~label (#!2 & sel) residues
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 2 models selected
> hide sel atoms
> save "C:/Users/avorkas/Desktop/ChR1 strucural images/CHR1.cxs" includeMaps
> true
——— End of log from Sat Sep 7 13:44:36 2024 ———
opened ChimeraX session
> ui tool show "Side View"
> find cavities
Unknown command: find cavities
> Find Cavieties
Unknown command: Find Cavieties
> Find Cavities
Unknown command: Find Cavities
> select /B:212
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
161 atoms, 161 bonds, 22 residues, 2 models selected
> select up
2160 atoms, 2234 bonds, 269 residues, 2 models selected
> select up
2162 atoms, 2234 bonds, 271 residues, 3 models selected
> select up
4340 atoms, 4468 bonds, 558 residues, 3 models selected
pyKVFinder module not installed; fetching from PyPi repository...
Traceback (most recent call last):
File "C:\Users\avorkas\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 37, in register_command
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\avorkas\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in register_command
run(logger.session, "pip install pyKVFinder", log=False)
File "C:\Users\avorkas\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\avorkas\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\avorkas\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Users\avorkas\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError
Could not install pyKVFinder module from PyPi repository:
RuntimeError
File "C:\Users\avorkas\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
See log for complete Python traceback.
>
Missing command
OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics 750
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: HP
Model: HP EliteDesk 800 G8 Tower PC
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 68,413,530,112
MaxProcessMemory: 137,438,953,344
CPU: 12 11th Gen Intel(R) Core(TM) i5-11500 @ 2.70GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.1.3
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Could not install pyKVFinder module from PyPi repository |
comment:2 by , 11 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Improved error reporting (I hope)
Note:
See TracTickets
for help on using tickets.
Needs even better error handling