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Opened 4 years ago
Closed 4 years ago
#5564 closed defect (fixed)
Build Structure: cannot change rotamer library
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3rc202111060828 (2021-11-06 08:28:15 UTC)
Description
When enter Build Structure windows under peptide, after apply button click small windows appear, in Rotamer library dropdown menu cannot select others except Dunbrack
Log:
UCSF ChimeraX version: 1.3rc202111060828 (2021-11-06)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/ich/Charisma/Alphafold2/1a2c_cxaf2.cxs format session
Log from Tue Nov 9 10:08:08 2021UCSF ChimeraX version: 1.3rc202111031842
(2021-11-03)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/ich/Charisma/MD_Simulation/Alphafold2/1a2c.pdb
Chain information for 1a2c.pdb #1
---
Chain | Description
H | No description available
I | No description available
> split #1
Split 1a2c.pdb (#1) into 2 models
Chain information for 1a2c.pdb H #1.1
---
Chain | Description
H | No description available
Chain information for 1a2c.pdb I #1.2
---
Chain | Description
I | No description available
> select #1.2/I:355-364
89 atoms, 91 bonds, 10 residues, 1 model selected
> set bgColor white
> select #1.1.1
1 pseudobond, 1 model selected
> ~select #1.1.1
Nothing selected
> select #1.1.1
1 pseudobond, 1 model selected
> ~select #1.1.1
Nothing selected
> select #1.1.1
1 pseudobond, 1 model selected
> color #1.2 #941100 transparency 0
> color #1.1 #005493 transparency 0
> ui tool show AlphaFold
> select #1.2
89 atoms, 91 bonds, 10 residues, 1 model selected
> select #1.1
2039 atoms, 2091 bonds, 1 pseudobond, 252 residues, 2 models selected
> ~select #1.1
Nothing selected
> select #1
2128 atoms, 2182 bonds, 1 pseudobond, 262 residues, 4 models selected
Alignment identifier is 1.1/H
Alignment identifier is 1.2/I
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/H:56-58,60-60,61-63,126-129,165-171,232-245
373 atoms, 380 bonds, 44 residues, 1 model selected
> select #1.2/I:361-363
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel pink
> select clear
> select #1.2/I:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/I:355-364
89 atoms, 91 bonds, 10 residues, 1 model selected
> style sel stick
Changed 89 atom styles
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select clear
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> view sel
> select clear
> color lightred
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel salmon
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> color sel salmon
> select clear
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/I:363
16 atoms, 16 bonds, 1 residue, 1 model selected
> color sel byelement
> ui tool show "Color Actions"
> color sel byhetero
> view
> select clear
> select #1.2/I:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/I:355-364
89 atoms, 91 bonds, 10 residues, 1 model selected
> select clear
> alphafold predict
> IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFEEIPEEYL
Running AlphaFold prediction
> select #1.2/I:364@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
89 atoms, 91 bonds, 10 residues, 1 model selected
> view sel
> select clear
> select #1.2/I:363@CD2
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 16 bonds, 1 residue, 1 model selected
> color sel & C salmon
> ui tool show H-Bonds
> select #1.2
89 atoms, 91 bonds, 10 residues, 1 model selected
> select #1
2128 atoms, 2182 bonds, 1 pseudobond, 262 residues, 4 models selected
> ~select #1
Nothing selected
> select #1.2
89 atoms, 91 bonds, 10 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fffb00 twoColors true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1.1 1a2c.pdb H
1.2 1a2c.pdb I
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1a2c.pdb I #1.2/I TYS 363 N 1a2c.pdb I #1.2/I PRO 360 O no hydrogen 2.351 N/A
1a2c.pdb I #1.2/I LEU 364 N 1a2c.pdb I #1.2/I GLU 361 O no hydrogen 3.116 N/A
2 hydrogen bonds found
0 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #fffb00 twoColors true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1.1 1a2c.pdb H
1.2 1a2c.pdb I
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1a2c.pdb I #1.2/I TYS 363 N 1a2c.pdb I #1.2/I PRO 360 O no hydrogen 2.351 N/A
1a2c.pdb I #1.2/I LEU 364 N 1a2c.pdb I #1.2/I GLU 361 O no hydrogen 3.116 N/A
2 hydrogen bonds found
0 strict hydrogen bonds found
> ui tool show Contacts
> contacts sel color #00fdff reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
48 contacts
atom1 atom2 overlap distance
1a2c.pdb I #1.2/I TYS 363 CD2 1a2c.pdb I #1.2/I PRO 360 CG 0.672 2.968
1a2c.pdb I #1.2/I TYS 363 CB 1a2c.pdb I #1.2/I PRO 360 O 0.558 2.742
1a2c.pdb I #1.2/I TYS 363 CE2 1a2c.pdb I #1.2/I PRO 360 CG 0.465 3.175
1a2c.pdb I #1.2/I ILE 359 CG1 1a2c.pdb I #1.2/I PRO 360 CD 0.372 3.388
1a2c.pdb I #1.2/I PRO 360 O 1a2c.pdb I #1.2/I TYS 363 CA 0.333 2.967
1a2c.pdb I #1.2/I TYS 363 N 1a2c.pdb I #1.2/I PRO 360 O 0.309 2.351
1a2c.pdb I #1.2/I PRO 360 CB 1a2c.pdb I #1.2/I GLU 362 CD 0.117 3.643
1a2c.pdb I #1.2/I PRO 360 CB 1a2c.pdb I #1.2/I GLU 362 OE1 0.089 3.211
1a2c.pdb I #1.2/I TYS 363 CD2 1a2c.pdb I #1.2/I PRO 360 CB 0.030 3.610
1a2c.pdb I #1.2/I PRO 360 CD 1a2c.pdb I #1.2/I TYS 363 CD2 0.028 3.612
1a2c.pdb I #1.2/I PHE 356 O 1a2c.pdb I #1.2/I GLU 357 O 0.013 2.827
1a2c.pdb I #1.2/I PRO 360 O 1a2c.pdb I #1.2/I GLU 362 N -0.009 2.669
1a2c.pdb I #1.2/I TYS 363 CE2 1a2c.pdb I #1.2/I GLU 362 CG -0.035 3.675
1a2c.pdb I #1.2/I PRO 360 CB 1a2c.pdb I #1.2/I GLU 362 CG -0.059 3.819
1a2c.pdb I #1.2/I PRO 360 O 1a2c.pdb I #1.2/I TYS 363 CD2 -0.061 3.241
1a2c.pdb I #1.2/I GLU 362 CG 1a2c.pdb I #1.2/I TYS 363 CE1 -0.065 3.705
1a2c.pdb I #1.2/I TYS 363 N 1a2c.pdb I #1.2/I GLU 361 CA -0.067 3.587
1a2c.pdb I #1.2/I LEU 364 CG 1a2c.pdb I #1.2/I TYS 363 O -0.095 3.395
1a2c.pdb I #1.2/I GLU 358 CD 1a2c.pdb I #1.2/I GLU 357 CG -0.113 3.873
1a2c.pdb I #1.2/I TYS 363 N 1a2c.pdb I #1.2/I GLU 361 O -0.114 2.774
1a2c.pdb I #1.2/I TYS 363 CD2 1a2c.pdb I #1.2/I GLU 362 CG -0.143 3.783
1a2c.pdb I #1.2/I GLU 362 CG 1a2c.pdb I #1.2/I TYS 363 CZ -0.146 3.636
1a2c.pdb I #1.2/I TYS 363 CE2 1a2c.pdb I #1.2/I GLU 362 CD -0.155 3.795
1a2c.pdb I #1.2/I PRO 360 C 1a2c.pdb I #1.2/I TYS 363 N -0.160 3.410
1a2c.pdb I #1.2/I GLU 362 C 1a2c.pdb I #1.2/I TYS 363 CD1 -0.164 3.534
1a2c.pdb I #1.2/I GLU 362 CG 1a2c.pdb I #1.2/I TYS 363 CD1 -0.167 3.807
1a2c.pdb I #1.2/I GLU 357 CG 1a2c.pdb I #1.2/I GLU 358 CA -0.174 3.934
1a2c.pdb I #1.2/I PRO 360 O 1a2c.pdb I #1.2/I TYS 363 CG -0.174 3.204
1a2c.pdb I #1.2/I LEU 364 CG 1a2c.pdb I #1.2/I ILE 359 CD1 -0.176 3.936
1a2c.pdb I #1.2/I TYS 363 CA 1a2c.pdb I #1.2/I GLU 361 C -0.182 3.672
1a2c.pdb I #1.2/I TYS 363 CB 1a2c.pdb I #1.2/I ILE 359 CD1 -0.190 3.950
1a2c.pdb I #1.2/I ILE 359 CD1 1a2c.pdb I #1.2/I LEU 364 CD2 -0.221 3.981
1a2c.pdb I #1.2/I ILE 359 CG1 1a2c.pdb I #1.2/I TYS 363 CB -0.229 3.989
1a2c.pdb I #1.2/I ILE 359 CD1 1a2c.pdb I #1.2/I TYS 363 O -0.234 3.534
1a2c.pdb I #1.2/I GLU 362 OE2 1a2c.pdb I #1.2/I TYS 363 OH -0.279 3.159
1a2c.pdb I #1.2/I TYS 363 CZ 1a2c.pdb I #1.2/I GLU 362 OE2 -0.281 3.311
1a2c.pdb I #1.2/I PRO 360 O 1a2c.pdb I #1.2/I GLU 362 CA -0.312 3.612
1a2c.pdb I #1.2/I ILE 359 CG1 1a2c.pdb I #1.2/I LEU 364 CG -0.318 4.078
1a2c.pdb I #1.2/I PRO 360 CB 1a2c.pdb I #1.2/I TYS 363 CE2 -0.324 3.964
1a2c.pdb I #1.2/I GLU 361 C 1a2c.pdb I #1.2/I LEU 364 N -0.348 3.598
1a2c.pdb I #1.2/I GLU 357 CA 1a2c.pdb I #1.2/I GLU 358 CD -0.354 4.114
1a2c.pdb I #1.2/I TYS 363 CG 1a2c.pdb I #1.2/I GLU 362 CG -0.356 3.846
1a2c.pdb I #1.2/I GLU 357 CG 1a2c.pdb I #1.2/I GLU 358 OE1 -0.360 3.660
1a2c.pdb I #1.2/I ILE 359 CG1 1a2c.pdb I #1.2/I PRO 360 CA -0.370 4.130
1a2c.pdb I #1.2/I GLU 362 CD 1a2c.pdb I #1.2/I TYS 363 CZ -0.372 3.862
1a2c.pdb I #1.2/I TYS 363 CA 1a2c.pdb I #1.2/I GLU 361 O -0.387 3.687
1a2c.pdb I #1.2/I PRO 360 O 1a2c.pdb I #1.2/I GLU 362 C -0.393 3.423
1a2c.pdb I #1.2/I TYS 363 CE2 1a2c.pdb I #1.2/I GLU 362 OE2 -0.397 3.577
48 contacts
> close #2
> close #1.2.1
> ui tool show H-Bonds
Restriction atom specifier must not be blank
> hbonds sel color #fffb00 restrict cross twoColors true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1.1 1a2c.pdb H
1.2 1a2c.pdb I
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> ui tool show Contacts
> contacts sel restrict cross color #00fdff reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> close #2
> close #1.2.1
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
AlphaFold prediction finished
Results in /Users/ich/Downloads/ChimeraX/AlphaFold/prediction_7
> color #2 #945200 transparency 0
> view
> select clear
> select #2
4429 atoms, 4485 bonds, 292 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #1.1
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 1a2c.pdb H, chain H (#1.1) with best_model.pdb, chain A (#2),
sequence alignment score = 1291
RMSD between 249 pruned atom pairs is 0.510 angstroms; (across all 252 pairs:
0.658)
> ~select #2
Nothing selected
Alignment identifier is 1.1/H
Alignment identifier is 1.2/I
Alignment identifier is 2/A
> select #2/A:251
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:251-282
232 atoms, 231 bonds, 32 residues, 1 model selected
> color sel green
> select #2/A:283
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:283-292
166 atoms, 168 bonds, 10 residues, 1 model selected
> color sel red
> color /1.2 red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1.2 red
> color #1.2 #941100 transparency 0
> style #1.2 stick
Changed 89 atom styles
> select #1.2
89 atoms, 91 bonds, 10 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> color #1.1.1 #00fdff models transparency 0
> ~select #1.1.2
89 atoms, 91 bonds, 10 residues, 1 model selected
> ~select #1.2
Nothing selected
> ~select #1.1.2
Nothing selected
> select #1.1.1
1 pseudobond, 1 model selected
> close #1.1.2
> color #1.1.1 #fffb00 models transparency 0
> select clear
Alignment identifier is 1.1/H
Alignment identifier is 1.2/I
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> select #1.1.1
1 pseudobond, 1 model selected
> select #1.1/H:56-58,60-60,61-63,126-129,165-171,232-245
373 atoms, 380 bonds, 44 residues, 1 model selected
> select
> #1.1/H:30-35,39-45,51-54,64-68,81-83,85-90,104-108,135-140,156-161,180-183,198-202,207-215,226-230
579 atoms, 582 bonds, 71 residues, 1 model selected
> select #1.1/H:56-58,60-60,61-63,126-129,165-171,232-245
373 atoms, 380 bonds, 44 residues, 1 model selected
> select
> #1.1/H:30-35,39-45,51-54,64-68,81-83,85-90,104-108,135-140,156-161,180-183,198-202,207-215,226-230
579 atoms, 582 bonds, 71 residues, 1 model selected
> select clear
> save /Users/ich/Charisma/Alphafold2/1a2c_cxaf2.cxs
——— End of log from Tue Nov 9 10:08:08 2021 ———
opened ChimeraX session
Drag select of 11 residues, 1 pseudobonds
> view sel
> select clear
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/H:150
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1.1/H:150
11 atoms, 9 bonds, 2 residues, 1 model selected
> select #2/A:147
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:147-148
21 atoms, 20 bonds, 2 residues, 1 model selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel tan
> select clear
> select #2/A:147
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:147-148
21 atoms, 20 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/H:147-150
11 atoms, 9 bonds, 1 pseudobond, 2 residues, 2 models selected
> color sel yellow
> color sel blue
> color sel skyblue
> select clear
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/H:147-150
11 atoms, 9 bonds, 1 pseudobond, 2 residues, 2 models selected
> label sel
> select #2/A:147
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:147-148
21 atoms, 20 bonds, 2 residues, 1 model selected
> label sel
> label sel color brown
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/H:147-150
11 atoms, 9 bonds, 1 pseudobond, 2 residues, 2 models selected
> label sel color steelblue
> select clear
> save /Users/ich/Desktop/image3.png supersample 3
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:147
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel red
> select add #1.1/H:147
21 atoms, 19 bonds, 2 residues, 2 models selected
> color sel red
> select clear
> select #1.1/H:150
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1.1/H:150
11 atoms, 9 bonds, 2 residues, 2 models selected
> color sel blue
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> label sel color red height 5
> label sel color red height 1
> select #2/A:147
14 atoms, 13 bonds, 1 residue, 1 model selected
> label sel color red height 1
> label sel color red height 1 offset 1,1,1
> label sel color red height 1 offset 1,0,1
> label sel color red height 1 offset -1,0,1
> label sel color red height 1 offset -2,0,1
> label sel color red height 1 offset -4,0,1
> label sel color red height 0.5 offset -4,0,1
> label sel color red offset -4,0,1
> label sel color red height 1 offset -6,0,1
> label sel color red height 1 offset -5,0,1
> select #2/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> label sel color blue height 1 offset -5,0,1
> label sel color blue height 1 offset -4,0,1
> select #1.1/H:150
4 atoms, 3 bonds, 1 residue, 1 model selected
> label sel color blue height 1 offset 0,0,-3
> label sel color blue height 1 offset 0,-3,-3
> label sel color blue height 1 offset 0,-2,-3
> label sel color blue height 1 offset 0,-2,-2
> label sel color blue height 1 offset 0,-2,-1
> select #2/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> label sel color blue height 1 offset 0,-2,0
> label sel color blue height 1 offset -3,0,0
> label sel color blue height 1 offset -4,0,0
> label sel color blue height 1 offset -3,0,0
> label sel color blue height 1 offset -3,1,0
> label sel color blue height 1 offset -3,0,0
> label sel color blue height 1 offset -3,-1,0
> label sel color blue height 1 offset -5,0,0
> label sel color blue height 1 offset -3.5,0,0
> save /Users/ich/Desktop/image4.png supersample 3
> ui tool show AlphaFold
QCssParser::parseHexColor: Unknown color name '#0C00'
[Repeated 1 time(s)]
Populating font family aliases took 371 ms. Replace uses of missing font
family "Calibri" with one that exists to avoid this cost.
> alphafold predict
> IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFEEIPEEXL
Running AlphaFold prediction
Alignment identifier is 2/A
> select clear
Alignment identifier is 1.1/H
Alignment identifier is 1.2/I
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> select #1.1/H:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/H:147-150
11 atoms, 9 bonds, 1 pseudobond, 2 residues, 2 models selected
> view orient
> close session
> ui tool show "Build Structure"
> build start peptide c3 GKITVKRCMKKTYEG -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> rotLib Dunbrack
Chain information for c3 #1
---
Chain | Description
A | No description available
OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10548.0.0,0)
OS Loader Version: 540.40.4~45
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 14 days 3:13
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
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: 1.3rc202111060828
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.2
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
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
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
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
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
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: 3.0.5
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: 2.1.0
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
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
File attachment: Screen Shot 2021-11-09 at 16.11.12.png
Attachments (1)
Change History (3)
by , 4 years ago
| Attachment: | Screen Shot 2021-11-09 at 16.11.12.png added |
|---|
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Build Structure: cannot change rotamer library |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Hi Charisma,
Thanks for reporting this problem. I have fixed it now and the fix will be in tomorrow's builds.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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