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Opened 4 years ago
Last modified 4 years ago
#5028 assigned enhancement
cylinder arrowheads
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Elaine Meng, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1160.31.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
How to add arrows to the end of helix cylinders? The "cartoon style arrowsHelix true" seems not working. I think it is a bug.
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/baocheng/Documents/phenix_folder2/hTERT-coot-27_final.pdb
Chain information for hTERT-coot-27_final.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
> open /home/baocheng/Documents/MBI_files/hTERT_model/model/PDB/5CQG.pdb
5CQG.pdb title:
Structure of tribolium telomerase In complex with the highly specific
inhibitor BIBR1532 [more info...]
Chain information for 5CQG.pdb #2
---
Chain | Description
A B | telomerase reverse transcriptase
Non-standard residues in 5CQG.pdb #2
---
55C — 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoicacid (bibr 1532)
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 hTERT-coot-27_final.pdb, chain A (#1) with 5CQG.pdb, chain A (#2),
sequence alignment score = 718.5
RMSD between 193 pruned atom pairs is 1.377 angstroms; (across all 561 pairs:
8.503)
> delete #2/b
> ui mousemode right zoom
> hide #2 models
> show #2 models
> hide #2 models
> dssp
> close #1
> open /home/baocheng/Documents/phenix_folder2/hTERT-coot-26_test.pdb
Chain information for hTERT-coot-26_test.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
> dssp
> close #1
> open /home/baocheng/Documents/phenix_folder2/hTERT-coot-27_final.pdb
Chain information for hTERT-coot-27_final.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
> open /home/baocheng/Documents/phenix_folder2/hTERT-coot-3.pdb
Chain information for hTERT-coot-3.pdb #3
---
Chain | Description
A | No description available
B | No description available
N | No description available
> close
> open /home/baocheng/Documents/phenix_folder2/hTERT-coot-27_final.pdb
Chain information for hTERT-coot-27_final.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
> open /home/baocheng/Documents/MBI_files/hTERT_model/model/PDB/5CQG.pdb
5CQG.pdb title:
Structure of tribolium telomerase In complex with the highly specific
inhibitor BIBR1532 [more info...]
Chain information for 5CQG.pdb #2
---
Chain | Description
A B | telomerase reverse transcriptase
Non-standard residues in 5CQG.pdb #2
---
55C — 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoicacid (bibr 1532)
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 hTERT-coot-27_final.pdb, chain A (#1) with 5CQG.pdb, chain A (#2),
sequence alignment score = 716.6
RMSD between 184 pruned atom pairs is 1.304 angstroms; (across all 560 pairs:
7.969)
> delete #2/b
> set bgColor white
> lighting soft
> lighting soft
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> lighting soft
> lighting soft
> lighting soft
> lighting full
> lighting soft
> lighting soft
> lighting soft
> lighting simple
> lighting simple
> lighting simple
> lighting soft
> hide #!1 models
> select #2/A:565
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/a :459-565
881 atoms, 899 bonds, 107 residues, 1 model selected
> select ~sel
17747 atoms, 18403 bonds, 6 pseudobonds, 2010 residues, 3 models selected
> ~select #1
4336 atoms, 4242 bonds, 700 residues, 1 model selected
> delete sel
> undo
Undo failed, probably because structures have been modified.
> open /home/baocheng/Documents/MBI_files/hTERT_model/model/PDB/5CQG.pdb
5CQG.pdb title:
Structure of tribolium telomerase In complex with the highly specific
inhibitor BIBR1532 [more info...]
Chain information for 5CQG.pdb #3
---
Chain | Description
A B | telomerase reverse transcriptase
Non-standard residues in 5CQG.pdb #3
---
55C — 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoicacid (bibr 1532)
> hide #2 models
> close #2
> ui tool show Matchmaker
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 hTERT-coot-27_final.pdb, chain A (#1) with 5CQG.pdb, chain A (#3),
sequence alignment score = 716.6
RMSD between 184 pruned atom pairs is 1.304 angstroms; (across all 560 pairs:
7.969)
> select #2/a :459-565
Nothing selected
> select #3/a :459-565
881 atoms, 899 bonds, 107 residues, 1 model selected
> select ~sel
22953 atoms, 23544 bonds, 6 pseudobonds, 2806 residues, 3 models selected
> select #3/A:601@C19
1 atom, 1 residue, 1 model selected
> select clear
> select #3/a :459-565, 601
906 atoms, 926 bonds, 108 residues, 1 model selected
> select ~sel
22928 atoms, 23517 bonds, 6 pseudobonds, 2805 residues, 3 models selected
> ~select #1
9517 atoms, 9356 bonds, 1495 residues, 1 model selected
> delete sel
> show #!1 models
> select #1/a:992-1107
917 atoms, 938 bonds, 116 residues, 1 model selected
> select ~sel
13400 atoms, 14149 bonds, 6 pseudobonds, 1302 residues, 3 models selected
> select sel /a
6571 atoms, 6730 bonds, 4 pseudobonds, 818 residues, 2 models selected
> ~ribbon sel
> select #1/C:211
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
131 atoms, 134 bonds, 15 residues, 1 model selected
> select up
1171 atoms, 1193 bonds, 152 residues, 1 model selected
> select up
13411 atoms, 14161 bonds, 1310 residues, 1 model selected
> select down
1171 atoms, 1193 bonds, 152 residues, 1 model selected
> ~ribbon sel
Drag select of 92 residues, 133 shapes, 20 atoms, 19 bonds
> select clear
Drag select of 99 residues, 1 pseudobonds, 140 shapes, 21 atoms, 17 bonds
> select ~sel
12500 atoms, 13095 bonds, 6 pseudobonds, 1315 residues, 3 models selected
> select sel /b:1-200
1625 atoms, 1811 bonds, 1 pseudobond, 77 residues, 2 models selected
> ~ribbon sel
> ~display sel
Drag select of 229 atoms, 2 residues, 242 bonds, 1 shapes
Drag select of 41 atoms, 45 bonds
Drag select of 245 atoms, 255 bonds
> ~display sel
> select clear
> select clear
> select #1/A:1011@CG
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ~display sel
> select clear
> ~display #1
Drag select of 52 residues
> select clear
Drag select of 55 residues
> select clear
Drag select of 60 residues
> ~ribbon sel
> ~display #2
> ~display #3
> display #3:601
> ui tool show Matchmaker
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 hTERT-coot-27_final.pdb, chain A (#1) with 5CQG.pdb, chain A (#3),
sequence alignment score = 244.4
RMSD between 69 pruned atom pairs is 1.091 angstroms; (across all 102 pairs:
4.361)
> save
> /home/baocheng/Documents/MBI_files/hTERT_model/Figures_preparation/bibr1532.cxs
> select #1/B:177
20 atoms, 21 bonds, 1 residue, 1 model selected
> display sel
> select #1/B:307
20 atoms, 21 bonds, 1 residue, 1 model selected
> display sel
> select clear
Drag select of 302 residues, 4 shapes, 25 atoms, 27 bonds
> select sel/b
1698 atoms, 1893 bonds, 80 residues, 1 model selected
> display sel
> select clear
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
> nucrib
> lighting simple
> lighting soft
> lighting simple
> select clear
> nucleotides sel atoms
> style nucleic & sel stick
Changed 40 atom styles
> select clear
> select #1/B:175
22 atoms, 24 bonds, 1 residue, 1 model selected
> color #1/b pink
> color #1/b hot pink
> select clear
> color #1/b:178-186 light blue
> color #1/b:178-186 blue
> color #1/b:106-115 blue
> color #1/b:173-176 blue
> color #1/b:187-190 magenta
> color #1/b:99-105 orange
> color #1/b:99-105 gold
> color #1/b:99-105 orange
> color #1/b:165-172 green
> color #1/b:163-172 green
Drag select of 9 residues, 15 shapes
> select subtract #1/B:126
171 atoms, 8 residues, 1 model selected
> select add #1/B:126
193 atoms, 24 bonds, 9 residues, 1 model selected
> select subtract #1/B:125
170 atoms, 24 bonds, 8 residues, 1 model selected
> select subtract #1/B:124
147 atoms, 24 bonds, 7 residues, 1 model selected
> ~ribbon sel
> ~display sel
> select clear
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
40 atoms, 42 bonds, 2 residues, 1 model selected
> color #1/b:177,307 red
> select clear
> select clear
> select clear
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
25 atoms, 27 bonds, 1 residue, 1 model selected
> style sel ball
Changed 25 atom styles
> color #3 silver
> transparency #3 70 target r
> select clear
> select #3/A:601@C16
1 atom, 1 residue, 1 model selected
> select up
25 atoms, 27 bonds, 1 residue, 1 model selected
> select up
906 atoms, 926 bonds, 108 residues, 1 model selected
> select down
25 atoms, 27 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
40 atoms, 42 bonds, 2 residues, 1 model selected
> color sel byhetero
> color sel grey,a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel grey target a
> color sel silver target a
> color sel byhetero
> select #1/B:311
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/B:310
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #1/B:312
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/B:313
83 atoms, 88 bonds, 4 residues, 1 model selected
> transparency sel 80
> transparency sel 80 target r
> transparency sel 80 target a
> transparency sel 80 target all
> transparency sel 80 target n
Invalid "target" argument: Character 'n' is not an allowed target, must be one
of acrsbpfl
> transparency sel 80 target
Missing "target" keyword's argument
> alias nucrib cartoon style nucleic xsect oval width 1 thick 1
> nucrib
> alias nucrib cartoon style nucleic xsect oval width 0.8 thick 0.8
> nucrib
> select clear
> ribbon style width 1.5 thickness 0.6
> nucrib
> ribbon style width 1.5 thickness 0.4
> nucrib
> select #1/A:1028
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1023
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:1028
17 atoms, 15 bonds, 2 residues, 1 model selected
> display #1/a:1023,1028
> select clear
> select add #1/B:307
20 atoms, 21 bonds, 1 residue, 1 model selected
> ~ribbon #1/b:307
> select #1/B:308
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:307@C4'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> ribbon #1/b:307
> select clear
> select #1/A:1028@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> ~display sle
> hide sle
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display sel
> select clear
> select #1/A:1023
9 atoms, 8 bonds, 1 residue, 1 model selected
> ribbonbackbone sel
Unknown command: ribbonbackbone sel
> ribbackbone sel
Unknown command: ribbackbone sel
> transparency sel 90 target r
> ~display sel
> display sel
> suppressBackboneDisplay false
Unknown command: suppressBackboneDisplay false
> carton style suppressBackboneDisplay false
Unknown command: carton style suppressBackboneDisplay false
> carton style sel suppressBackboneDisplay false
Unknown command: carton style sel suppressBackboneDisplay false
> carton sel suppressBackboneDisplay false
Unknown command: carton sel suppressBackboneDisplay false
> cartoon sel suppressBackboneDisplay false
> select clear
> select #1/A:1023@NE2
1 atom, 1 residue, 1 model selected
> select add #1/A:1023@OE1
2 atoms, 1 residue, 1 model selected
> select add #1/A:1023@CD
3 atoms, 1 residue, 1 model selected
> select add #1/A:1023@CG
4 atoms, 1 residue, 1 model selected
> select add #1/A:1023@CB
5 atoms, 1 residue, 1 model selected
> ~display sel
> select clear
> select #1/B:307@N3
1 atom, 1 residue, 1 model selected
> select add #1/A:1023@O
2 atoms, 2 residues, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> display sel
> select #1/A:1023@NE2
1 atom, 1 residue, 1 model selected
> select add #1/A:1023@OE1
2 atoms, 1 residue, 1 model selected
> select add #1/A:1023@CD
3 atoms, 1 residue, 1 model selected
> select add #1/A:1023@CG
4 atoms, 1 residue, 1 model selected
> transparency sel 80
> transparency sel 80 target a
> select clear
> select #1/A:1023@OE1
1 atom, 1 residue, 1 model selected
> select add #1/A:1023@NE2
2 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/A:1023@CG
3 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:1023@CB
4 atoms, 4 bonds, 1 residue, 1 model selected
> transparency sel 80 target a
> select clear
> graphics silhouettes true
> color #1/a #9775a448eb78
> select #1/A:1023@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> transparency #3/a 90 target r
> select clear
> select #1/A:1019
8 atoms, 7 bonds, 1 residue, 1 model selected
Unknown or unsupported skia image format
> transparency #3/a 90 target r
> transparency sel 90 target r
> select clear
> select #1/A:1019
8 atoms, 7 bonds, 1 residue, 1 model selected
> display sel
> cartoon sel suppressBackboneDisplay false
> color sel byhetero
> select clear
> select #1/A:1019@CD2
1 atom, 1 residue, 1 model selected
> select add #1/A:1019@CG
2 atoms, 1 residue, 1 model selected
> select add #1/A:1019@CD1
3 atoms, 1 residue, 1 model selected
> transparency sel 80 target a
> select clear
> select add #1/A:1019@CB
1 atom, 2 bonds, 1 residue, 1 model selected
> transparency sel 80 target a
> select clear
> select #1/B:177@N3
1 atom, 1 residue, 1 model selected
> select add #1/A:1019@O
2 atoms, 2 residues, 1 model selected
> ui tool show Contacts
> ui tool show Distances
> distance #1/B:177@N3 #1/A:1019@O
Distance between hTERT-coot-27_final.pdb #1/B U 177 N3 and /A LEU 1019 O:
3.359Å
> select #1/A:1023@O
1 atom, 1 residue, 1 model selected
> select add #1/B:307@N3
2 atoms, 2 residues, 1 model selected
> distance #1/A:1023@O #1/B:307@N3
Distance between hTERT-coot-27_final.pdb #1/A GLN 1023 O and /B U 307 N3:
3.746Å
> select clear
> select #1/A:1019@O
1 atom, 1 residue, 1 model selected
> select add #1/A:1023
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
54 atoms, 56 bonds, 6 residues, 1 model selected
> select down
17 atoms, 15 bonds, 2 residues, 1 model selected
> cartoon sel suppressBackboneDisplay true
> select clear
> select add #1/A:1023
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:1019
17 atoms, 15 bonds, 2 residues, 1 model selected
> transparency sel 80 target a
> transparency sel 0 target r
> select clear
> select #1/A:1023@CD
1 atom, 1 residue, 1 model selected
> select add #1/A:1019@CG
2 atoms, 2 residues, 1 model selected
> select up
17 atoms, 15 bonds, 2 residues, 1 model selected
> ~display sle
> hide sle
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display sel
> select clear
> select clear
> ~label sel
> select clear
> select #1/A:1024
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:1017
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/A:1016
24 atoms, 21 bonds, 3 residues, 1 model selected
> display sel
> color sel byhetero
> cartoon sel suppressBackboneDisplay false
> select clear
> select #1/A:1017@CG
1 atom, 1 residue, 1 model selected
> select add #3/A:486
12 atoms, 10 bonds, 2 residues, 2 models selected
> select clear
> select #1/A:1016@CB
1 atom, 1 residue, 1 model selected
> select add #1/A:1017@CB
2 atoms, 2 residues, 1 model selected
> select up
15 atoms, 14 bonds, 2 residues, 1 model selected
> ~display sel
> select clear
> select #1/A:1024@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> ~display sel
> select clear
> transparency #3/a 80 target r
> select clear
> transparency sel 80 target a
> transparency sel 80 target r
> select clear
> select #1/a:1033,1032,1016,1012,1089
49 atoms, 48 bonds, 5 residues, 1 model selected
> display sel
> color sel byhetero
> select clear
> select #1/a:1033,1032,1016,1012,1089,1025
56 atoms, 54 bonds, 6 residues, 1 model selected
> display sel
> color sel byhetero
> select clear
> select #1/B:311
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
4605 atoms, 5136 bonds, 217 residues, 1 model selected
> transparency sel 0 target r
> select clear
> save
> /home/baocheng/Documents/MBI_files/hTERT_model/Figures_preparation/bibr1532_2.cxs
> transparency #3/a 85 target r
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
25 atoms, 27 bonds, 1 residue, 1 model selected
> surface sel
> color sel byhetero target s
> select clear
> transparency sel 85 target s
> select #3/A:601@C21
1 atom, 1 residue, 1 model selected
> select up
25 atoms, 27 bonds, 1 residue, 2 models selected
> select up
906 atoms, 926 bonds, 108 residues, 2 models selected
> select down
25 atoms, 27 bonds, 1 residue, 2 models selected
> transparency sel 85 target s
> color sel cyan target s
> transparency sel 85 target s
> color sel byhetero target s
> select clear
> select clear
> save
> /home/baocheng/Documents/MBI_files/hTERT_model/Figures_preparation/bibr1532_3.cxs
> save bibr-v3.png width 3000 height 3000 supersample 3 transparentBackground
> true
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> select #3/A:601@O22
1 atom, 1 residue, 1 model selected
> select up
25 atoms, 27 bonds, 1 residue, 2 models selected
> transparency sel 75 target s
> select #1/A:1023
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:1019
17 atoms, 15 bonds, 2 residues, 1 model selected
> display sel
> transparency sel 80 target r
> cartoon sel supressbackbone false
Expected a keyword
> cartoon sel suppressBackboneDisplay false
> select clear
> select #1/A:1023@CA
1 atom, 1 residue, 1 model selected
> select add #1/A:1019
9 atoms, 7 bonds, 2 residues, 1 model selected
> cartoon sel suppressBackboneDisplay true
> select clear
> select #1/A:1023
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:1023
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:1019
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
54 atoms, 56 bonds, 6 residues, 1 model selected
> select down
17 atoms, 15 bonds, 2 residues, 1 model selected
> transparency sel 50 target r
> transparency sel 50 target a
> transparency sel 0 target r
> select clear
> select #1/B:163
23 atoms, 25 bonds, 1 residue, 1 model selected
> ~ribbon sel
> ~distance sel
> ~display sel
> select clear
> transparency #3/a 80 target r
> select clear
> save bibr-v4.png width 3000 height 3000 supersample 3 transparentBackground
> true
> color #1/b:163-172 limo green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1/b:163-172 lemonchiffon green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/b:163-172 lemonchiffon green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/b:163-172 lemonchiffon green all
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/b:163-172 green
> color #1/b:163-172 lime green
> select #1/b:163-164
45 atoms, 50 bonds, 2 residues, 1 model selected
> riboon sel
Unknown command: riboon sel
> ribbon sel
> select clear
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> select #1/B:164
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/B:165
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #1/B:95
68 atoms, 74 bonds, 3 residues, 1 model selected
> select add #1/B:94
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #1/B:96
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #1/B:311
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #1/B:312
148 atoms, 158 bonds, 7 residues, 1 model selected
> transparency sel 75
> transparency sel 75 target all
> transparency sel 75 target r
> select clear
> save
> /home/baocheng/Documents/MBI_files/hTERT_model/Figures_preparation/bibr1532_4.cxs
> save bibr-v5.png width 3000 height 3000 supersample 3 transparentBackground
> true
> save
> /home/baocheng/Documents/MBI_files/hTERT_model/Figures_preparation/bibr1532_5.cxs
> hide #2 models
> hide #!3 models
> ribbon #1
> close #1
> close #2
> open /home/baocheng/Documents/phenix_folder2/RealSpaceRefine_131/hTERT-
> coot-26_test_real_space_refined.pdb
Chain information for hTERT-coot-26_test_real_space_refined.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
> close #1
> open /home/baocheng/Documents/phenix_folder2/hTERT-coot-27.pdb
Chain information for hTERT-coot-27.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
No distances to delete!
No distances to delete!
> ~display #1
> select #1/a:1-300,721-815
2001 atoms, 2045 bonds, 1 pseudobond, 255 residues, 2 models selected
> select ~
Expected an objects specifier or a keyword
> select ~sel
12316 atoms, 13042 bonds, 5 pseudobonds, 1163 residues, 3 models selected
> delete sel
> hide #1.1 models
> open /home/baocheng/Documents/MBI_files/hTERT_model/model/PDB/7LMA.pdb
7LMA.pdb title:
Tetrahymena telomerase T3D2 structure At 3.3 angstrom [more info...]
Chain information for 7LMA.pdb #2
---
Chain | Description
A | telomerase reverse transcriptase
B | telomerase RNA
C | telomere DNA
D | telomerase holoenzyme TEB1 subunit
E | telomerase holoenzyme TEB2 subunit
F | telomerase holoenzyme TEB3 subunit
G | P50
H | telomerase La-related protein P65
Non-standard residues in 7LMA.pdb #2
---
ZN — zinc ion
> hide atoms
> show cartoons
> select #2/a:1-190,627-756
2324 atoms, 2367 bonds, 1 pseudobond, 276 residues, 2 models selected
> select ~sel
18349 atoms, 19045 bonds, 13 pseudobonds, 1987 residues, 5 models selected
> select sel 
16348 atoms, 17000 bonds, 11 pseudobonds, 1732 residues, 3 models selected
> delete sel
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 hTERT-coot-27.pdb, chain A (#1) with 7LMA.pdb, chain A (#2),
sequence alignment score = 347.7
RMSD between 98 pruned atom pairs is 1.185 angstroms; (across all 239 pairs:
6.316)
> color #2 silver
> color #2 silver
> color #1/a:1-300 cyan
> color #1/a:721-815 dark violet
> color #1/a:736-801 salmon
> cartoon style protein modeHelix tube radius 1.3 sides 24
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> ~select #2.1
Nothing selected
> open /home/baocheng/Documents/MBI_files/hTERT_model/Figures_preparation/hT-
> temp_TEN-TRAP-IFD.pdb
Chain information for hT-temp_TEN-TRAP-IFD.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
> hide #!3 models
> cartoon style protein modeHelix wrap radius 1.3 sides 24
> cartoon style protein modeHelix tube radius 1.3 sides 24
> cartoon style protein modeHelix tube radius 1.3 sides 24 arrowsHelix true
> cartoon style protein modeHelix tube radius 1.3 sides 24 arrowsHelix true
> cartoon style protein modeHelix tube radius 1.3 sides 24 arrowHelix true
Expected a keyword
> cartoon style protein modeHelix tube radius 1.3 sides 24 Helixarrows true
Expected a keyword
> cartoon style protein modeHelix tube radius 1.3 sides 24 arrows true
> cartoon style protein modeHelix tube radius 1.3 sides 24 arrowsHelix true
OpenGL version: 3.3.0 NVIDIA 440.82
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-5039A-I
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 Intel(R) Xeon(R) W-2265 CPU @ 3.50GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 125G 19G 89G 468M 17G 105G
Swap: 31G 0B 31G
Graphics:
65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:12a0]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
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: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Depiction |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → cylinder arrowheads |
| Type: | defect → enhancement |
comment:2 by , 4 years ago
Hi Baocheng,
There is currently no capability in ChimeraX for showing arrowheads on helix cylinders -- only on ribbon depictions. Sorry!
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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Reported by Baocheng Liu