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Opened 3 years ago
Last modified 3 years ago
#8848 assigned defect
Install StarMap from toolshed: ImportError: No module named pip
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/michaelmatthias/R01.PAR.22.241/preChop2.cxs format session
Log from Sat Apr 15 11:43:38 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/michaelmatthias/R01.PAR.22.241/preChop1.cxs format session
Log from Fri Apr 14 18:25:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/michaelmatthias/R01.PAR.22.241/preChop.cxs format session
Log from Fri Apr 14 17:32:31 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/michaelmatthias/R01.PAR.22.241/stillNoCigarButBetter.cxs format
> session
Log from Thu Apr 13 11:56:51 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Mon Apr 10 12:10:39 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/michaelmatthias/Downloads/prediction_test_a3c0a/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> lighting full
> lighting soft
> lighting full
> color orange red
> color purple
> ui tool show "Color Actions"
> color light sea green
> color blue
> color cornflower blue
> color medium blue
> color purple
> color hot pink
> color magenta
> color white
> color light gray
> color black
> color red
> color orange red
> color red
> color coral
> color indian red
> color orange
> color dark orange
> color light sea green
> color steel blue
> color magenta
> color rosy brown
> color dim gray
> color gray
> color black
> color dark green
> color light blue
> color silver
> color powder blue
> color chartreuse
> color green
[Repeated 1 time(s)]
> color maroon
> color dark red
> color brown
> color sienna
> color light salmon
> color dark khaki
> color salmon
> color olive
> set bgColor white
[Repeated 1 time(s)]
> set bgColor black
> set bgColor gray
> set bgColor black
> lighting soft
Alignment identifier is 1/A
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-393
841 atoms, 866 bonds, 52 residues, 1 model selected
> ui tool show "Color Actions"
> color sel white
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> hbonds sel reveal true
13 hydrogen bonds found
> select /A:236-237,342-393
869 atoms, 894 bonds, 9 pseudobonds, 54 residues, 2 models selected
> select
> /A:45-47,53-61,64-70,80-82,88-92,95-100,112-114,116-119,129-132,135-138,146-148,151-155,185-187,197-200,205-210,215-218,223-225,240-242,252-254
1409 atoms, 1421 bonds, 82 residues, 1 model selected
> select /A:94
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:94
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:163-164
31 atoms, 31 bonds, 2 residues, 1 model selected
> select /A:123
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:122-123
33 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:140
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:140
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:140,334-393
964 atoms, 990 bonds, 11 pseudobonds, 61 residues, 2 models selected
> hbonds sel reveal true
25 hydrogen bonds found
> style sel ball
Changed 964 atom styles
> color sel byhetero
> select /A:376
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:376-379
45 atoms, 46 bonds, 4 residues, 1 model selected
> select /A:360
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:360-362
42 atoms, 41 bonds, 3 residues, 1 model selected
> select /A:358
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:358-359
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-349
70 atoms, 73 bonds, 3 residues, 1 model selected
> select /A:348
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:348-349
48 atoms, 51 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-348
46 atoms, 47 bonds, 2 residues, 1 model selected
> style sel ball
Changed 46 atom styles
> hide sel cartoons
> select /A:353
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:353
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select /A:355
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:355
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:354
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:354
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:360
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:360
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:368
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:368-370
51 atoms, 50 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:371
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:371-373
56 atoms, 55 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:374-375
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /A:374-375
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:378
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:378-379
21 atoms, 21 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:376
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:376-377
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select /A:378
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:378-379
21 atoms, 21 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select /A:378
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:378
7 atoms, 6 bonds, 1 residue, 1 model selected
> swapaa :378 ALA
Using Dunbrack library
Swapping /A GLY 378 to ALA
> select /A:380
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:380-385
108 atoms, 110 bonds, 6 residues, 1 model selected
> show sel atoms
> select /A:380
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:380-385
108 atoms, 110 bonds, 6 residues, 1 model selected
> hide sel cartoons
> hbonds sel reveal true
0 hydrogen bonds found
> swapaa :378 THR
Using Dunbrack library
/A ALA 378: phi -73.4, psi 149.8 trans
Applying THR rotamer (chi angles: 60.0) to /A THR 378
> swapaa :376 HIS
Using Dunbrack library
/A ALA 376: phi -39.0, psi 136.4 trans
Applying HIS rotamer (chi angles: -67.2 56.0) to /A HIS 376
> swapaa :376 THR
Using Dunbrack library
/A HIS 376: phi -39.0, psi 136.4 trans
Applying THR rotamer (chi angles: -59.1) to /A THR 376
> swapaa :376 SER
Using Dunbrack library
/A THR 376: phi -39.0, psi 136.4 trans
Applying SER rotamer (chi angles: 176.1) to /A SER 376
> swapaa :378 SER
Using Dunbrack library
/A THR 378: phi -73.4, psi 149.8 trans
Applying SER rotamer (chi angles: -63.6) to /A SER 378
> swapaa :378 GLU
Using Dunbrack library
/A SER 378: phi -73.4, psi 149.8 trans
Applying GLU rotamer (chi angles: 69.8 -81.8 67.6) to /A GLU 378
> swapaa :376 GLU
Using Dunbrack library
/A SER 376: phi -39.0, psi 136.4 trans
Applying GLU rotamer (chi angles: -65.8 85.2 -8.2) to /A GLU 376
> swapaa :380 GLU
Using Dunbrack library
/A LYS 380: phi -38.3, psi 125.7 trans
Applying GLU rotamer (chi angles: -65.7 85.2 -9.2) to /A GLU 380
> swapaa :382 GLU
Using Dunbrack library
/A LYS 382: phi -53.8, psi 132.8 trans
Applying GLU rotamer (chi angles: -65.7 85.1 -9.7) to /A GLU 382
> select /A:267
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:255-267
199 atoms, 201 bonds, 13 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 199 atom styles
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_c9c29/rank_1_model_1_ptm_seed_1_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_1_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
275 hydrogen bonds found
Alignment identifier is 1/A
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363-365
53 atoms, 53 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:351
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-355
52 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:356
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:356-357
29 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:356
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:341-356
269 atoms, 282 bonds, 6 pseudobonds, 16 residues, 2 models selected
> select /A:362
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:362-370
150 atoms, 151 bonds, 9 residues, 1 model selected
> show sel atoms
> select /A:346
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:308-346
569 atoms, 577 bonds, 23 pseudobonds, 39 residues, 2 models selected
> select /A:350
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:346-350
100 atoms, 106 bonds, 2 pseudobonds, 5 residues, 2 models selected
> show sel atoms
> select /A:345
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:341-345
98 atoms, 102 bonds, 2 pseudobonds, 5 residues, 2 models selected
> show sel atoms
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_c9c29/rank_2_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_2_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363-365
53 atoms, 53 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:341
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:341-350
198 atoms, 209 bonds, 10 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
6 hydrogen bonds found
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-26
414 atoms, 418 bonds, 26 residues, 1 model selected
> hbonds sel reveal true
4 hydrogen bonds found
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_a3c0a/rank_1_model_1_ptm_seed_2_relaxed.pdb
> format pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
267 hydrogen bonds found
Alignment identifier is 1/A
> select /A:367
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:367-370
68 atoms, 67 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:371
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:371-373
56 atoms, 55 bonds, 3 residues, 1 model selected
> select /A:372
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:372
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:374-375
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /A:374-393
307 atoms, 316 bonds, 20 residues, 1 model selected
> select /A:373
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:1-373
5860 atoms, 5959 bonds, 267 pseudobonds, 373 residues, 2 models selected
> select /A:359
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-359
119 atoms, 123 bonds, 9 residues, 1 model selected
> show sel atoms
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-373
534 atoms, 549 bonds, 9 pseudobonds, 32 residues, 2 models selected
> color (#!1 & sel) white
> select /A:358
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:358-359
21 atoms, 21 bonds, 2 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /A:360
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:360
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-349
70 atoms, 73 bonds, 3 residues, 1 model selected
> select clear
> hide atoms
> hide cartoons
[Repeated 1 time(s)]
> show cartoons
> select /A:125
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:125-127
50 atoms, 50 bonds, 3 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select /A:103
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:103-106
72 atoms, 71 bonds, 4 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> show sel atoms
> select /A:102
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:101-102
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /A:107
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:107-111
83 atoms, 82 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-349
70 atoms, 73 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:345
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:345-346
33 atoms, 33 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:350
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:350
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:351
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-352
21 atoms, 21 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:353
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:353-354
30 atoms, 30 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:350
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:350-351
35 atoms, 36 bonds, 2 residues, 1 model selected
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-349
70 atoms, 73 bonds, 3 residues, 1 model selected
> select /A:349
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:349-350
45 atoms, 47 bonds, 2 residues, 1 model selected
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-348
46 atoms, 47 bonds, 2 residues, 1 model selected
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-348
46 atoms, 47 bonds, 2 residues, 1 model selected
> style sel ball
Changed 46 atom styles
> hide sel cartoons
> color sel byhetero
> select /A:355
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:355
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:356
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:356-357
28 atoms, 29 bonds, 2 residues, 1 model selected
> select /A:358
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:358-360
37 atoms, 37 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:236
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:236
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:103
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:103-110
141 atoms, 140 bonds, 5 pseudobonds, 8 residues, 2 models selected
> color (#!1 & sel) orange
> color sel byhetero
> select /A:355
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:355
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:358
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:358
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> swapaa :358 PHE
Using Dunbrack library
/A GLY 358: phi 178.1, psi 164.9 trans
Applying PHE rotamer (chi angles: -65.0 115.8) to /A PHE 358
> swapaa :358 TRP
Using Dunbrack library
/A PHE 358: phi 178.1, psi 164.9 trans
Applying TRP rotamer (chi angles: -66.3 90.6) to /A TRP 358
> swapaa :358 LEU
Using Dunbrack library
/A TRP 358: phi 178.1, psi 164.9 trans
Applying LEU rotamer (chi angles: -64.7 174.3) to /A LEU 358
> select /A:357
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:356-357
28 atoms, 29 bonds, 2 residues, 1 model selected
> show sel atoms
> swapaa :358 LYS
Using Dunbrack library
/A LEU 358: phi 178.1, psi 164.9 trans
Applying LYS rotamer (chi angles: 64.8 -176.8 -70.3 -65.5) to /A LYS 358
> hbonds sel reveal true
0 hydrogen bonds found
> select clear
> swapaa :358 MET
Using Dunbrack library
/A LYS 358: phi 178.1, psi 164.9 trans
Applying MET rotamer (chi angles: 63.5 -172.5 72.0) to /A MET 358
> hide cartoons
> undo
> select /A:358
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:358
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> color sel byhetero
> swapaa :358 ALA
Using Dunbrack library
Swapping /A MET 358 to ALA
> style sel ball
Changed 4 atom styles
> select clear
> select /A:357
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:357-359
33 atoms, 34 bonds, 3 residues, 1 model selected
> style sel ball
Changed 33 atom styles
> select /A:350-351
35 atoms, 36 bonds, 2 residues, 1 model selected
> select /A:346-351
119 atoms, 125 bonds, 6 residues, 1 model selected
> select clear
> style ball
Changed 6165 atom styles
> select /A:360
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:350-360
154 atoms, 159 bonds, 11 residues, 1 model selected
> style sel sphere
Changed 154 atom styles
> hide sel cartoons
> select /A:358
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:358-360
35 atoms, 35 bonds, 3 residues, 1 model selected
> select clear
> show atoms
> hide cartoons
> style sphere
Changed 6165 atom styles
> select /A:361
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:361-363
43 atoms, 42 bonds, 3 residues, 1 model selected
> select /A:362
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:362
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:350
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:350-365
226 atoms, 232 bonds, 16 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_492c0/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
275 hydrogen bonds found
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_492c0/rank_2_model_1_ptm_seed_0_relaxed.pdb
Chain information for rank_2_model_1_ptm_seed_0_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
276 hydrogen bonds found
Alignment identifier is 1/A
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-349
70 atoms, 73 bonds, 3 residues, 1 model selected
> select /A:366
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:366-368
47 atoms, 46 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:369
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:369
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363-368
100 atoms, 100 bonds, 6 residues, 1 model selected
> show sel atoms
> select /A:350
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:350-360
152 atoms, 155 bonds, 3 pseudobonds, 11 residues, 2 models selected
> show sel atoms
> select /A:345
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:345-349
103 atoms, 107 bonds, 1 pseudobond, 5 residues, 2 models selected
> show sel atoms
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-344
65 atoms, 68 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:351
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-355
52 atoms, 53 bonds, 1 pseudobond, 5 residues, 2 models selected
> hide sel cartoons
> swapaa :353 LEU
Using Dunbrack library
/A ALA 353: phi -70.8, psi 80.0 trans
Applying LEU rotamer (chi angles: -78.7 -61.2) to /A LEU 353
> swapaa :353 ILE
Using Dunbrack library
/A LEU 353: phi -70.8, psi 80.0 trans
Applying ILE rotamer (chi angles: -56.3 -60.0) to /A ILE 353
> swapaa :353 TRP
Using Dunbrack library
/A ILE 353: phi -70.8, psi 80.0 trans
Applying TRP rotamer (chi angles: -67.7 -135.9) to /A TRP 353
> select
> /A:45-47,53-61,64-70,80-82,88-92,95-100,112-114,116-119,129-132,135-138,146-148,151-155,185-187,197-200,205-210,215-218,223-225,240-242,252-254,265-267,363-365
1508 atoms, 1519 bonds, 64 pseudobonds, 88 residues, 2 models selected
> select /A:360
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:360
17 atoms, 17 bonds, 1 residue, 1 model selected
> swapaa :360 TRP
Using Dunbrack library
/A HIS 360: phi -69.4, psi 66.6 trans
Applying TRP rotamer (chi angles: -67.4 99.5) to /A TRP 360
> swapaa :360 ARG
Using Dunbrack library
/A TRP 360: phi -69.4, psi 66.6 trans
Applying ARG rotamer (chi angles: 60.7 88.3 169.5 85.7) to /A ARG 360
> swapaa :358 ILE
Using Dunbrack library
/A VAL 358: phi -84.6, psi 67.0 trans
Applying ILE rotamer (chi angles: -171.0 166.9) to /A ILE 358
> swapaa :358 LEU
Using Dunbrack library
/A ILE 358: phi -84.6, psi 67.0 trans
Applying LEU rotamer (chi angles: -171.1 62.2) to /A LEU 358
> swapaa :358 ILE
Using Dunbrack library
/A LEU 358: phi -84.6, psi 67.0 trans
Applying ILE rotamer (chi angles: -171.0 166.9) to /A ILE 358
> swapaa :353 ILE
Using Dunbrack library
/A TRP 353: phi -70.8, psi 80.0 trans
Applying ILE rotamer (chi angles: -56.3 -60.0) to /A ILE 353
> select /A:353
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:353
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:357
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:357
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:355
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:355-356
33 atoms, 33 bonds, 2 residues, 1 model selected
> select /A:351-352
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:351-353
31 atoms, 31 bonds, 3 residues, 1 model selected
> select /A:354
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:354-355
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:381-382
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:381-388
119 atoms, 121 bonds, 8 residues, 1 model selected
> show sel atoms
> select /A:380
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:371-380
135 atoms, 139 bonds, 10 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
0 hydrogen bonds found
> select /A:381
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:381-382
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:268
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:268-282
242 atoms, 244 bonds, 15 residues, 1 model selected
> show sel atoms
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A
6044 atoms, 6149 bonds, 388 residues, 1 model selected
> select /A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:371-388
254 atoms, 261 bonds, 18 residues, 1 model selected
> hide sel cartoons
> style sel sphere
Changed 254 atom styles
> color sel orange red
> color sel byhetero
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select /A:385-386
33 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:385-388
65 atoms, 66 bonds, 4 residues, 1 model selected
> color sel light sea green
> color sel byhetero
> select /A:384
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:381-384
54 atoms, 54 bonds, 4 residues, 1 model selected
> color sel cornflower blue
> color sel hot pink
> color sel byhetero
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_39e76/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
275 hydrogen bonds found
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_39e76/rank_2_model_1_ptm_seed_0_relaxed.pdb
Chain information for rank_2_model_1_ptm_seed_0_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
280 hydrogen bonds found
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_39e76/rank_3_model_1_ptm_seed_3_relaxed.pdb
Chain information for rank_3_model_1_ptm_seed_3_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
282 hydrogen bonds found
Alignment identifier is 1/A
> select /A:362
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:362-365
67 atoms, 67 bonds, 4 residues, 1 model selected
> close session
> open "/Users/michaelmatthias/Downloads/prediction_test_39e76
> 2/rank_1_model_1_ptm_seed_2_relaxed.pdb"
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
275 hydrogen bonds found
Alignment identifier is 1/A
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363-365
53 atoms, 53 bonds, 3 residues, 1 model selected
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_492c0/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_492c0/rank_2_model_1_ptm_seed_0_relaxed.pdb
Chain information for rank_2_model_1_ptm_seed_0_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
276 hydrogen bonds found
Alignment identifier is 1/A
> select /A:351
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-355
52 atoms, 53 bonds, 1 pseudobond, 5 residues, 2 models selected
> show sel cartoons
> show sel atoms
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-350
189 atoms, 198 bonds, 4 pseudobonds, 9 residues, 2 models selected
> select /A:341
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:341-350
203 atoms, 213 bonds, 5 pseudobonds, 10 residues, 2 models selected
> show sel atoms
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363-365
53 atoms, 53 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:366
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:366-368
47 atoms, 46 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:369
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:369-370
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_0ff3c/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_63a81/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
283 hydrogen bonds found
Alignment identifier is 1/A
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363-365
55 atoms, 54 bonds, 3 residues, 1 model selected
> show sel atoms
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_63a81/rank_2_model_1_ptm_seed_0_relaxed.pdb
Chain information for rank_2_model_1_ptm_seed_0_relaxed.pdb #1
---
Chain | Description
A | No description available
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_63a81/rank_2_model_1_ptm_seed_0_unrelaxed.pdb
Chain information for rank_2_model_1_ptm_seed_0_unrelaxed.pdb #1
---
Chain | Description
A | No description available
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_63a81/rank_1_model_1_ptm_seed_2_relaxed.pdb
> format pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select /A:351
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-362
157 atoms, 159 bonds, 12 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
6 hydrogen bonds found
> hbonds sel reveal true
6 hydrogen bonds found
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-350
189 atoms, 198 bonds, 9 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
7 hydrogen bonds found
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-365
401 atoms, 413 bonds, 5 pseudobonds, 24 residues, 2 models selected
> show sel atoms
> hbonds sel reveal true
14 hydrogen bonds found
> select /A:268
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:268-269
34 atoms, 33 bonds, 2 residues, 1 model selected
> select /A:267-268
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:267-283
278 atoms, 280 bonds, 17 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
30 hydrogen bonds found
> select /A:291
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:291-299
112 atoms, 114 bonds, 9 residues, 1 model selected
> show sel atoms
> select /A:300
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:300-306
107 atoms, 107 bonds, 7 residues, 1 model selected
> show sel atoms
> select /A:103
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:103-106
72 atoms, 71 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:366
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:366-370
75 atoms, 75 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:263
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:263-267
85 atoms, 85 bonds, 5 residues, 1 model selected
> show sel atoms
> swapaa :353 ILE
Using Dunbrack library
/A ALA 353: phi -69.8, psi 82.4 trans
Applying ILE rotamer (chi angles: -56.3 -60.0) to /A ILE 353
> swapaa :357 LEU
Using Dunbrack library
/A ALA 357: phi -70.7, psi 69.3 trans
Applying LEU rotamer (chi angles: -80.2 -61.5) to /A LEU 357
> swapaa :357 VAL
Using Dunbrack library
/A LEU 357: phi -70.7, psi 69.3 trans
Applying VAL rotamer (chi angles: 177.0) to /A VAL 357
> swapaa :358 ASN
Using Dunbrack library
/A VAL 358: phi -5.6, psi 106.1 trans
Applying ASN rotamer (chi angles: -67.7 -119.0) to /A ASN 358
> swapaa :359 TRP
Using Dunbrack library
/A GLN 359: phi -49.9, psi 117.3 trans
Applying TRP rotamer (chi angles: -175.9 -102.3) to /A TRP 359
> select /A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:371-379
121 atoms, 124 bonds, 9 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
0 hydrogen bonds found
> select /A:24
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:24-32
153 atoms, 153 bonds, 9 residues, 1 model selected
> show sel atoms
> select /A:33
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:32-33
36 atoms, 35 bonds, 2 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
4 hydrogen bonds found
> select clear
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> mlp
Map values for surface "rank_1_model_1_ptm_seed_2_relaxed.pdb_A SES surface":
minimum -26.54, mean -3.518, maximum 27.75
To also show corresponding color key, enter the above mlp command and add key
true
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:20-23
58 atoms, 57 bonds, 4 residues, 1 model selected
> hide sel surfaces
> select /A:24
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:24-32
153 atoms, 153 bonds, 9 residues, 1 model selected
> hide sel surfaces
> style sel ball
Changed 153 atom styles
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select ::name="CYS"
100 atoms, 90 bonds, 10 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 100 atom styles
> select /A:313
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:313-316
44 atoms, 43 bonds, 4 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select /A:362
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:362-363
31 atoms, 30 bonds, 2 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
1 hydrogen bonds found
> select /A:361
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:350-361
156 atoms, 161 bonds, 12 residues, 1 model selected
> show sel atoms
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-344
65 atoms, 68 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:291
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:291-299
112 atoms, 114 bonds, 9 residues, 1 model selected
> show sel cartoons
> show sel atoms
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> color (#!1 & sel) white
> select clear
> select /A:299
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:292-299
98 atoms, 99 bonds, 8 residues, 1 model selected
> color sel byhetero
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A
6062 atoms, 6170 bonds, 1 pseudobond, 389 residues, 2 models selected
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:341
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:329-341
177 atoms, 178 bonds, 13 residues, 1 model selected
> select /A:345
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:345-346
33 atoms, 33 bonds, 2 residues, 1 model selected
> select /A:351
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-355
52 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
4 hydrogen bonds found
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-350
91 atoms, 95 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:345
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:345-346
33 atoms, 33 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:313
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:313-316
44 atoms, 43 bonds, 4 residues, 1 model selected
> select /A:317
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:313-317
56 atoms, 55 bonds, 5 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select /A:188
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:188-196
142 atoms, 144 bonds, 9 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> show sel atoms
> select /A:371
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:371-380
135 atoms, 139 bonds, 10 residues, 1 model selected
> show sel atoms
> select /A:381
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:381-389
133 atoms, 136 bonds, 9 residues, 1 model selected
> show sel atoms
> select /A:388-389
29 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:388-389
29 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:389
15 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:389
15 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:19
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 5 residues, 1 model selected
> show sel atoms
> select clear
> mlp
Map values for surface "rank_1_model_1_ptm_seed_2_relaxed.pdb_A SES surface":
minimum -26.54, mean -3.518, maximum 27.75
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color byhetero
> mlp
Map values for surface "rank_1_model_1_ptm_seed_2_relaxed.pdb_A SES surface":
minimum -26.54, mean -3.518, maximum 27.75
To also show corresponding color key, enter the above mlp command and add key
true
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_0a254/rank_1_model_1_ptm_seed_1_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_1_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
278 hydrogen bonds found
Alignment identifier is 1/A
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-344
65 atoms, 68 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:353
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:353-356
59 atoms, 59 bonds, 1 pseudobond, 4 residues, 2 models selected
> show sel atoms
> select /A:360
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:358-360
58 atoms, 60 bonds, 1 pseudobond, 3 residues, 2 models selected
> show sel atoms
> select /A:350
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:350-363
218 atoms, 223 bonds, 4 pseudobonds, 14 residues, 2 models selected
> show sel atoms
> select /A:364
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:364-389
381 atoms, 390 bonds, 26 residues, 1 model selected
> show sel atoms
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_0a254/rank_2_model_1_ptm_seed_0_relaxed.pdb
Chain information for rank_2_model_1_ptm_seed_0_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
275 hydrogen bonds found
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_63a81/rank_1_model_1_ptm_seed_2_relaxed.pdb
> format pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
283 hydrogen bonds found
Alignment identifier is 1/A
> select /A:389
15 atoms, 15 bonds, 1 residue, 1 model selected
> select /A
6070 atoms, 6176 bonds, 283 pseudobonds, 389 residues, 2 models selected
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:1-2
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A
6070 atoms, 6176 bonds, 283 pseudobonds, 389 residues, 2 models selected
> select /A:266
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:266-269
64 atoms, 63 bonds, 1 pseudobond, 4 residues, 2 models selected
> select /A:263
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:263-267
85 atoms, 85 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel white
> select /A:357
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:353-357
60 atoms, 60 bonds, 2 pseudobonds, 5 residues, 2 models selected
> show sel atoms
> select /A:346
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:346-359
219 atoms, 226 bonds, 7 pseudobonds, 14 residues, 2 models selected
> show sel atoms
> open
> /Users/michaelmatthias/Downloads/prediction_test1_63a81/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #2
---
Chain | Description
A | No description available
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test1_63a81/rank_1_model_1_ptm_seed_2_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_2_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> set bgColor white
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-389
744 atoms, 766 bonds, 48 residues, 1 model selected
> color sel dim gray
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> hbonds sel reveal true
15 hydrogen bonds found
> hbonds sel reveal true
15 hydrogen bonds found
> select /A:341
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:341-389
758 atoms, 781 bonds, 10 pseudobonds, 49 residues, 2 models selected
> hbonds sel reveal true
15 hydrogen bonds found
> select /A:342-343
41 atoms, 42 bonds, 2 residues, 1 model selected
> select /A:342-344
65 atoms, 68 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-349
70 atoms, 73 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:345-346
33 atoms, 33 bonds, 2 residues, 1 model selected
> select /A:345-346
33 atoms, 33 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:363
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:363-365
55 atoms, 54 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:265
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:265-267
46 atoms, 45 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:362
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:362
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:359
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:359-362
60 atoms, 60 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A
6070 atoms, 6176 bonds, 15 pseudobonds, 389 residues, 2 models selected
> select clear
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select /A:139-140
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:104-139
621 atoms, 631 bonds, 36 residues, 1 model selected
> select /A:291
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:291-298
98 atoms, 99 bonds, 8 residues, 1 model selected
> select /A:291-292
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:291-299
112 atoms, 114 bonds, 9 residues, 1 model selected
> color sel orange
> select /A:342
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:342-389
744 atoms, 766 bonds, 9 pseudobonds, 48 residues, 2 models selected
> color (#!1 & sel) orange red
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 5 residues, 1 model selected
> color sel light sea green
> select /A:17-18
43 atoms, 43 bonds, 2 residues, 1 model selected
> select /A:1-18
292 atoms, 296 bonds, 18 residues, 1 model selected
> color sel forest green
> select /A:24
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:24-32
153 atoms, 153 bonds, 9 residues, 1 model selected
> color sel cornflower blue
> select /A:192
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:192-258
1054 atoms, 1073 bonds, 67 residues, 1 model selected
> color sel cornflower blue
> select /A:291-292
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:291-298
98 atoms, 99 bonds, 8 residues, 1 model selected
> select /A:300-301
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:300-341
589 atoms, 593 bonds, 42 residues, 1 model selected
> color sel blue
[Repeated 1 time(s)]
> color sel medium blue
> select /A:33
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:33-191
2564 atoms, 2606 bonds, 159 residues, 1 model selected
> color sel medium blue
> ui tool show "Color Actions"
> color sel dark blue
> select clear
> select /A:342-343
41 atoms, 42 bonds, 2 residues, 1 model selected
> select /A:342-350
189 atoms, 198 bonds, 4 pseudobonds, 9 residues, 2 models selected
> style sel ball
Changed 189 atom styles
> color (#!1 & sel) byelement
> ui tool show "Color Actions"
> color sel white target l
> select clear
> select /A:297
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:296-297
26 atoms, 25 bonds, 2 residues, 1 model selected
> color sel byhetero
> select /A:294
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:294
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel byhetero
> select /A:361
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:361-370
156 atoms, 156 bonds, 10 residues, 1 model selected
> style sel ball
Changed 156 atom styles
> ui tool show "Color Actions"
> color sel light goldenrod yellow target l
> save "/Users/michaelmatthias/New Folder/nearDn.cxs"
[Errno 20] Not a directory: '/Users/michaelmatthias/New Folder'
> save /Users/michaelmatthias/R01.PAR.22.241/nearDn.cxs
——— End of log from Mon Apr 10 12:10:39 2023 ———
opened ChimeraX session
Alignment identifier is 1/A
> select /A:348
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:348-349
48 atoms, 51 bonds, 2 residues, 1 model selected
> select /A:347
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:347-350
91 atoms, 95 bonds, 1 pseudobond, 4 residues, 2 models selected
> select /A:345
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:345-355
176 atoms, 183 bonds, 4 pseudobonds, 11 residues, 2 models selected
> style sel ball
Changed 176 atom styles
> select /A:356
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:356-358
45 atoms, 44 bonds, 1 pseudobond, 3 residues, 2 models selected
> select /A:359-360
34 atoms, 34 bonds, 2 residues, 1 model selected
> select /A:359-389
458 atoms, 468 bonds, 31 residues, 1 model selected
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_438e1/rank_1_model_1_ptm_seed_3_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_3_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select /A:493
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:489-493
97 atoms, 101 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:133
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:133-135
50 atoms, 50 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:147-148
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:147-150
51 atoms, 51 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:486
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:486-489
63 atoms, 64 bonds, 4 residues, 1 model selected
> hbonds sel reveal true
4 hydrogen bonds found
> select /A:494
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:494-497
91 atoms, 95 bonds, 4 residues, 1 model selected
> show sel atoms
> hbonds sel reveal true
2 hydrogen bonds found
> select /A:109
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:109-119
179 atoms, 179 bonds, 11 residues, 1 model selected
> show sel atoms
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-18
292 atoms, 296 bonds, 18 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select /A:19
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:24
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:24-31
111 atoms, 112 bonds, 8 residues, 1 model selected
> show sel atoms
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:1-23
362 atoms, 366 bonds, 23 residues, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select /A:40
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-40
618 atoms, 625 bonds, 2 pseudobonds, 40 residues, 2 models selected
> hbonds sel reveal true
8 hydrogen bonds found
> select /A:37
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:37
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:36
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:36-37
36 atoms, 36 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:36
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:36-38
47 atoms, 47 bonds, 3 residues, 1 model selected
> show sel atoms
> select /A:24
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:24-28
73 atoms, 74 bonds, 2 pseudobonds, 5 residues, 2 models selected
> select /A:31
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:24-31
111 atoms, 112 bonds, 2 pseudobonds, 8 residues, 2 models selected
> select /A:489
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:489-502
241 atoms, 252 bonds, 14 residues, 1 model selected
> select /A:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:498-502
53 atoms, 54 bonds, 5 residues, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> show sel atoms
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 5 residues, 1 model selected
> hide sel cartoons
> style sel sphere
Changed 70 atom styles
> color sel orange red
> select /A:18
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:1-18
292 atoms, 296 bonds, 18 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> style sel sphere
Changed 292 atom styles
> color sel light sea green
> select /A:494
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:494-502
144 atoms, 150 bonds, 9 residues, 1 model selected
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_test_c481a/rank_1_model_1_ptm_seed_0_relaxed.pdb
Chain information for rank_1_model_1_ptm_seed_0_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 5 residues, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select /A:33
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:23-33
184 atoms, 184 bonds, 11 residues, 1 model selected
> hbonds sel reveal true
3 hydrogen bonds found
> select /A:489
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:486-489
94 atoms, 97 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:485
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:481-485
97 atoms, 101 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:490
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:490-495
73 atoms, 75 bonds, 6 residues, 1 model selected
> show sel atoms
> select /A:495
15 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:481-495
264 atoms, 275 bonds, 15 residues, 1 model selected
> hbonds sel reveal true
9 hydrogen bonds found
> save /Users/michaelmatthias/R01.PAR.22.241/stillNoCigarButBetter.cxs
——— End of log from Thu Apr 13 11:56:51 2023 ———
opened ChimeraX session
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_testB_593d3/rank_1_model_2_ptm_seed_3_relaxed.pdb
> format pdb
Chain information for rank_1_model_2_ptm_seed_3_relaxed.pdb #1
---
Chain | Description
A | No description available
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_testB_593d3/rank_2_model_2_ptm_seed_1_relaxed.pdb
> format pdb
Chain information for rank_2_model_2_ptm_seed_1_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select /A:342
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:342-382
633 atoms, 645 bonds, 41 residues, 1 model selected
> select /A:396
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:305-396
1467 atoms, 1490 bonds, 92 residues, 1 model selected
> select /A:397
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:397-402
81 atoms, 82 bonds, 6 residues, 1 model selected
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_testB_8c286/rank_1_model_4_ptm_seed_1_relaxed.pdb
> format pdb
Chain information for rank_1_model_4_ptm_seed_1_relaxed.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select /A:344
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:324-344
345 atoms, 349 bonds, 21 residues, 1 model selected
> select /A:345
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:345-347
45 atoms, 44 bonds, 3 residues, 1 model selected
> select /A:347-348
32 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:347-349
49 atoms, 49 bonds, 3 residues, 1 model selected
> select /A:351-352
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /A:348-351
70 atoms, 70 bonds, 4 residues, 1 model selected
> select /A:332-333
29 atoms, 28 bonds, 2 residues, 1 model selected
> select /A:332-351
340 atoms, 343 bonds, 20 residues, 1 model selected
> select /A:332-351,408-484
1470 atoms, 1489 bonds, 97 residues, 1 model selected
> select /A:324-325
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:324-351
460 atoms, 465 bonds, 28 residues, 1 model selected
> select /A:484
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:484-486
64 atoms, 67 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 64 atom styles
> select /A:481
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:481-483
43 atoms, 43 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 43 atom styles
> select /A:106-107
37 atoms, 36 bonds, 2 residues, 1 model selected
> select /A:106-109
72 atoms, 71 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 72 atom styles
> select /A:126
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:126-131
100 atoms, 100 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 100 atom styles
> select /A:435
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:435-449
233 atoms, 235 bonds, 15 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 233 atom styles
> color sel light gray
> select /A:475
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:475-483
114 atoms, 114 bonds, 9 residues, 1 model selected
> select /A:474
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:474-484
144 atoms, 145 bonds, 11 residues, 1 model selected
> color sel orange
> show sel atoms
> style sel ball
Changed 144 atom styles
> select /A:471
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:471-473
47 atoms, 46 bonds, 3 residues, 1 model selected
> color sel orange
> show sel atoms
> style sel ball
Changed 47 atom styles
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select /A:471-472
30 atoms, 29 bonds, 2 residues, 1 model selected
> select /A:471-484
191 atoms, 192 bonds, 14 residues, 1 model selected
> color sel orange red
> select /A:435
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:435-443
138 atoms, 139 bonds, 9 residues, 1 model selected
> select /A:438
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:438-449
200 atoms, 202 bonds, 12 residues, 1 model selected
> color sel purple
> select /A:438
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:438-439
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /A:440
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:438-440
57 atoms, 57 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tan
> select /A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:332-336
64 atoms, 64 bonds, 5 residues, 1 model selected
> color sel light sea green
> select /A:443
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:443-445
52 atoms, 53 bonds, 3 residues, 1 model selected
> select /A:485-486
44 atoms, 46 bonds, 2 residues, 1 model selected
> select /A:485-499
277 atoms, 288 bonds, 15 residues, 1 model selected
> hide sel atoms
> select /A:131
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:128-131
74 atoms, 74 bonds, 4 residues, 1 model selected
> color sel orange red
> select /A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:126
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:126-127
26 atoms, 25 bonds, 2 residues, 1 model selected
> select /A:132
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:132
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:109-110
41 atoms, 40 bonds, 2 residues, 1 model selected
> select /A:106-110
94 atoms, 93 bonds, 5 residues, 1 model selected
> select /A:106
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:106-109
72 atoms, 71 bonds, 4 residues, 1 model selected
> color sel lime
> select /A:110
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:110
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel lime
> select /A:111
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:111-112
25 atoms, 24 bonds, 2 residues, 1 model selected
> select /A:111
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:111
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel lime
> select /A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:113-114
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:112
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:111-112
25 atoms, 24 bonds, 2 residues, 1 model selected
> color sel lime
> select /A:110
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:110
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:109
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:106-109
72 atoms, 71 bonds, 4 residues, 1 model selected
> select /A:109
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:109
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:112
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:111-112
25 atoms, 24 bonds, 2 residues, 1 model selected
> select /A:114
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:113-114
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:440
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:440
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel purple
> select /A:89
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:89
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel cornflower blue
> select /A:90
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:90
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:89
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:87-89
53 atoms, 53 bonds, 3 residues, 1 model selected
> select /A:86-87
28 atoms, 27 bonds, 2 residues, 1 model selected
> select clear
> select /A:484
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:484
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:337
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:337-338
38 atoms, 37 bonds, 2 residues, 1 model selected
> select /A:337-340
72 atoms, 73 bonds, 4 residues, 1 model selected
> select /A:337
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:337-339
55 atoms, 55 bonds, 3 residues, 1 model selected
> color sel light sea green
> select /A:438
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:438-439
40 atoms, 40 bonds, 2 residues, 1 model selected
> color sel purple
> select clear
> mlp
Map values for surface "rank_1_model_4_ptm_seed_1_relaxed.pdb_A SES surface":
minimum -26.58, mean -3.419, maximum 28.46
To also show corresponding color key, enter the above mlp command and add key
true
> hide cartoons
> hide surfaces
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-484
7578 atoms, 7704 bonds, 484 residues, 1 model selected
> select /A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:330-332
31 atoms, 31 bonds, 3 residues, 1 model selected
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:345
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:340-345
120 atoms, 120 bonds, 6 residues, 1 model selected
> select /A:25
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:25
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:23-24
44 atoms, 43 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!1 & sel) hot pink
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!1 & sel) hot pink
> color (#!1 & sel) magenta
> select /A:25
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:25
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 5 residues, 1 model selected
> color (#!1 & sel) orange
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:275
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:275-276
43 atoms, 43 bonds, 2 residues, 1 model selected
> select /A:274
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:274-277
62 atoms, 62 bonds, 4 residues, 1 model selected
> select /A:278
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:274-278
76 atoms, 76 bonds, 5 residues, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> color (#!1 & sel) light gray
> color (#!1 & sel) black
> select /A:74
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:74-76
51 atoms, 52 bonds, 3 residues, 1 model selected
> select /A:76
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:76-78
58 atoms, 59 bonds, 3 residues, 1 model selected
> select /A:76-80
91 atoms, 93 bonds, 5 residues, 1 model selected
> select /A:77
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:77-79
51 atoms, 51 bonds, 3 residues, 1 model selected
> select /A:81
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:81
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:76
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:76-77
41 atoms, 42 bonds, 2 residues, 1 model selected
> select /A:76-77,79
58 atoms, 59 bonds, 3 residues, 1 model selected
> select /A:76
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:76-77
41 atoms, 42 bonds, 2 residues, 1 model selected
> select /A:74,76-77
58 atoms, 58 bonds, 3 residues, 1 model selected
> select /A:74-77
68 atoms, 69 bonds, 4 residues, 1 model selected
> graphics silhouettes true color grey]
Invalid "color" argument: Invalid color name or specifier
> graphics silhouettes true color grey
> select clear
> select /A:275
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:275-276
43 atoms, 43 bonds, 2 residues, 1 model selected
> select /A:74
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:74-77
68 atoms, 69 bonds, 4 residues, 1 model selected
> color (#!1 & sel) black
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /A:75
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:75
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel byhetero
> select /A:246
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:246-248
70 atoms, 73 bonds, 3 residues, 1 model selected
> color (#!1 & sel) black
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> color (#!1 & sel) medium blue
> select /A:151-152
35 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:151-154
80 atoms, 83 bonds, 4 residues, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /A:32-33
32 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:30-32
49 atoms, 49 bonds, 3 residues, 1 model selected
> color (#!1 & sel) forest green
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /A:29
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:29
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel ball
Changed 14 atom styles
> color sel byhetero
> select /A:28
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:28-35
124 atoms, 125 bonds, 8 residues, 1 model selected
> select /A:25-26
29 atoms, 29 bonds, 2 residues, 1 model selected
> select /A:1-26
413 atoms, 418 bonds, 26 residues, 1 model selected
> select /A:28
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:1-28
442 atoms, 448 bonds, 28 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /A:16
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:16-19
67 atoms, 67 bonds, 4 residues, 1 model selected
> show sel atoms
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /A:275
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:275-276
43 atoms, 43 bonds, 2 residues, 1 model selected
> color sel byhetero
> select /A:277
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:274-277
62 atoms, 62 bonds, 4 residues, 1 model selected
> select /A:270
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:269-270
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:36
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:36-38
53 atoms, 53 bonds, 3 residues, 1 model selected
> select /A:40
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:40-43
62 atoms, 63 bonds, 4 residues, 1 model selected
> select /A:259
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:259-262
74 atoms, 76 bonds, 4 residues, 1 model selected
> select /A:250
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:250-255
73 atoms, 72 bonds, 6 residues, 1 model selected
> select /A:30
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:30-33
60 atoms, 60 bonds, 4 residues, 1 model selected
> select /A:12
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:12-14
41 atoms, 41 bonds, 3 residues, 1 model selected
> select /A:333
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:333-334
39 atoms, 39 bonds, 2 residues, 1 model selected
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:340-341
41 atoms, 41 bonds, 2 residues, 1 model selected
> select /A:216
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:216-217
42 atoms, 43 bonds, 2 residues, 1 model selected
> select /A:115
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:115-117
57 atoms, 59 bonds, 3 residues, 1 model selected
> style sel ball
Changed 57 atom styles
> select /A:166
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:166-167
31 atoms, 31 bonds, 2 residues, 1 model selected
> select /A:449
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:449-451
42 atoms, 41 bonds, 3 residues, 1 model selected
> select /A:440
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:440-441
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:439
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:439-441
52 atoms, 52 bonds, 3 residues, 1 model selected
> select /A:41
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:41-42
28 atoms, 29 bonds, 2 residues, 1 model selected
> style sel ball
Changed 28 atom styles
> color sel byhetero
> select /A:28
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:24-25
36 atoms, 36 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select /A:29
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:28-29
29 atoms, 29 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 29 atom styles
> color sel byhetero
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:24-25
36 atoms, 36 bonds, 2 residues, 1 model selected
> select /A:29
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:29-30
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /A:274
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:274-278
76 atoms, 76 bonds, 5 residues, 1 model selected
> style sel ball
Changed 76 atom styles
> color sel byhetero
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-236
3762 atoms, 3825 bonds, 236 residues, 1 model selected
> select /A:352
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:352-407
862 atoms, 877 bonds, 56 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /A:352-353
28 atoms, 29 bonds, 2 residues, 1 model selected
> select /A:352-353
28 atoms, 29 bonds, 2 residues, 1 model selected
> select /A:354
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:354-355
31 atoms, 31 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select /A:422
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:422-425
60 atoms, 59 bonds, 4 residues, 1 model selected
> select /A:420
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:413-420
133 atoms, 134 bonds, 8 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:412
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:408-412
67 atoms, 68 bonds, 5 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select
> /A:106-109,128-130,171-177,256-258,290-295,309-323,352-363,385-392,394-407,414-425,443-445,468-470,484-486
1528 atoms, 1542 bonds, 93 residues, 1 model selected
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:421-425
81 atoms, 81 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:352
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:352-353
28 atoms, 29 bonds, 2 residues, 1 model selected
> select /A:346-347
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:346-351
101 atoms, 101 bonds, 6 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> style sel ball
Changed 101 atom styles
> select clear
> select /A:353
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:352-353
28 atoms, 29 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:355
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:354-355
31 atoms, 31 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:351
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:351-353
42 atoms, 43 bonds, 3 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select /A:354
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:354-355
31 atoms, 31 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select /A:353
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:351-353
42 atoms, 43 bonds, 3 residues, 1 model selected
> select /A:315-347
535 atoms, 541 bonds, 33 residues, 1 model selected
> select /A:315-346
523 atoms, 529 bonds, 32 residues, 1 model selected
> select /A:350
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:346-350
87 atoms, 87 bonds, 5 residues, 1 model selected
> show sel cartoons
> select /A:352
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:352-356
76 atoms, 78 bonds, 5 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:350
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:350
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:346
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:346-347
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:348
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:348-351
70 atoms, 70 bonds, 4 residues, 1 model selected
> show sel atoms
> select /A:422
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:422-425
60 atoms, 59 bonds, 4 residues, 1 model selected
> hide sel atoms
> select /A:424
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:424
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:422
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:422-423
29 atoms, 28 bonds, 2 residues, 1 model selected
> show sel cartoons
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select /A:422
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:422-424
43 atoms, 42 bonds, 3 residues, 1 model selected
> hbonds sel reveal true
5 hydrogen bonds found
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:422
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:422-426
79 atoms, 78 bonds, 1 pseudobond, 5 residues, 2 models selected
> select /A:399
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:399-401
44 atoms, 43 bonds, 3 residues, 1 model selected
> select /A:346
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:346-347
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:348
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:348-351
70 atoms, 70 bonds, 4 residues, 1 model selected
> select /A:345
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:345-347
45 atoms, 44 bonds, 3 residues, 1 model selected
> select /A:399
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:399-402
56 atoms, 55 bonds, 4 residues, 1 model selected
> select /A:345-346
33 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:345-347
45 atoms, 44 bonds, 3 residues, 1 model selected
> select /A:348
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:348-351
70 atoms, 70 bonds, 4 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:324
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:324-346
378 atoms, 382 bonds, 23 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select /A:348
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:348-349
37 atoms, 37 bonds, 2 residues, 1 model selected
> select /A:346-347
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:346-347
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:421-425
81 atoms, 81 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:392
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:386-392
135 atoms, 136 bonds, 7 residues, 1 model selected
> select /A:345
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:345-346
33 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:347
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:347-350
68 atoms, 68 bonds, 4 residues, 1 model selected
> select /A:354-355
31 atoms, 31 bonds, 2 residues, 1 model selected
> select /A:354-359
94 atoms, 94 bonds, 6 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select /A:347-348
32 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:347-356
158 atoms, 161 bonds, 10 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select /A:421
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:408-421
221 atoms, 225 bonds, 14 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:352
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:352-364
209 atoms, 212 bonds, 13 residues, 1 model selected
> hide sel atoms
> hide sel surfaces
> hide sel cartoons
> select /A:484
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:484-486
64 atoms, 67 bonds, 3 residues, 1 model selected
> show sel atoms
> close session
> open
> /Users/michaelmatthias/Downloads/prediction_testB_732fc/rank_1_model_3_ptm_seed_0_relaxed.pdb
Chain information for rank_1_model_3_ptm_seed_0_relaxed.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
Alignment identifier is 1/A
> select /A:359
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:359-374
264 atoms, 267 bonds, 16 residues, 1 model selected
> select /A:354-355
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:354-358
67 atoms, 68 bonds, 5 residues, 1 model selected
> select /A:345
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:345-352
129 atoms, 131 bonds, 8 residues, 1 model selected
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:340-344
106 atoms, 106 bonds, 5 residues, 1 model selected
> select /A:339
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:339-340
34 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:340-346
139 atoms, 139 bonds, 7 residues, 1 model selected
> select /A:381
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:381-391
170 atoms, 172 bonds, 11 residues, 1 model selected
> show sel atoms
> select /A:368
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:368-380
205 atoms, 209 bonds, 13 residues, 1 model selected
> select /A:367
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:359-367
154 atoms, 156 bonds, 9 residues, 1 model selected
> select /A:342
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:342-346
98 atoms, 97 bonds, 5 residues, 1 model selected
> select /A:340
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:340-353
249 atoms, 252 bonds, 14 residues, 1 model selected
> select /A:346
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:346-353
129 atoms, 131 bonds, 8 residues, 1 model selected
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-430
6751 atoms, 6862 bonds, 430 residues, 1 model selected
> open "/Users/michaelmatthias/Downloads/prediction_testB_732fc
> 2/rank_1_model_3_ptm_seed_3_relaxed.pdb"
Chain information for rank_1_model_3_ptm_seed_3_relaxed.pdb #2
---
Chain | Description
A | No description available
> close session
> open "/Users/michaelmatthias/Downloads/prediction_testB_732fc
> 2/rank_1_model_3_ptm_seed_3_relaxed.pdb" format pdb
Chain information for rank_1_model_3_ptm_seed_3_relaxed.pdb #1
---
Chain | Description
A | No description available
> hbonds reveal true
402 hydrogen bonds found
Alignment identifier is 1/A
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:23-34
205 atoms, 208 bonds, 12 residues, 1 model selected
> show sel atoms
> select /A:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:23-26
79 atoms, 79 bonds, 4 residues, 1 model selected
> select /A:482
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:482-483
35 atoms, 36 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-18
292 atoms, 296 bonds, 1 pseudobond, 18 residues, 2 models selected
> show sel atoms
> select /A:19
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 1 pseudobond, 5 residues, 2 models selected
> select /A:17
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:17-18
43 atoms, 43 bonds, 2 residues, 1 model selected
> select /A:19-20
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:19-23
70 atoms, 69 bonds, 1 pseudobond, 5 residues, 2 models selected
> show sel atoms
> set bgColor white
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select /A:441
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:441-445
85 atoms, 86 bonds, 1 pseudobond, 5 residues, 2 models selected
> color (#!1 & sel) purple
> select /A:331
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:331-339
143 atoms, 144 bonds, 9 residues, 1 model selected
> select /A:331
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:331-335
64 atoms, 64 bonds, 5 residues, 1 model selected
> color sel orange
> select /A:482
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:482-483
35 atoms, 36 bonds, 2 residues, 1 model selected
> color sel black
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> ui tool show "Color Actions"
> color sel light gray target l
> select /A:480
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:480-481
29 atoms, 28 bonds, 2 residues, 1 model selected
> color sel dark gray
> select /A:440
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:438-440
52 atoms, 52 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple target l
> ui tool show "Color Actions"
> color sel light gray target l
> color sel medium purple
> select /A:305
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:305-308
69 atoms, 68 bonds, 4 residues, 1 model selected
> select /A:300
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:300-307
125 atoms, 126 bonds, 2 pseudobonds, 8 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> select /A:294
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:294
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:308
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:307-308
34 atoms, 33 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pink
> select /A:298
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:292-298
110 atoms, 109 bonds, 2 pseudobonds, 7 residues, 2 models selected
> select /A:308
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:308-315
145 atoms, 146 bonds, 5 pseudobonds, 8 residues, 2 models selected
> select /A:104-105
29 atoms, 29 bonds, 2 residues, 1 model selected
> select /A:105-108
72 atoms, 71 bonds, 4 residues, 1 model selected
> select /A:109
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:109
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:104
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:104-109
108 atoms, 108 bonds, 4 pseudobonds, 6 residues, 2 models selected
> select /A:110
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:110-111
25 atoms, 24 bonds, 2 residues, 1 model selected
> select /A:103
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:103-113
179 atoms, 179 bonds, 7 pseudobonds, 11 residues, 2 models selected
> color (#!1 & sel) light sea green
> select /A:136
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:135-136
28 atoms, 27 bonds, 2 residues, 1 model selected
> select /A:130
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:125-130
100 atoms, 100 bonds, 4 pseudobonds, 6 residues, 2 models selected
> color (#!1 & sel) dark gray
> select /A:131
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:131-134
84 atoms, 85 bonds, 4 residues, 1 model selected
> select /A:130
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:129
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:126-129
62 atoms, 62 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select /A:125
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:125
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:124
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:124-125
33 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:123
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:123
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel dark gray
> select /A:312
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:308-312
83 atoms, 82 bonds, 2 pseudobonds, 5 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> select /A:278
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:278-280
53 atoms, 52 bonds, 3 residues, 1 model selected
> select /A:251
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:251
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:266
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:266-269
43 atoms, 42 bonds, 1 pseudobond, 4 residues, 2 models selected
> select /A:270
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:270-273
62 atoms, 61 bonds, 4 residues, 1 model selected
> select /A:266
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:266-269
43 atoms, 42 bonds, 1 pseudobond, 4 residues, 2 models selected
> color (#!1 & sel) lime
> select /A:197
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:197
14 atoms, 13 bonds, 1 residue, 1 model selected
> select
> /A:47-49,55-63,66-72,82-84,90-94,97-102,114-116,118-121,131-134,137-140,147-150,153-157,187-189,192-195,198-203,206-208,214-217,222-227,232-239,242-248,278-280,285-287
1797 atoms, 1814 bonds, 83 pseudobonds, 104 residues, 2 models selected
> select /A:187
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:187-189
50 atoms, 49 bonds, 3 residues, 1 model selected
> color sel gray
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select /A:303
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:303-307
86 atoms, 86 bonds, 5 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select /A:278
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:278-280
53 atoms, 52 bonds, 3 residues, 1 model selected
> select /A:187-188
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:187-189
50 atoms, 49 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light gray target l
> select /A:125
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:125-130
100 atoms, 100 bonds, 4 pseudobonds, 6 residues, 2 models selected
> select /A:128
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:125-128
59 atoms, 59 bonds, 1 pseudobond, 4 residues, 2 models selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> ui tool show "Color Actions"
> color sel white target l
> select /A:158
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:158-169
189 atoms, 190 bonds, 1 pseudobond, 12 residues, 2 models selected
> select /A:158-169,299-307
325 atoms, 327 bonds, 3 pseudobonds, 21 residues, 2 models selected
> select /A:292
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:292-298
110 atoms, 109 bonds, 2 pseudobonds, 7 residues, 2 models selected
> select /A:299-300
25 atoms, 25 bonds, 2 residues, 1 model selected
> select /A:299-307
136 atoms, 137 bonds, 2 pseudobonds, 9 residues, 2 models selected
> select /A:158
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:158-169
189 atoms, 190 bonds, 1 pseudobond, 12 residues, 2 models selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /A:169
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:169-177
131 atoms, 132 bonds, 7 pseudobonds, 9 residues, 2 models selected
> style sel ball
Changed 131 atom styles
> select /A:158
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:158-169
189 atoms, 190 bonds, 1 pseudobond, 12 residues, 2 models selected
> select /A:103
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:103-113
179 atoms, 179 bonds, 7 pseudobonds, 11 residues, 2 models selected
> save /Users/michaelmatthias/R01.PAR.22.241/preChop.cxs
——— End of log from Fri Apr 14 17:32:31 2023 ———
opened ChimeraX session
> select
> /A:105-108,127-129,170-176,289-291,308-322,351-362,384-391,393-406,410-424,441-445,467-469
1448 atoms, 1460 bonds, 59 pseudobonds, 89 residues, 2 models selected
> select /A:406
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:340-406
1066 atoms, 1082 bonds, 50 pseudobonds, 67 residues, 2 models selected
> select /A:344
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:344-345
33 atoms, 32 bonds, 2 residues, 1 model selected
> select /A:348-349
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /A:346-349
68 atoms, 68 bonds, 4 residues, 1 model selected
> select /A:434
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:434-483
705 atoms, 711 bonds, 25 pseudobonds, 50 residues, 2 models selected
> select /A:431
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:353-431
1239 atoms, 1261 bonds, 62 pseudobonds, 79 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> show sel atoms
> select /A:434
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:434-440
104 atoms, 104 bonds, 7 residues, 1 model selected
> color sel medium blue
> color sel purple
> save /Users/michaelmatthias/R01.PAR.22.241/preChop1.cxs
——— End of log from Fri Apr 14 18:25:24 2023 ———
opened ChimeraX session
> select /A:435
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:434-435
26 atoms, 25 bonds, 2 residues, 1 model selected
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select /A:432
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:432-433
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:436
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:436-437
26 atoms, 25 bonds, 2 residues, 1 model selected
> select /A:432
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:432-433
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:434
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:434-435
26 atoms, 25 bonds, 2 residues, 1 model selected
> select /A:436
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:436-437
26 atoms, 25 bonds, 2 residues, 1 model selected
> select /A:410
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:410-424
249 atoms, 252 bonds, 10 pseudobonds, 15 residues, 2 models selected
> select /A:407
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:407-411
67 atoms, 68 bonds, 5 residues, 1 model selected
> select /A:307
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:299-307
136 atoms, 137 bonds, 2 pseudobonds, 9 residues, 2 models selected
> select /A:288
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:288-298
178 atoms, 179 bonds, 6 pseudobonds, 11 residues, 2 models selected
> select /A:198
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:198-203
123 atoms, 124 bonds, 6 residues, 1 model selected
> select /A:252
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:252-277
394 atoms, 400 bonds, 17 pseudobonds, 26 residues, 2 models selected
> select /A:448
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:345-448
1622 atoms, 1651 bonds, 72 pseudobonds, 104 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /A:362
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:362-364
53 atoms, 54 bonds, 3 residues, 1 model selected
> select clear
> show cartoons
> select clear
> select /A:433
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:432-433
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:434
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:434-438
73 atoms, 73 bonds, 5 residues, 1 model selected
> select /A:436
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:434-436
33 atoms, 32 bonds, 3 residues, 1 model selected
> select /A:431
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:430-431
38 atoms, 39 bonds, 2 residues, 1 model selected
> select /A:391
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:391-392
45 atoms, 45 bonds, 2 residues, 1 model selected
> select /A:392-393
35 atoms, 36 bonds, 2 residues, 1 model selected
> select /A:392-393
35 atoms, 36 bonds, 2 residues, 1 model selected
> select /A:383
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:376-383
106 atoms, 107 bonds, 2 pseudobonds, 8 residues, 2 models selected
> select /A:375
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:353-375
342 atoms, 347 bonds, 11 pseudobonds, 23 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /A:382
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:374-382
135 atoms, 138 bonds, 2 pseudobonds, 9 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /A:383
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:383-385
46 atoms, 47 bonds, 1 pseudobond, 3 residues, 2 models selected
> select /A:345
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:345-346
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /A:483
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A
7580 atoms, 7705 bonds, 402 pseudobonds, 483 residues, 2 models selected
> select clear
> show cartoons
> select /A:365-366
28 atoms, 27 bonds, 2 residues, 1 model selected
> select /A:365-376
164 atoms, 167 bonds, 12 residues, 1 model selected
> select /A:384
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:371-384
185 atoms, 189 bonds, 4 pseudobonds, 14 residues, 2 models selected
> select /A:385
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:385-416
529 atoms, 537 bonds, 25 pseudobonds, 32 residues, 2 models selected
> select /A:384
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:384-406
386 atoms, 391 bonds, 21 pseudobonds, 23 residues, 2 models selected
> show sel atoms
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> hide sel atoms
> select /A:240
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:240-241
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:196
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:196-203
144 atoms, 145 bonds, 8 residues, 1 model selected
> show sel atoms
> select /A:203
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:203
24 atoms, 23 bonds, 1 residue, 1 model selected
> select
> /A:47-49,55-63,66-72,82-84,90-94,97-102,114-116,118-121,131-134,137-140,147-150,153-157,187-189,192-195,198-203,206-208,214-217,222-227,232-239,242-248,278-280,285-287
1797 atoms, 1814 bonds, 83 pseudobonds, 104 residues, 2 models selected
> select /A:281
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:281-288
111 atoms, 111 bonds, 8 residues, 1 model selected
> show sel atoms
> select /A:289
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:289-294
102 atoms, 103 bonds, 2 pseudobonds, 6 residues, 2 models selected
> show sel atoms
> select /A:437
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:435-437
33 atoms, 32 bonds, 3 residues, 1 model selected
> select /A:428
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:428-433
95 atoms, 98 bonds, 6 residues, 1 model selected
> select /A:465-466
25 atoms, 25 bonds, 2 residues, 1 model selected
> select /A:465-469
61 atoms, 61 bonds, 4 pseudobonds, 5 residues, 2 models selected
> select /A:407
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:407-411
67 atoms, 68 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:288
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:288
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:283
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:283
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:286
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:286-287
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:286
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:286
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:288
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:288-298
178 atoms, 179 bonds, 6 pseudobonds, 11 residues, 2 models selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> hide atoms
> select /A:288-289
36 atoms, 36 bonds, 2 residues, 1 model selected
> select /A:288-289
36 atoms, 36 bonds, 2 residues, 1 model selected
> color sel light sea green
> select /A:407
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:407-409
32 atoms, 32 bonds, 3 residues, 1 model selected
> color sel light sea green
> select /A:290
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:290-295
100 atoms, 100 bonds, 3 pseudobonds, 6 residues, 2 models selected
> select /A:410
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:410-412
49 atoms, 49 bonds, 3 residues, 1 model selected
> select /A:141
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:141-146
96 atoms, 97 bonds, 1 pseudobond, 6 residues, 2 models selected
> ui tool show "Color Actions"
> select
> /A:47-49,55-63,66-72,82-84,90-94,97-102,114-116,118-121,131-134,137-140,147-150,153-157,187-189,192-195,198-203,206-208,214-217,222-227,232-239,242-248,278-280,285-287
1797 atoms, 1814 bonds, 83 pseudobonds, 104 residues, 2 models selected
> select /A:407
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:407-408
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:409
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:409
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:407-408
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:407-409
32 atoms, 32 bonds, 3 residues, 1 model selected
> color sel light sea green target l
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> color sel light sea green target l
> select /A:289
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:289-291
46 atoms, 47 bonds, 3 residues, 1 model selected
> color sel light sea green target acpl
> color sel light green target acpl
> color sel light sea green target acpl
> select /A:307
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:303-307
86 atoms, 86 bonds, 5 residues, 1 model selected
> select /A:250
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:250-253
55 atoms, 54 bonds, 4 residues, 1 model selected
> select /A:29
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:29-34
95 atoms, 95 bonds, 6 residues, 1 model selected
> color sel red
> select /A:441
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:441-448
129 atoms, 130 bonds, 2 pseudobonds, 8 residues, 2 models selected
> select /A:450
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:438-450
209 atoms, 211 bonds, 3 pseudobonds, 13 residues, 2 models selected
> select /A:407
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:407-410
53 atoms, 54 bonds, 4 residues, 1 model selected
> select /A:441
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:441-450
157 atoms, 158 bonds, 2 pseudobonds, 10 residues, 2 models selected
> color (#!1 & sel) red
> select /A:451
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:451-460
135 atoms, 134 bonds, 4 pseudobonds, 10 residues, 2 models selected
> select /A:451
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:451-457
80 atoms, 79 bonds, 7 residues, 1 model selected
> color sel red
> select /A:323
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:323-331
127 atoms, 128 bonds, 9 residues, 1 model selected
> color sel red
> select /A:332-333
39 atoms, 39 bonds, 2 residues, 1 model selected
> select /A:332-343
225 atoms, 226 bonds, 1 pseudobond, 12 residues, 2 models selected
> color (#!1 & sel) purple
> color (#!1 & sel) blue
> select /A:440
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:434-440
104 atoms, 104 bonds, 7 residues, 1 model selected
> color sel blue
> select clear
> select /A:330
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:323-330
120 atoms, 121 bonds, 8 residues, 1 model selected
> select /A:323
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:323-327
86 atoms, 86 bonds, 5 residues, 1 model selected
> select /A:322
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:322-324
43 atoms, 42 bonds, 3 residues, 1 model selected
> select /A:324-325
26 atoms, 25 bonds, 2 residues, 1 model selected
> select /A:322-325
55 atoms, 54 bonds, 4 residues, 1 model selected
> color sel forest green
> select /A:458
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:458-466
136 atoms, 137 bonds, 2 pseudobonds, 9 residues, 2 models selected
> select /A:458
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:458-463
90 atoms, 89 bonds, 2 pseudobonds, 6 residues, 2 models selected
> color (#!1 & sel) forest green
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> ui windowfill toggle
[Repeated 4 time(s)]
> view sel
[Repeated 1 time(s)]
> save /Users/michaelmatthias/R01.PAR.22.241/preChop2.cxs
——— End of log from Sat Apr 15 11:43:38 2023 ———
opened ChimeraX session
> ui tool show "Color Actions"
> lighting soft
> graphics silhouettes true
> lighting full
> graphics silhouettes false
> view sel
Must select at least one chain from each list
> toolshed show
Downloading bundle ChimeraX_StarMap-1.1.75-py3-none-any.whl
ERROR:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 87, in _run_code
exec(code, run_globals)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/__main__.py", line 1035, in <module>
exit_code = init(sys.argv)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/__main__.py", line 796, in init
runpy.run_module(opts.module, init_globals=global_dict,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 206, in run_module
mod_name, mod_spec, code = _get_module_details(mod_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 141, in _get_module_details
raise error("No module named %s" % mod_name)
ImportError: No module named pip
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
AttributeError: 'PasswordDialog' object has no attribute 'exec_'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 289, in authorize
p.exec_()
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14X000GDLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 50 days, 22 hours, 52 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.1.70
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
pyqtgraph: 0.13.1
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
Send2Trash: 1.8.0
SEQCROW: 1.5.10
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (1)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Install StarMap from toolshed: ImportError: No module named pip |
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