The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
I am trying to mutate a threonine (Thr) to a phosphorylated threonine (TPO):
Using Dunbrack library EBP1_rank_1.pdb #14/A THR 46: phi -164.3, psi 140.7 trans Traceback (most recent call last): File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/cmd.py", line 40, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params return self._get_params(res_name, file_name, cache, archive) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params "%s library does not support residue type '%s'" % (self.display_name, base_name)) AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params "%s library does not support residue type '%s'" % (self.display_name, base_name))
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB1763-4-15/Refine_20/FB1763-4-15_refine_020.pdb
Chain information for FB1763-4-15_refine_020.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB2623-1-39/Refine_28/FB2623-1-39_refine_028.pdb
Chain information for FB2623-1-39_refine_028.pdb #2
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB1763-4-15/Refine_20/FB1763-4-15_refine_020.pdb
> format pdb
Chain information for FB1763-4-15_refine_020.pdb #3
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB1201-4-38/Refine_17/FB1201-4-38_refine_017.pdb
Chain information for FB1201-4-38_refine_017.pdb #4
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB7412-4-10/Refine_38/FB7412-4-10_refine_038.pdb
Chain information for FB7412-4-10_refine_038.pdb #5
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB3775-1-22/Refine_18/FB3775-1-22_refine_018.pdb
Chain information for FB3775-1-22_refine_018.pdb #6
---
Chain | Description
A | No description available
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec222024/Processed_data/FB6476-E3/Refine_21/FB6476-E3_refine_021.pdb
Chain information for FB6476-E3_refine_021.pdb #7
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!2-7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FB1763-4-15_refine_020.pdb, chain B (#1) with
FB2623-1-39_refine_028.pdb, chain B (#2), sequence alignment score = 1633.1
RMSD between 316 pruned atom pairs is 0.703 angstroms; (across all 335 pairs:
0.953)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB1763-4-15_refine_020.pdb, chain A (#3), sequence alignment score = 1733.2
RMSD between 336 pruned atom pairs is 0.000 angstroms; (across all 336 pairs:
0.000)
Matchmaker FB1763-4-15_refine_020.pdb, chain B (#1) with
FB1201-4-38_refine_017.pdb, chain A (#4), sequence alignment score = 1682.1
RMSD between 323 pruned atom pairs is 0.994 angstroms; (across all 334 pairs:
1.106)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB7412-4-10_refine_038.pdb, chain B (#5), sequence alignment score = 1667.5
RMSD between 312 pruned atom pairs is 0.552 angstroms; (across all 336 pairs:
1.171)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB3775-1-22_refine_018.pdb, chain A (#6), sequence alignment score = 1593.5
RMSD between 326 pruned atom pairs is 0.715 angstroms; (across all 335 pairs:
0.875)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB6476-E3_refine_021.pdb, chain A (#7), sequence alignment score = 1625.5
RMSD between 328 pruned atom pairs is 0.703 angstroms; (across all 336 pairs:
0.841)
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> select #5/A
2392 atoms, 2433 bonds, 2 pseudobonds, 320 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select #1/A
2552 atoms, 2597 bonds, 1 pseudobond, 337 residues, 2 models selected
> select #1/B
2495 atoms, 2539 bonds, 1 pseudobond, 336 residues, 2 models selected
> close #3
> close #5
> open
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB7412-4-10/Refine_38/FB7412-4-10_refine_038.pdb
Chain information for FB7412-4-10_refine_038.pdb #3
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB7412-4-10_refine_038.pdb, chain B (#3), sequence alignment score = 1667.5
RMSD between 312 pruned atom pairs is 0.552 angstroms; (across all 336 pairs:
1.171)
> select clear
> select #3/A
2392 atoms, 2433 bonds, 2 pseudobonds, 320 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #1/B:233
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
56 atoms, 55 bonds, 8 residues, 1 model selected
> select up
2113 atoms, 2151 bonds, 287 residues, 1 model selected
> select up
2186 atoms, 2225 bonds, 297 residues, 1 model selected
> select up
2481 atoms, 2524 bonds, 335 residues, 1 model selected
> select up
2495 atoms, 2539 bonds, 336 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> hide #!3 models
> select #2/B:201
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
65 atoms, 64 bonds, 8 residues, 1 model selected
> select up
2079 atoms, 2117 bonds, 288 residues, 1 model selected
> select up
2147 atoms, 2186 bonds, 298 residues, 1 model selected
> select up
2421 atoms, 2464 bonds, 336 residues, 1 model selected
> select up
2435 atoms, 2479 bonds, 337 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/C:10@O1
6 atoms, 4 bonds, 2 residues, 2 models selected
> select up
10 atoms, 8 bonds, 2 residues, 2 models selected
> select up
12 atoms, 9 bonds, 3 residues, 2 models selected
> select up
15 atoms, 12 bonds, 3 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select #1/C:3@O2
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/C:8@O4
6 atoms, 4 bonds, 2 residues, 1 model selected
> select up
10 atoms, 8 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!2 models
> show #!4 models
> select #4/B:260
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 3 residues, 1 model selected
> select up
2186 atoms, 2226 bonds, 288 residues, 1 model selected
> select up
2350 atoms, 2393 bonds, 309 residues, 1 model selected
> select up
2572 atoms, 2617 bonds, 336 residues, 1 model selected
> select up
5220 atoms, 5297 bonds, 685 residues, 1 model selected
> select down
2572 atoms, 2617 bonds, 336 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!6 models
> hide #!4 models
> show #!7 models
> show #!4 models
> show #!3 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!2-4,6-7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB2623-1-39_refine_028.pdb, chain A (#2), sequence alignment score = 1512.5
RMSD between 312 pruned atom pairs is 0.622 angstroms; (across all 321 pairs:
3.470)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB7412-4-10_refine_038.pdb, chain B (#3), sequence alignment score = 1667.5
RMSD between 312 pruned atom pairs is 0.552 angstroms; (across all 336 pairs:
1.171)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB1201-4-38_refine_017.pdb, chain A (#4), sequence alignment score = 1675.7
RMSD between 314 pruned atom pairs is 0.867 angstroms; (across all 335 pairs:
1.144)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB3775-1-22_refine_018.pdb, chain A (#6), sequence alignment score = 1593.5
RMSD between 326 pruned atom pairs is 0.715 angstroms; (across all 335 pairs:
0.875)
Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with
FB6476-E3_refine_021.pdb, chain A (#7), sequence alignment score = 1625.5
RMSD between 328 pruned atom pairs is 0.703 angstroms; (across all 336 pairs:
0.841)
> select #3/C:2@O2
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Color Actions"
> set bgColor white
> select ::name="SO4"
70 atoms, 56 bonds, 14 residues, 6 models selected
> hide sel atoms
> select ::name="HOH"
48 atoms, 48 residues, 6 models selected
> hide sel atoms
> select
15303 atoms, 15497 bonds, 8 pseudobonds, 2067 residues, 12 models selected
> hide sel atoms
> select clear
> select ::name="V12"
15 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="V17"
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="V26"
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="V37"
18 atoms, 19 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="V64"
13 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="V74"
15 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #7/A:83
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 4 residues, 1 model selected
> select up
2164 atoms, 2201 bonds, 288 residues, 1 model selected
> select up
2244 atoms, 2282 bonds, 298 residues, 1 model selected
> select up
2548 atoms, 2590 bonds, 336 residues, 1 model selected
> select up
2561 atoms, 2603 bonds, 337 residues, 1 model selected
> select down
2548 atoms, 2590 bonds, 336 residues, 1 model selected
> select up
2561 atoms, 2603 bonds, 337 residues, 1 model selected
> show sel surfaces
> mlp sel
Map values for surface "FB6476-E3_refine_021.pdb_A SES surface": minimum
-28.6, mean -4.513, maximum 23.45
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select #1/A:44
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 12 residues, 1 model selected
> select up
2164 atoms, 2203 bonds, 288 residues, 1 model selected
> select up
2244 atoms, 2284 bonds, 298 residues, 1 model selected
> select up
2538 atoms, 2582 bonds, 336 residues, 1 model selected
> hide sel cartoons
> select #2/A:43
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 2 residues, 1 model selected
> select up
2029 atoms, 2067 bonds, 275 residues, 1 model selected
> select up
2152 atoms, 2188 bonds, 294 residues, 1 model selected
> select up
2360 atoms, 2398 bonds, 321 residues, 1 model selected
> hide sel cartoons
> select #3/B:244
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
54 atoms, 54 bonds, 7 residues, 1 model selected
> select up
2203 atoms, 2242 bonds, 288 residues, 1 model selected
> select up
2342 atoms, 2382 bonds, 309 residues, 1 model selected
> select up
2564 atoms, 2606 bonds, 336 residues, 1 model selected
> hide sel cartoons
> select #7/A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide surfaces
> select #7/A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 2 models selected
> select up
2164 atoms, 2201 bonds, 288 residues, 2 models selected
> select up
2244 atoms, 2282 bonds, 298 residues, 2 models selected
> select up
2548 atoms, 2590 bonds, 336 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> hide surfaces
> select #4/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
44 atoms, 44 bonds, 6 residues, 1 model selected
> select up
2211 atoms, 2250 bonds, 287 residues, 1 model selected
> select up
2291 atoms, 2331 bonds, 297 residues, 1 model selected
> select up
2604 atoms, 2648 bonds, 335 residues, 1 model selected
> show sel surfaces
> select clear
> mlp
Map values for surface "FB3775-1-22_refine_018.pdb_A SES surface": minimum
-27.32, mean -3.845, maximum 21.48
Map values for surface "FB1201-4-38_refine_017.pdb_A SES surface": minimum
-28.13, mean -4.243, maximum 22.28
Map values for surface "FB2623-1-39_refine_028.pdb_A SES surface": minimum
-26.88, mean -4.383, maximum 23.05
Map values for surface "FB1763-4-15_refine_020.pdb_A SES surface": minimum
-25.7, mean -3.937, maximum 21.78
Map values for surface "FB6476-E3_refine_021.pdb_A SES surface": minimum
-28.6, mean -4.513, maximum 23.45
Map values for surface "FB7412-4-10_refine_038.pdb_B SES surface": minimum
-26.12, mean -4.304, maximum 24.01
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> hide surfaces
> select #4/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
2211 atoms, 2250 bonds, 287 residues, 2 models selected
> select up
2291 atoms, 2331 bonds, 297 residues, 2 models selected
> select up
2604 atoms, 2648 bonds, 335 residues, 2 models selected
> show sel surfaces
> select clear
> save
> /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB7412-4-10/Refine_38/FEM1BOverlay.cxs
> close session
> open "/Users/katinaj/Downloads/7uhy (1).pdb" format pdb
7uhy (1).pdb title:
Human GATOR2 complex [more info...]
Chain information for 7uhy (1).pdb #1
---
Chain | Description | UniProt
A B | missing oocyte meiosis regulator homolog | MIO_HUMAN 1-875
C | WD repeat-containing protein 24 | WDR24_HUMAN 1-790
D | WD repeat-containing protein 59 | WDR59_HUMAN 1-974
E F G | isoform B of nucleoporin SEH1 | SEH1_HUMAN 1-421
H | protein SEC13 homolog | SEC13_HUMAN 1-322
I | unknown |
J | unknown |
Non-standard residues in 7uhy (1).pdb #1
---
ZN — zinc ion
> close session
> open "/Users/katinaj/Downloads/7pe8 (1).pdb"
7pe8 (1).pdb title:
Cryo-em structure of deptor bound to human mtor complex 2, focussed on one
protomer [more info...]
Chain information for 7pe8 (1).pdb #1
---
Chain | Description | UniProt
A | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-2549
C | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326
E | rapamycin-insensitive companion of mtor | RICTR_HUMAN 1-1708
G | target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522
I | DEP domain-containing protein 6 | DPTOR_HUMAN 1-409
Non-standard residues in 7pe8 (1).pdb #1
---
ACE — acetyl group
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
ZN — zinc ion
> hide cartoons
> show atoms
> select
29291 atoms, 29830 bonds, 31 pseudobonds, 3835 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
Drag select of 22 residues
> close session
> open /Users/katinaj/Downloads/4drh.pdb
4drh.pdb title:
Co-crystal structure of the ppiase domain of FKBP51, rapamycin and the FRB
fragment of mtor At low pH [more info...]
Chain information for 4drh.pdb #1
---
Chain | Description | UniProt
A D | peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 1-140
B E | serine/threonine-protein kinase mtor | MTOR_HUMAN 2025-2114
Non-standard residues in 4drh.pdb #1
---
RAP — rapamycin immunosuppressant drug
SO4 — sulfate ion
> select /D
1099 atoms, 1097 bonds, 157 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /E
758 atoms, 763 bonds, 1 pseudobond, 103 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select
1964 atoms, 1937 bonds, 299 residues, 1 model selected
> hide sel atoms
> select clear
> select ::name="RAP"
65 atoms, 68 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel lime
> color sel byhetero
> select clear
> open
> /Users/katinaj/Documents/Vanderbilt/Longevity/FRB/xraydata/FRBVU4592_xtalstructure/FRB4592_01_refine_8.pdb
Chain information for FRB4592_01_refine_8.pdb #2
---
Chain | Description
B | No description available
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4drh.pdb, chain B (#1) with FRB4592_01_refine_8.pdb, chain B (#2),
sequence alignment score = 480.5
RMSD between 88 pruned atom pairs is 0.783 angstroms; (across all 92 pairs:
2.086)
> hide #!1 models
> show #!1 models
> hide #2 models
> hide #!1 models
> show #2 models
> show #!1 models
> hide #!1 models
> select #2/B:2037
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
199 atoms, 206 bonds, 19 residues, 1 model selected
> select up
947 atoms, 969 bonds, 92 residues, 1 model selected
> show sel surfaces
> mlp sel
Map values for surface "FRB4592_01_refine_8.pdb_B SES surface": minimum
-24.26, mean -3.975, maximum 21.45
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> transparency #2 70
> select clear
> transparency #2 30
> select clear
> close session
> open
> /Users/katinaj/Documents/Vanderbilt/Longevity/FRB/xraydata/FRBVU4592_xtalstructure/FRB4592_01_refine_8.pdb
> format pdb
Chain information for FRB4592_01_refine_8.pdb #1
---
Chain | Description
B | No description available
> open
> /Users/katinaj/Documents/Vanderbilt/Longevity/FRB/xraydata/FRBVU4592_xtalstructure/FRB4592_01_refine_8.pdb
> format pdb
Chain information for FRB4592_01_refine_8.pdb #2
---
Chain | Description
B | No description available
> ui tool show "Color Actions"
> set bgColor white
> select #1/B:2031
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
199 atoms, 206 bonds, 19 residues, 1 model selected
> select up
947 atoms, 969 bonds, 92 residues, 1 model selected
> mlp sel
Map values for surface "FRB4592_01_refine_8.pdb_B SES surface": minimum
-24.87, mean -3.982, maximum 21.39
To also show corresponding color key, enter the above mlp command and add key
true
> select #1/A:2@NA
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 3 residues, 1 model selected
> hide sel atoms
> select #2/A:2@NA
1 atom, 1 residue, 1 model selected
> select add #2/A:3@NA
2 atoms, 2 residues, 1 model selected
> select add #2/A:1@NA
3 atoms, 3 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 1 residue, 1 model selected
> show sel surfaces
> color sel byhetero
Drag select of 2 residues
> select up
298 atoms, 306 bonds, 28 residues, 3 models selected
> select up
1894 atoms, 1938 bonds, 184 residues, 3 models selected
> hide sel surfaces
> show sel surfaces
> transparency (#!1-2 & sel) 60
> select clear
> select #1/B:2201@C10
1 atom, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 1 residue, 2 models selected
> color (#!1 & sel) gray
> color sel byhetero
> select clear
> select #1/B:2040@O
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
199 atoms, 206 bonds, 19 residues, 2 models selected
> select up
947 atoms, 969 bonds, 92 residues, 2 models selected
> select down
199 atoms, 206 bonds, 19 residues, 2 models selected
> select up
947 atoms, 969 bonds, 92 residues, 2 models selected
> mlp sel
Map values for surface "FRB4592_01_refine_8.pdb_B SES surface": minimum
-24.87, mean -3.982, maximum 21.39
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select #2/B:2033@O
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 2 models selected
> select up
199 atoms, 206 bonds, 19 residues, 2 models selected
> select up
947 atoms, 969 bonds, 92 residues, 2 models selected
> close #2
> select /B:2111
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
46 atoms, 46 bonds, 3 residues, 2 models selected
> select up
947 atoms, 969 bonds, 92 residues, 2 models selected
> show sel surfaces
> select clear
> select /B:2201@C10
1 atom, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 1 residue, 2 models selected
> color sel byhetero
> color sel bychain
> color sel bypolymer
> color sel bychain
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue VU9 (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/77/52vr4r5963q7wss_q3pgqvdm0000gp/T/tmp855l3krm/ante.in.mol2 -fi
mol2 -o
/var/folders/77/52vr4r5963q7wss_q3pgqvdm0000gp/T/tmp855l3krm/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(VU9) ``
(VU9) `Welcome to antechamber 20.0: molecular input file processor.`
(VU9) ``
(VU9) `Info: Finished reading file
(/var/folders/77/52vr4r5963q7wss_q3pgqvdm0000gp/T/tmp855l3krm/ante.in.mol2);
atoms read (30), bonds read (32).`
(VU9) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(VU9) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(VU9) ``
(VU9) ``
(VU9) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(VU9) `Info: Total number of electrons: 126; net charge: 0`
(VU9) ``
(VU9) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(VU9) ``
(VU9) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(VU9) ``
(VU9) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(VU9) ``
Charges for residue VU9 determined
Coulombic values for FRB4592_01_refine_8.pdb_B SES surface #1.2: minimum,
-2.65, mean -0.07, maximum 3.08
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select /B:2201@C04
1 atom, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 1 residue, 2 models selected
> color (#!1 & sel) dark gray
> select /B:2110@NE
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 2 models selected
> select up
46 atoms, 46 bonds, 3 residues, 2 models selected
> select up
947 atoms, 969 bonds, 92 residues, 2 models selected
> hide sel surfaces
> color (#!1 & sel) dim gray
> color sel byhetero
> select /B:2201@C11
1 atom, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 1 residue, 2 models selected
> hide sel surfaces
> color (#!1 & sel) cyan
> select sel :< 5
146 atoms, 144 bonds, 14 residues, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select /A:2@NA
1 atom, 1 residue, 1 model selected
> select add /A:3@NA
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select /B:2107
13 atoms, 13 bonds, 1 residue, 1 model selected
> select up
149 atoms, 153 bonds, 14 residues, 2 models selected
> select up
947 atoms, 969 bonds, 92 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "FRB4592_01_refine_8.pdb_B SES surface": minimum
-24.87, mean -3.982, maximum 21.39
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 1 residue, 2 models selected
> color (#!1 & sel) magenta
> select clear
> transparency 60
> transparency 40
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
30 atoms, 32 bonds, 1 residue, 2 models selected
> show sel surfaces
> transparency (#!1 & sel) 0
> select clear
> select /B:2037@CB
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 2 models selected
> select up
199 atoms, 206 bonds, 19 residues, 2 models selected
> select up
947 atoms, 969 bonds, 92 residues, 2 models selected
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 30
> select clear
[Repeated 1 time(s)]
> close session
> open /Users/katinaj/Downloads/7pea.pdb /Users/katinaj/Downloads/5wbj.pdb
7pea.pdb title:
Cryo-em structure of deptor bound to human mtor complex 1, overall refinement
[more info...]
Chain information for 7pea.pdb #1
---
Chain | Description | UniProt
A B | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-16 31-36 54-355
381-2549
C D | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326
E F | regulatory-associated protein of mtor | RPTOR_HUMAN 1-1335
I J | DEP domain-containing protein 6 | DPTOR_HUMAN 1-409
Non-standard residues in 7pea.pdb #1
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
5wbj.pdb title:
Crystal structure of the arabidopsis thaliana raptor In complex with the tos
peptide of human 4EBP1 [more info...]
Chain information for 5wbj.pdb #2
---
Chain | Description | UniProt
A | regulatory-associated protein of tor 1 | RTOR1_ARATH 1-942 943-1344
T | eukaryotic translation initiation factor 4E-binding protein 1 |
4EBP1_HUMAN 99-118
> select
66631 atoms, 68063 bonds, 56 pseudobonds, 8402 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> select clear
> open "/Users/katinaj/Downloads/3fap (2).pdb"
3fap (2).pdb title:
Atomic structures of the rapamycin analogs In complex with both human FKBP12
and FRB domain of frap [more info...]
Chain information for 3fap (2).pdb #3
---
Chain | Description | UniProt
A | FKBP12 | FKB1A_HUMAN 1-107
B | FRAP | FRAP_HUMAN 108-201
Non-standard residues in 3fap (2).pdb #3
---
ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug)
> ui tool show Matchmaker
> matchmaker #3#!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain A (#1) with 3fap (2).pdb, chain B (#3), sequence
alignment score = 505
RMSD between 92 pruned atom pairs is 0.742 angstroms; (across all 94 pairs:
1.152)
Matchmaker 7pea.pdb, chain E (#1) with 5wbj.pdb, chain A (#2), sequence
alignment score = 2894.7
RMSD between 591 pruned atom pairs is 1.038 angstroms; (across all 1013 pairs:
3.563)
> select #1/C:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
53 atoms, 54 bonds, 6 residues, 1 model selected
> select up
2456 atoms, 2514 bonds, 317 residues, 1 model selected
> hide sel cartoons
> select #1/A:2183
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
63 atoms, 64 bonds, 7 residues, 1 model selected
> select up
4623 atoms, 4724 bonds, 570 residues, 1 model selected
> select down
63 atoms, 64 bonds, 7 residues, 1 model selected
> select #1/I
795 atoms, 811 bonds, 106 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/J
795 atoms, 811 bonds, 106 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/T
68 atoms, 68 bonds, 8 residues, 1 model selected
> select #1/E
8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected
> select #1/F
8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/E
8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected
> select #2/A
8311 atoms, 8503 bonds, 6 pseudobonds, 1058 residues, 2 models selected
> select #1/A
17490 atoms, 17836 bonds, 20 pseudobonds, 2193 residues, 2 models selected
> select #1/B
17490 atoms, 17836 bonds, 20 pseudobonds, 2193 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/D:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
39 atoms, 39 bonds, 5 residues, 1 model selected
> select up
2456 atoms, 2514 bonds, 317 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/C
2456 atoms, 2514 bonds, 317 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> matchmaker #2/A to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain E (#1) with 5wbj.pdb, chain A (#2), sequence
alignment score = 2894.7
RMSD between 591 pruned atom pairs is 1.038 angstroms; (across all 1013 pairs:
3.563)
> select #2/T
68 atoms, 68 bonds, 8 residues, 1 model selected
> color sel orange
> select clear
> ui tool show "Color Actions"
> set bgColor white
> hide #3 models
> select add #1/A:2020
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
147 atoms, 146 bonds, 19 residues, 1 model selected
> select add #1/A:2161
156 atoms, 154 bonds, 20 residues, 1 model selected
> select up
170 atoms, 168 bonds, 22 residues, 1 model selected
> select add #1/A:2131
178 atoms, 175 bonds, 23 residues, 1 model selected
> select up
222 atoms, 220 bonds, 29 residues, 1 model selected
> select add #1/A:2155
228 atoms, 225 bonds, 30 residues, 1 model selected
> select up
253 atoms, 250 bonds, 33 residues, 1 model selected
> select add #1/A:2174
261 atoms, 257 bonds, 34 residues, 1 model selected
> select up
280 atoms, 276 bonds, 37 residues, 1 model selected
> select add #1/A:2182
291 atoms, 287 bonds, 38 residues, 1 model selected
> select up
343 atoms, 340 bonds, 44 residues, 1 model selected
> select #1/A:2179
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 4 residues, 1 model selected
> select add #1/A:2159
34 atoms, 33 bonds, 5 residues, 1 model selected
> select up
51 atoms, 50 bonds, 7 residues, 1 model selected
> select add #1/A:2155
57 atoms, 55 bonds, 8 residues, 1 model selected
> select up
82 atoms, 80 bonds, 11 residues, 1 model selected
> select add #1/A:2158
89 atoms, 87 bonds, 12 residues, 1 model selected
> select up
94 atoms, 94 bonds, 13 residues, 1 model selected
> select add #1/A:2174
102 atoms, 101 bonds, 14 residues, 1 model selected
> select up
121 atoms, 121 bonds, 17 residues, 1 model selected
> select add #1/A:2171
130 atoms, 129 bonds, 18 residues, 1 model selected
> select up
213 atoms, 215 bonds, 28 residues, 1 model selected
> select add #1/A:2184
224 atoms, 226 bonds, 29 residues, 1 model selected
> select up
276 atoms, 280 bonds, 35 residues, 1 model selected
> select add #1/A:2134
287 atoms, 290 bonds, 36 residues, 1 model selected
> select up
428 atoms, 436 bonds, 54 residues, 1 model selected
> select add #1/A:2189
438 atoms, 446 bonds, 55 residues, 1 model selected
> select up
459 atoms, 468 bonds, 58 residues, 1 model selected
> select add #1/A:2232
466 atoms, 474 bonds, 59 residues, 1 model selected
> select up
494 atoms, 502 bonds, 63 residues, 1 model selected
> select add #1/A:2237
502 atoms, 509 bonds, 64 residues, 1 model selected
> select up
518 atoms, 526 bonds, 67 residues, 1 model selected
> select add #1/A:1983
525 atoms, 532 bonds, 68 residues, 1 model selected
> select up
531 atoms, 538 bonds, 69 residues, 1 model selected
> select add #1/A:1987
542 atoms, 548 bonds, 70 residues, 1 model selected
> select up
678 atoms, 687 bonds, 88 residues, 1 model selected
> select add #1/A:1980
684 atoms, 692 bonds, 89 residues, 1 model selected
> select up
755 atoms, 766 bonds, 98 residues, 1 model selected
> hide sel cartoons
> select #1/A:2090
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
158 atoms, 161 bonds, 18 residues, 1 model selected
> select up
4623 atoms, 4724 bonds, 570 residues, 1 model selected
> select down
158 atoms, 161 bonds, 18 residues, 1 model selected
> select add #1/A:2071
166 atoms, 168 bonds, 19 residues, 1 model selected
> select up
237 atoms, 241 bonds, 28 residues, 1 model selected
> select add #1/A:2060
248 atoms, 251 bonds, 29 residues, 1 model selected
> select up
268 atoms, 273 bonds, 32 residues, 1 model selected
> select add #1/A:2056
273 atoms, 277 bonds, 33 residues, 1 model selected
> select up
403 atoms, 411 bonds, 49 residues, 1 model selected
> select add #1/A:2107
410 atoms, 417 bonds, 50 residues, 1 model selected
> select up
608 atoms, 621 bonds, 72 residues, 1 model selected
> select add #1/A:2026
616 atoms, 628 bonds, 73 residues, 1 model selected
> select up
773 atoms, 793 bonds, 90 residues, 1 model selected
> select add #1/A:2116
780 atoms, 800 bonds, 91 residues, 1 model selected
> select up
797 atoms, 818 bonds, 93 residues, 1 model selected
> select add #1/A:2119
804 atoms, 824 bonds, 94 residues, 1 model selected
> select up
4623 atoms, 4724 bonds, 570 residues, 1 model selected
> select down
804 atoms, 824 bonds, 94 residues, 1 model selected
> select add #1/A:2131
812 atoms, 831 bonds, 95 residues, 1 model selected
> select up
856 atoms, 877 bonds, 101 residues, 1 model selected
> select add #1/A:2019
863 atoms, 883 bonds, 102 residues, 1 model selected
> select up
1003 atoms, 1024 bonds, 120 residues, 1 model selected
> color sel forest green
> select #1/A:2124
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
36 atoms, 36 bonds, 4 residues, 1 model selected
> color sel forest green
> select #1/A:2120
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> color sel forest green
> hide #!1 models
> show #!1 models
> hide #!2 models
> open /Users/katinaj/Downloads/7pea.pdb
7pea.pdb title:
Cryo-em structure of deptor bound to human mtor complex 1, overall refinement
[more info...]
Chain information for 7pea.pdb #4
---
Chain | Description | UniProt
A B | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-16 31-36 54-355
381-2549
C D | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326
E F | regulatory-associated protein of mtor | RPTOR_HUMAN 1-1335
I J | DEP domain-containing protein 6 | DPTOR_HUMAN 1-409
Non-standard residues in 7pea.pdb #4
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
> hide sel atoms
> select
94396 atoms, 96226 bonds, 81 pseudobonds, 12042 residues, 7 models selected
> hide sel & #!1,4 atoms
> show sel & #!1,4 cartoons
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain A (#1) with 7pea.pdb, chain A (#4), sequence
alignment score = 12654.3
RMSD between 2192 pruned atom pairs is 0.000 angstroms; (across all 2192
pairs: 0.000)
> select clear
> select #4/B:461
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
106 atoms, 107 bonds, 13 residues, 1 model selected
> select up
453 atoms, 460 bonds, 57 residues, 1 model selected
> select up
467 atoms, 473 bonds, 59 residues, 1 model selected
> select up
708 atoms, 717 bonds, 90 residues, 1 model selected
> select up
728 atoms, 736 bonds, 94 residues, 1 model selected
> select up
833 atoms, 841 bonds, 115 residues, 1 model selected
> select up
939 atoms, 951 bonds, 129 residues, 1 model selected
> select up
17490 atoms, 17836 bonds, 2193 residues, 1 model selected
> select up
58252 atoms, 59492 bonds, 7336 residues, 1 model selected
> select down
17490 atoms, 17836 bonds, 2193 residues, 1 model selected
> select down
939 atoms, 951 bonds, 129 residues, 1 model selected
> select up
17490 atoms, 17836 bonds, 2193 residues, 1 model selected
> select up
58252 atoms, 59492 bonds, 7336 residues, 1 model selected
> select down
17490 atoms, 17836 bonds, 2193 residues, 1 model selected
> ui tool show "Color Actions"
> color sel olive drab target acs
> select #1/A:64
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
130 atoms, 134 bonds, 14 residues, 1 model selected
> select up
135 atoms, 139 bonds, 15 residues, 1 model selected
> select up
17490 atoms, 17836 bonds, 2193 residues, 1 model selected
> color sel olive drab target acs
> select clear
> select #1/A:1286
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
176 atoms, 179 bonds, 20 residues, 1 model selected
> select add #1/A:1325
182 atoms, 184 bonds, 21 residues, 1 model selected
> select up
280 atoms, 286 bonds, 33 residues, 1 model selected
> select add #1/A:1264
288 atoms, 293 bonds, 34 residues, 1 model selected
> select up
345 atoms, 352 bonds, 41 residues, 1 model selected
> select add #1/A:1273
356 atoms, 362 bonds, 42 residues, 1 model selected
> select up
384 atoms, 392 bonds, 46 residues, 1 model selected
> color sel forest green target acs
[Repeated 1 time(s)]
> select add #1/A:1336
393 atoms, 400 bonds, 47 residues, 1 model selected
> select up
520 atoms, 527 bonds, 63 residues, 1 model selected
> select add #1/A:1330
528 atoms, 534 bonds, 64 residues, 1 model selected
> select add #1/A:1386
539 atoms, 544 bonds, 65 residues, 1 model selected
> select up
600 atoms, 607 bonds, 74 residues, 1 model selected
> select add #1/A:1349
608 atoms, 614 bonds, 75 residues, 1 model selected
> select up
617 atoms, 624 bonds, 76 residues, 1 model selected
> select add #1/A:1352
626 atoms, 632 bonds, 77 residues, 1 model selected
> select up
759 atoms, 768 bonds, 94 residues, 1 model selected
> color sel forest green target acs
> select add #1/A:1296
765 atoms, 773 bonds, 95 residues, 1 model selected
> select up
4498 atoms, 4603 bonds, 554 residues, 1 model selected
> color sel forest green target acs
> select #1/A:1638
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
112 atoms, 113 bonds, 13 residues, 1 model selected
> select add #1/A:1647
122 atoms, 123 bonds, 14 residues, 1 model selected
> select up
144 atoms, 146 bonds, 17 residues, 1 model selected
> select clear
> select #1/A:2263
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
94 atoms, 94 bonds, 11 residues, 1 model selected
> select add #1/A:2256
103 atoms, 102 bonds, 12 residues, 1 model selected
> select up
202 atoms, 203 bonds, 23 residues, 1 model selected
> select add #1/A:2305
210 atoms, 210 bonds, 24 residues, 1 model selected
> select up
293 atoms, 295 bonds, 34 residues, 1 model selected
> color sel forest green target acs
> select #1/A:970
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
135 atoms, 138 bonds, 17 residues, 1 model selected
> select add #1/A:955
143 atoms, 145 bonds, 18 residues, 1 model selected
> select up
292 atoms, 299 bonds, 36 residues, 1 model selected
> select add #1/A:961
300 atoms, 306 bonds, 37 residues, 1 model selected
> select up
2339 atoms, 2391 bonds, 290 residues, 1 model selected
> color sel magenta target acs
> select clear
> select #1/A:2113
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
205 atoms, 210 bonds, 23 residues, 1 model selected
> select #1/A:2028
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
165 atoms, 172 bonds, 18 residues, 1 model selected
> select add #1/A:2113
174 atoms, 180 bonds, 19 residues, 1 model selected
> select up
370 atoms, 382 bonds, 41 residues, 1 model selected
> select add #1/A:2077
378 atoms, 389 bonds, 42 residues, 1 model selected
> select up
528 atoms, 543 bonds, 59 residues, 1 model selected
> select add #1/A:2069
534 atoms, 548 bonds, 60 residues, 1 model selected
> select up
607 atoms, 623 bonds, 69 residues, 1 model selected
> select add #1/A:2051
615 atoms, 630 bonds, 70 residues, 1 model selected
> select up
742 atoms, 760 bonds, 86 residues, 1 model selected
> select add #1/A:2040
746 atoms, 763 bonds, 87 residues, 1 model selected
> select up
766 atoms, 785 bonds, 89 residues, 1 model selected
> color sel cornflower blue target acs
> select #1/A:2117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> color sel cornflower blue target acs
> select #1/E:193
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
52 atoms, 53 bonds, 6 residues, 1 model selected
> select up
1633 atoms, 1672 bonds, 202 residues, 1 model selected
> color sel thistle target acs
> color sel lavender target acs
> select #1/E:324
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
176 atoms, 181 bonds, 22 residues, 1 model selected
> select up
3568 atoms, 3656 bonds, 451 residues, 1 model selected
> select up
3574 atoms, 3661 bonds, 452 residues, 1 model selected
> select up
3849 atoms, 3944 bonds, 486 residues, 1 model selected
> color sel lavender target acs
> select #1/E:1096
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
54 atoms, 55 bonds, 6 residues, 1 model selected
> select up
1375 atoms, 1411 bonds, 167 residues, 1 model selected
> color sel lavender target acs
> select #1/E:1237
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
45 atoms, 45 bonds, 5 residues, 1 model selected
> select clear
> select #4/B:1012
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
153 atoms, 155 bonds, 19 residues, 1 model selected
> select up
2339 atoms, 2391 bonds, 290 residues, 1 model selected
> color sel magenta target acs
> select #4/B:1284
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
176 atoms, 179 bonds, 20 residues, 1 model selected
> select up
4498 atoms, 4603 bonds, 554 residues, 1 model selected
> color sel forest green target acs
> select #4/B:2270
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
94 atoms, 94 bonds, 11 residues, 1 model selected
> select up
4623 atoms, 4724 bonds, 570 residues, 1 model selected
> select up
4646 atoms, 4745 bonds, 573 residues, 1 model selected
> color sel pale green target acs
> select up
9594 atoms, 9810 bonds, 1182 residues, 1 model selected
> select down
4646 atoms, 4745 bonds, 573 residues, 1 model selected
> color sel dark sea green target acs
> select #1/A:1986
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
147 atoms, 148 bonds, 19 residues, 1 model selected
> select up
4623 atoms, 4724 bonds, 570 residues, 1 model selected
> color sel dark sea green target acs
> select clear
> select #1/A:2117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
4623 atoms, 4724 bonds, 570 residues, 1 model selected
> select down
24 atoms, 24 bonds, 3 residues, 1 model selected
> select add #1/A:2115
32 atoms, 31 bonds, 4 residues, 1 model selected
> select up
229 atoms, 235 bonds, 26 residues, 1 model selected
> select add #1/A:2074
241 atoms, 247 bonds, 27 residues, 1 model selected
> select up
387 atoms, 396 bonds, 44 residues, 1 model selected
> select add #1/A:2073
392 atoms, 400 bonds, 45 residues, 1 model selected
> select up
466 atoms, 476 bonds, 54 residues, 1 model selected
> select add #1/A:2024
476 atoms, 486 bonds, 55 residues, 1 model selected
> select up
631 atoms, 648 bonds, 72 residues, 1 model selected
> select add #1/A:2054
639 atoms, 655 bonds, 73 residues, 1 model selected
> select up
766 atoms, 785 bonds, 89 residues, 1 model selected
> select add #1/A:2040
770 atoms, 788 bonds, 90 residues, 1 model selected
> select up
790 atoms, 810 bonds, 92 residues, 1 model selected
> color sel cornflower blue target acs
> select clear
> color cornflower blue target acs
> select #1/A:2061
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
31 atoms, 31 bonds, 4 residues, 1 model selected
> color sel cornflower blue target acs
> select clear
> select #4/B:2095
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
205 atoms, 210 bonds, 23 residues, 1 model selected
> select add #4/B:2051
213 atoms, 217 bonds, 24 residues, 1 model selected
> select up
340 atoms, 347 bonds, 40 residues, 1 model selected
> select add #4/B:2035
346 atoms, 352 bonds, 41 residues, 1 model selected
> select up
505 atoms, 519 bonds, 58 residues, 1 model selected
> select add #4/B:2041
514 atoms, 527 bonds, 59 residues, 1 model selected
> select up
529 atoms, 544 bonds, 61 residues, 1 model selected
> color sel cornflower blue target acs
> select add #4/B:2077
537 atoms, 551 bonds, 62 residues, 1 model selected
> select up
687 atoms, 705 bonds, 79 residues, 1 model selected
> color sel cornflower blue target acs
> select #4/B:2068
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
79 atoms, 79 bonds, 10 residues, 1 model selected
> select add #4/B:2060
90 atoms, 89 bonds, 11 residues, 1 model selected
> select up
110 atoms, 111 bonds, 14 residues, 1 model selected
> select add #4/B:2118
118 atoms, 118 bonds, 15 residues, 1 model selected
> select up
134 atoms, 135 bonds, 17 residues, 1 model selected
> select add #4/B:2119
141 atoms, 141 bonds, 18 residues, 1 model selected
> select add #4/B:2121
149 atoms, 148 bonds, 19 residues, 1 model selected
> select up
164 atoms, 165 bonds, 21 residues, 1 model selected
> color sel cornflower blue target acs
> select clear
> select #4/F:215
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
179 atoms, 180 bonds, 22 residues, 1 model selected
> select up
1633 atoms, 1672 bonds, 202 residues, 1 model selected
> color sel lavender target acs
> select #4/F:473
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
70 atoms, 72 bonds, 8 residues, 1 model selected
> select up
3568 atoms, 3656 bonds, 451 residues, 1 model selected
> color sel lavender target acs
> select #4/F:987
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
246 atoms, 248 bonds, 27 residues, 1 model selected
> select up
1375 atoms, 1411 bonds, 167 residues, 1 model selected
> select down
246 atoms, 248 bonds, 27 residues, 1 model selected
> select up
1375 atoms, 1411 bonds, 167 residues, 1 model selected
> select up
1384 atoms, 1419 bonds, 169 residues, 1 model selected
> select down
1375 atoms, 1411 bonds, 167 residues, 1 model selected
> select down
246 atoms, 248 bonds, 27 residues, 1 model selected
> select add #4/F:965
257 atoms, 258 bonds, 28 residues, 1 model selected
> select up
348 atoms, 354 bonds, 39 residues, 1 model selected
> select add #4/F:953
353 atoms, 358 bonds, 40 residues, 1 model selected
> select up
385 atoms, 391 bonds, 44 residues, 1 model selected
> select add #4/F:839
397 atoms, 403 bonds, 45 residues, 1 model selected
> select up
517 atoms, 525 bonds, 61 residues, 1 model selected
> select add #4/F:955
524 atoms, 531 bonds, 62 residues, 1 model selected
> select up
540 atoms, 549 bonds, 64 residues, 1 model selected
> select add #4/F:971
547 atoms, 555 bonds, 65 residues, 1 model selected
> select up
639 atoms, 652 bonds, 76 residues, 1 model selected
> select add #4/F:816
647 atoms, 659 bonds, 77 residues, 1 model selected
> select up
758 atoms, 774 bonds, 90 residues, 1 model selected
> select add #4/F:821
766 atoms, 781 bonds, 91 residues, 1 model selected
> select up
773 atoms, 791 bonds, 92 residues, 1 model selected
> color sel lavender target acs
> select clear
> show #3 models
> hide #!4 models
> hide #!1 models
> select #3/A:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 4 residues, 1 model selected
> select up
832 atoms, 851 bonds, 107 residues, 1 model selected
> select up
1006 atoms, 924 bonds, 213 residues, 1 model selected
> select up
1890 atoms, 1742 bonds, 395 residues, 1 model selected
> hide sel atoms
> select clear
> select #3/A
1006 atoms, 924 bonds, 213 residues, 1 model selected
> color sel cornflower blue
> color sel cyan
> select #3/B:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
180 atoms, 185 bonds, 20 residues, 1 model selected
> select up
796 atoms, 818 bonds, 94 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet target acs
> select ::name="ARD"
69 atoms, 73 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> color sel byhetero
> select clear
> select #3/B:190
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
180 atoms, 185 bonds, 20 residues, 1 model selected
> select up
796 atoms, 818 bonds, 94 residues, 1 model selected
> show sel surfaces
> select #3/A:52
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
46 atoms, 45 bonds, 6 residues, 1 model selected
> select up
832 atoms, 851 bonds, 107 residues, 1 model selected
> select up
1006 atoms, 924 bonds, 213 residues, 1 model selected
> select down
832 atoms, 851 bonds, 107 residues, 1 model selected
> hide sel cartoons
> mlp sel
Map values for surface "3fap (2).pdb_A SES surface": minimum -28.01, mean
-4.647, maximum 24.6
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select #3/B:194@CE2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
180 atoms, 185 bonds, 20 residues, 2 models selected
> select up
796 atoms, 818 bonds, 94 residues, 2 models selected
> select up
884 atoms, 818 bonds, 182 residues, 2 models selected
> select down
796 atoms, 818 bonds, 94 residues, 2 models selected
> mlp sel
Map values for surface "3fap (2).pdb_B SES surface": minimum -27.62, mean
-3.547, maximum 21.62
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> transparency #3 60
> select clear
> hide #!3 surfaces
> select #3/A:402@C18
1 atom, 1 residue, 1 model selected
> select up
69 atoms, 73 bonds, 1 residue, 1 model selected
> select sel :< 5
644 atoms, 620 bonds, 78 residues, 3 models selected
> show sel & #!3 atoms
> select #3/A:54@N
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
46 atoms, 45 bonds, 6 residues, 2 models selected
> select up
832 atoms, 851 bonds, 107 residues, 2 models selected
> hide sel atoms
> select #3/A:234@O
1 atom, 1 residue, 1 model selected
> select up
1006 atoms, 924 bonds, 213 residues, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select add #3/A:315@O
2 atoms, 2 residues, 1 model selected
> select add #3/A:214@O
3 atoms, 3 residues, 1 model selected
> select add #3/A:317@O
4 atoms, 4 residues, 1 model selected
> select add #3/A:343@O
5 atoms, 5 residues, 1 model selected
> select add #3/A:364@O
6 atoms, 6 residues, 1 model selected
> select add #3/A:249@O
7 atoms, 7 residues, 1 model selected
> select add #3/A:221@O
8 atoms, 8 residues, 1 model selected
> select add #3/A:258@O
9 atoms, 9 residues, 1 model selected
> hide sel atoms
> select #3/B:194
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
180 atoms, 185 bonds, 20 residues, 2 models selected
> select up
796 atoms, 818 bonds, 94 residues, 2 models selected
> color sel byhetero
> select clear
> select #3/B:194
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
180 atoms, 185 bonds, 20 residues, 2 models selected
> select up
796 atoms, 818 bonds, 94 residues, 2 models selected
> select up
884 atoms, 818 bonds, 182 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "3fap (2).pdb_B SES surface": minimum -27.62, mean
-3.547, maximum 21.62
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> transparency #3 50
> select clear
> select add #3/A:402@C20
1 atom, 5 bonds, 1 residue, 1 model selected
> select add #3/A:402@C45
2 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/A:402@O8
3 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/A:402@O9
4 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime
> select add #3/A:402@C18
1 atom, 13 bonds, 1 residue, 1 model selected
> color sel lime
[Repeated 2 time(s)]
> select clear
> select #3/A:402@C43
1 atom, 1 residue, 1 model selected
> color sel lime
> select clear
> select #3/A:402@C44
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C23
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C15
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/B:178@CB
1 atom, 1 residue, 1 model selected
> select #3/B:178@CB
1 atom, 1 residue, 1 model selected
> select #3/A:402@C26
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C25
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C24
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C50
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C22
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C21
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C19
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C17
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C16
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C49
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C54
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C53
1 atom, 1 residue, 1 model selected
> color sel lime
> select #3/A:402@C55
1 atom, 1 residue, 1 model selected
> color sel lime
> select clear
[Repeated 1 time(s)]
> select #3/A:402@C52
1 atom, 1 residue, 1 model selected
> color sel lime
> open "/Users/katinaj/Downloads/4drh (1).pdb" "/Users/katinaj/Downloads/5gpg
> (4).pdb"
4drh (1).pdb title:
Co-crystal structure of the ppiase domain of FKBP51, rapamycin and the FRB
fragment of mtor At low pH [more info...]
Chain information for 4drh (1).pdb #5
---
Chain | Description | UniProt
A D | peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 1-140
B E | serine/threonine-protein kinase mtor | MTOR_HUMAN 2025-2114
Non-standard residues in 4drh (1).pdb #5
---
RAP — rapamycin immunosuppressant drug
SO4 — sulfate ion
5gpg (4).pdb title:
Co-crystal structure of the FK506 binding domain of human FKBP25, rapamycin
and the FRB domain of human mtor [more info...]
Chain information for 5gpg (4).pdb #6
---
Chain | Description | UniProt
A | peptidyl-prolyl cis-trans isomerase FKBP3 | FKBP3_HUMAN 109-224
B | serine/threonine-protein kinase mtor | MTOR_HUMAN 2021-2112
Non-standard residues in 5gpg (4).pdb #6
---
RAP — rapamycin immunosuppressant drug
> ui tool show Matchmaker
> matchmaker #!5-6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fap (2).pdb, chain B (#3) with 4drh (1).pdb, chain B (#5),
sequence alignment score = 474.6
RMSD between 88 pruned atom pairs is 0.612 angstroms; (across all 93 pairs:
2.315)
Matchmaker 3fap (2).pdb, chain B (#3) with 5gpg (4).pdb, chain B (#6),
sequence alignment score = 510.9
RMSD between 84 pruned atom pairs is 0.556 angstroms; (across all 93 pairs:
1.149)
> select #5/D
1099 atoms, 1097 bonds, 157 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/E
758 atoms, 763 bonds, 1 pseudobond, 103 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select
98369 atoms, 99928 bonds, 82 pseudobonds, 12833 residues, 10 models selected
> hide sel & #!3,5-6 atoms
> hide sel & #!3,5-6 surfaces
> select ::name="ARD"
69 atoms, 73 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
100 atoms, 102 bonds, 11 residues, 1 model selected
> select up
1001 atoms, 1021 bonds, 132 residues, 1 model selected
> select up
1136 atoms, 1117 bonds, 175 residues, 1 model selected
> select up
1964 atoms, 1937 bonds, 299 residues, 1 model selected
> select down
1136 atoms, 1117 bonds, 175 residues, 1 model selected
> hide sel cartoons
> select #6/A:221
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
82 atoms, 82 bonds, 10 residues, 1 model selected
> select up
523 atoms, 534 bonds, 67 residues, 1 model selected
> select up
548 atoms, 558 bonds, 70 residues, 1 model selected
> select up
864 atoms, 883 bonds, 110 residues, 1 model selected
> hide sel cartoons
> select ::name="RAP"
130 atoms, 136 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> show #!1 models
> hide #!1 models
> show #!2 models
> open "/Users/katinaj/Downloads/5wbk (1).pdb"
5wbk (1).pdb title:
Crystal structure of the arabidopsis thaliana raptor In complex with the tos
peptide of human S6K1 [more info...]
Chain information for 5wbk (1).pdb #7
---
Chain | Description | UniProt
A | regulatory-associated protein of tor 1 | RTOR1_ARATH 1-942 943-1344
T | ribosomal protein S6 kinase β-1 | KS6B1_HUMAN 1-14
> hide #!3 models
> hide #!5 models
> hide #!6 models
> ui tool show Matchmaker
> matchmaker #!7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wbj.pdb, chain A (#2) with 5wbk (1).pdb, chain A (#7), sequence
alignment score = 6225.2
RMSD between 1053 pruned atom pairs is 0.308 angstroms; (across all 1053
pairs: 0.308)
> open "/Users/katinaj/Downloads/4l46 (1).pdb"
4l46 (1).pdb title:
Crystal structures of human P70S6K1-WT [more info...]
Chain information for 4l46 (1).pdb #8
---
Chain | Description | UniProt
A | RPS6KB1 protein | Q7Z721_HUMAN 52-394
Non-standard residues in 4l46 (1).pdb #8
---
5FI —
2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole
SO4 — sulfate ion
ZN — zinc ion
> hide #!2 models
> open /Users/katinaj/Downloads/5wbh.pdb
5wbh.pdb title:
Structure of the FRB domain of mtor bound to A substrate recruitment peptide
of S6K1 [more info...]
Chain information for 5wbh.pdb #9
---
Chain | Description | UniProt
A B C D E | serine/threonine-protein kinase mtor | MTOR_HUMAN 2018-2114
W | ribosomal protein S6 kinase β-1 | KS6B1_HUMAN 389-414
> hide #!8 models
> hide #!7 models
> show #!2 models
> show #!3 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #!3 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wbh.pdb, chain C (#9) with 3fap (2).pdb, chain B (#3), sequence
alignment score = 514.6
RMSD between 92 pruned atom pairs is 0.555 angstroms; (across all 94 pairs:
0.825)
> undo
> hide #!3 models
> hide #!2 models
> show #!3 models
> select
117659 atoms, 119245 bonds, 94 pseudobonds, 15034 residues, 16 models selected
> hide sel & #9#!3 atoms
> show sel & #9#!3 cartoons
> select clear
> select #9/C:2026
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
355 atoms, 362 bonds, 21 residues, 1 model selected
> select up
1586 atoms, 1608 bonds, 96 residues, 1 model selected
> select up
1637 atoms, 1608 bonds, 147 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/B:2076
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
472 atoms, 476 bonds, 29 residues, 1 model selected
> select up
1532 atoms, 1554 bonds, 92 residues, 1 model selected
> select up
1579 atoms, 1554 bonds, 139 residues, 1 model selected
> select add #9/A:2076
1603 atoms, 1577 bonds, 140 residues, 1 model selected
> select up
2051 atoms, 2030 bonds, 168 residues, 1 model selected
> select up
3111 atoms, 3108 bonds, 231 residues, 1 model selected
> select up
3179 atoms, 3108 bonds, 299 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/E:2075
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
472 atoms, 476 bonds, 29 residues, 1 model selected
> select up
1560 atoms, 1582 bonds, 94 residues, 1 model selected
> select up
1626 atoms, 1582 bonds, 160 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> matchmaker #9 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fap (2).pdb, chain B (#3) with 5wbh.pdb, chain D (#9), sequence
alignment score = 514
RMSD between 91 pruned atom pairs is 0.615 angstroms; (across all 91 pairs:
0.615)
> show #!8 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!8 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wbh.pdb, chain W (#9) with 4l46 (1).pdb, chain A (#8), sequence
alignment score = 25.3
RMSD between 3 pruned atom pairs is 0.048 angstroms; (across all 3 pairs:
0.048)
> ui tool show Matchmaker
> matchmaker #8/A to #9/W pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wbh.pdb, chain W (#9) with 4l46 (1).pdb, chain A (#8), sequence
alignment score = 25.3
RMSD between 3 pruned atom pairs is 0.048 angstroms; (across all 3 pairs:
0.048)
> ui tool show "Show Sequence Viewer"
> sequence chain #9/W
Alignment identifier is 9/W
> sequence chain #8/A
Alignment identifier is 8/A
> select #9/W:394-409
268 atoms, 270 bonds, 16 residues, 1 model selected
> select
> #8/A:68-76,80-87,96-103,135-141,144-150,155-156,201-203,209-211,390-391
409 atoms, 407 bonds, 49 residues, 1 model selected
> select clear
> show #!1 models
> ui tool show Matchmaker
> matchmaker #9#!2-8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain A (#1) with 5wbh.pdb, chain D (#9), sequence
alignment score = 511.3
RMSD between 92 pruned atom pairs is 0.699 angstroms; (across all 92 pairs:
0.699)
Matchmaker 7pea.pdb, chain E (#1) with 5wbj.pdb, chain A (#2), sequence
alignment score = 2894.7
RMSD between 591 pruned atom pairs is 1.038 angstroms; (across all 1013 pairs:
3.563)
Matchmaker 7pea.pdb, chain A (#1) with 3fap (2).pdb, chain B (#3), sequence
alignment score = 505
RMSD between 92 pruned atom pairs is 0.742 angstroms; (across all 94 pairs:
1.152)
Matchmaker 7pea.pdb, chain A (#1) with 7pea.pdb, chain A (#4), sequence
alignment score = 12654.3
RMSD between 2192 pruned atom pairs is 0.000 angstroms; (across all 2192
pairs: 0.000)
Matchmaker 7pea.pdb, chain A (#1) with 4drh (1).pdb, chain B (#5), sequence
alignment score = 478.5
RMSD between 88 pruned atom pairs is 0.747 angstroms; (across all 92 pairs:
2.026)
Matchmaker 7pea.pdb, chain A (#1) with 5gpg (4).pdb, chain B (#6), sequence
alignment score = 498.3
RMSD between 85 pruned atom pairs is 0.857 angstroms; (across all 93 pairs:
1.174)
Matchmaker 7pea.pdb, chain E (#1) with 5wbk (1).pdb, chain A (#7), sequence
alignment score = 2918.1
RMSD between 589 pruned atom pairs is 1.039 angstroms; (across all 1006 pairs:
3.430)
Matchmaker 7pea.pdb, chain A (#1) with 4l46 (1).pdb, chain A (#8), sequence
alignment score = 87.7
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 232 pairs:
25.097)
> hide #!8 models
> hide #9 models
> show #9 models
> show #!7 models
> hide #!7 models
> show #!6 models
> show #!8 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> open /Users/katinaj/Downloads/3ihy.pdb
3ihy.pdb title:
Human PIK3C3 crystal structure [more info...]
Chain information for 3ihy.pdb #10
---
Chain | Description | UniProt
A B C D E | phosphatidylinositol 3-kinase catalytic subunit type 3 |
PK3C3_HUMAN 282-879
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> hide #9 models
> select #10/A:471@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
34 atoms, 32 bonds, 4 residues, 1 model selected
> select up
4343 atoms, 4428 bonds, 536 residues, 1 model selected
> select up
21670 atoms, 22093 bonds, 2675 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #!10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain A (#1) with 3ihy.pdb, chain B (#10), sequence
alignment score = 555
RMSD between 153 pruned atom pairs is 1.221 angstroms; (across all 456 pairs:
21.078)
> select #10/B
4340 atoms, 4423 bonds, 2 pseudobonds, 536 residues, 2 models selected
> select #10/A
4343 atoms, 4428 bonds, 1 pseudobond, 536 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> select #10/C
4344 atoms, 4430 bonds, 1 pseudobond, 537 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> select #4/E
8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected
> select #10/D
4303 atoms, 4387 bonds, 1 pseudobond, 531 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> select #10/E
4340 atoms, 4425 bonds, 1 pseudobond, 535 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> ui tool show Matchmaker
> matchmaker #!10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain A (#1) with 3ihy.pdb, chain B (#10), sequence
alignment score = 555
RMSD between 153 pruned atom pairs is 1.221 angstroms; (across all 456 pairs:
21.078)
> hide #!4 models
> select #10/B:829
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
44 atoms, 44 bonds, 6 residues, 1 model selected
> select up
3220 atoms, 3281 bonds, 400 residues, 1 model selected
> select up
3228 atoms, 3288 bonds, 401 residues, 1 model selected
> select up
4331 atoms, 4416 bonds, 534 residues, 1 model selected
> select clear
> select ::name="5FI"
28 atoms, 31 bonds, 1 residue, 1 model selected
> show #!10 atoms
> hide #!10 atoms
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #10/B
Alignment identifier is 10/B
> select
> #10/B:289-301,309-337,341-355,359-367,373-385,388-414,474-561,565-584,606-609,641-661,690-708,713-740,780-787,792-822,828-847,851-870
2991 atoms, 3023 bonds, 365 residues, 1 model selected
> select clear
> select
> #10/B:289-301,309-337,341-355,359-367,373-385,388-414,474-561,565-584,606-609,641-661,690-708,713-740,780-787,792-822,828-847,851-870
2991 atoms, 3023 bonds, 365 residues, 1 model selected
> select #10/B:328
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select ::name="5FI"
28 atoms, 31 bonds, 1 residue, 1 model selected
> show #!10 atoms
> hide #!10 atoms
> select #10/B:354
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> color sel byhetero
> color sel yellow
> select #10/B:356
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> color sel yellow
> color sel byhetero
> select clear
> show #!4 models
> show #!1 models
> hide #!4 models
> select #1/A:1438
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
127 atoms, 130 bonds, 17 residues, 1 model selected
> select up
4498 atoms, 4603 bonds, 554 residues, 1 model selected
> select up
4534 atoms, 4638 bonds, 558 residues, 1 model selected
> select up
11460 atoms, 11718 bonds, 1414 residues, 1 model selected
> select down
4534 atoms, 4638 bonds, 558 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:869
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
107 atoms, 107 bonds, 13 residues, 1 model selected
> select up
891 atoms, 905 bonds, 113 residues, 1 model selected
> select up
906 atoms, 920 bonds, 115 residues, 1 model selected
> select up
2008 atoms, 2039 bonds, 256 residues, 1 model selected
> select up
2028 atoms, 2059 bonds, 259 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:316
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
111 atoms, 114 bonds, 15 residues, 1 model selected
> select add #1/A:180
118 atoms, 121 bonds, 16 residues, 1 model selected
> select up
165 atoms, 171 bonds, 21 residues, 1 model selected
> select up
728 atoms, 742 bonds, 101 residues, 1 model selected
> select up
734 atoms, 747 bonds, 102 residues, 1 model selected
> select up
879 atoms, 895 bonds, 120 residues, 1 model selected
> select up
886 atoms, 901 bonds, 121 residues, 1 model selected
> select up
1332 atoms, 1355 bonds, 177 residues, 1 model selected
> select up
1339 atoms, 1361 bonds, 178 residues, 1 model selected
> select up
1436 atoms, 1459 bonds, 191 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:528
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
115 atoms, 116 bonds, 15 residues, 1 model selected
> select up
409 atoms, 412 bonds, 53 residues, 1 model selected
> select up
9492 atoms, 9677 bonds, 1185 residues, 1 model selected
> select down
409 atoms, 412 bonds, 53 residues, 1 model selected
> select add #1/A:624
420 atoms, 422 bonds, 54 residues, 1 model selected
> select up
540 atoms, 543 bonds, 69 residues, 1 model selected
> select add #1/A:607
545 atoms, 547 bonds, 70 residues, 1 model selected
> select up
651 atoms, 657 bonds, 82 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
[Repeated 1 time(s)]
> select #1/A:593
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
57 atoms, 54 bonds, 7 residues, 1 model selected
> select add #1/A:588
64 atoms, 60 bonds, 8 residues, 1 model selected
> select up
157 atoms, 155 bonds, 21 residues, 1 model selected
> select add #1/A:578
162 atoms, 159 bonds, 22 residues, 1 model selected
> select add #1/A:44
167 atoms, 163 bonds, 23 residues, 1 model selected
> select up
242 atoms, 239 bonds, 38 residues, 1 model selected
> select add #1/A:95
246 atoms, 242 bonds, 39 residues, 1 model selected
> select up
350 atoms, 346 bonds, 54 residues, 1 model selected
> select add #1/A:280
359 atoms, 354 bonds, 55 residues, 1 model selected
> select up
468 atoms, 463 bonds, 68 residues, 1 model selected
> select add #1/A:28
473 atoms, 467 bonds, 69 residues, 1 model selected
> select up
533 atoms, 527 bonds, 81 residues, 1 model selected
> select add #1/A:271
541 atoms, 534 bonds, 82 residues, 1 model selected
> select up
649 atoms, 644 bonds, 96 residues, 1 model selected
> select add #1/A:127
655 atoms, 649 bonds, 97 residues, 1 model selected
> select up
757 atoms, 751 bonds, 111 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #1/A:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
133 atoms, 134 bonds, 16 residues, 1 model selected
> select add #1/A:118
141 atoms, 141 bonds, 17 residues, 1 model selected
> select up
193 atoms, 195 bonds, 25 residues, 1 model selected
> select add #1/A:239
202 atoms, 203 bonds, 26 residues, 1 model selected
> select up
308 atoms, 313 bonds, 38 residues, 1 model selected
> select add #1/A:150
317 atoms, 321 bonds, 39 residues, 1 model selected
> select up
459 atoms, 469 bonds, 55 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:64
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
130 atoms, 134 bonds, 14 residues, 1 model selected
> select add #1/A:60
135 atoms, 138 bonds, 15 residues, 1 model selected
> select add #1/A:259
143 atoms, 145 bonds, 1 pseudobond, 16 residues, 2 models selected
> select up
199 atoms, 199 bonds, 1 pseudobond, 23 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/E:1182
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
32 atoms, 31 bonds, 5 residues, 1 model selected
> select up
1296 atoms, 1316 bonds, 168 residues, 1 model selected
> select up
1333 atoms, 1351 bonds, 174 residues, 1 model selected
> select up
2903 atoms, 2969 bonds, 364 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/E:677
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 101 bonds, 12 residues, 1 model selected
> select up
3568 atoms, 3656 bonds, 451 residues, 1 model selected
> select up
3574 atoms, 3661 bonds, 452 residues, 1 model selected
> select up
3849 atoms, 3944 bonds, 486 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/E:34
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
54 atoms, 54 bonds, 6 residues, 1 model selected
> select up
1633 atoms, 1672 bonds, 202 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:2038
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
165 atoms, 172 bonds, 18 residues, 1 model selected
> select up
4614 atoms, 4715 bonds, 569 residues, 1 model selected
> select down
165 atoms, 172 bonds, 18 residues, 1 model selected
> select add #1/A:2045
174 atoms, 180 bonds, 19 residues, 1 model selected
> select up
300 atoms, 309 bonds, 35 residues, 1 model selected
> select add #1/A:2067
309 atoms, 317 bonds, 36 residues, 1 model selected
> select up
379 atoms, 388 bonds, 45 residues, 1 model selected
> select add #1/A:2082
388 atoms, 396 bonds, 46 residues, 1 model selected
> select up
537 atoms, 550 bonds, 63 residues, 1 model selected
> select add #1/A:2097
545 atoms, 557 bonds, 64 residues, 1 model selected
> select up
742 atoms, 760 bonds, 86 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:2061
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
59 atoms, 57 bonds, 8 residues, 1 model selected
> select add #1/A:2116
66 atoms, 64 bonds, 9 residues, 1 model selected
> select up
83 atoms, 81 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:945
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
157 atoms, 161 bonds, 19 residues, 1 model selected
> select up
2303 atoms, 2354 bonds, 286 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> matchmaker #!10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain A (#1) with 3ihy.pdb, chain B (#10), sequence
alignment score = 451.2
RMSD between 153 pruned atom pairs is 1.221 angstroms; (across all 371 pairs:
12.792)
> show #9 models
> hide #9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #9 models
> open /Users/katinaj/Downloads/6bcx.cif
Summary of feedback from opening /Users/katinaj/Downloads/6bcx.cif
---
warnings | Atom HB3 is not in the residue template for UNK /A:17
Atom HB3 is not in the residue template for UNK /A:18
Atom HB3 is not in the residue template for UNK /A:19
Atom HB3 is not in the residue template for UNK /A:20
Atom HB3 is not in the residue template for UNK /A:21
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
note | Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
6bcx.cif title:
mTORC1 structure refined to 3.0 angstroms [more info...]
Chain information for 6bcx.cif #11
---
Chain | Description | UniProt
A B | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 579-2549
D E | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326
W Y | Regulatory-associated protein of mTOR | RPTOR_HUMAN 2-1335
X Z | Eukaryotic translation initiation factor 4E-binding protein 1 |
4EBP1_HUMAN 1-118
Non-standard residues in 6bcx.cif #11
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> hide #9 models
> hide #!10 models
> hide #!11 models
> hide #!1 models
> show #!1 models
> show #!4 models
> hide #!1 models
> show #!11 models
> select
207590 atoms, 210143 bonds, 131 pseudobonds, 19366 residues, 21 models
selected
> hide sel & #!4,11 atoms
> show sel & #!4,11 cartoons
> ui tool show Matchmaker
> matchmaker #!11 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain A (#4) with 6bcx.cif, chain A (#11), sequence
alignment score = 12420.3
RMSD between 2107 pruned atom pairs is 0.865 angstroms; (across all 2178
pairs: 0.969)
> hide #!4 models
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel magenta
> color sel byhetero
> show #9 models
> select clear
> show #!2 models
> hide #!2 models
> show #!3 models
> select clear
> select ::name="RAP"
130 atoms, 136 bonds, 2 residues, 2 models selected
> show #9#!3,11 atoms
> hide #9#!3,11 atoms
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> show sel atoms
> select ::name="ARD"
69 atoms, 73 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select #11/A:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
266 atoms, 267 bonds, 16 residues, 1 model selected
> select up
938 atoms, 945 bonds, 57 residues, 1 model selected
> select up
968 atoms, 974 bonds, 59 residues, 1 model selected
> select up
1473 atoms, 1482 bonds, 90 residues, 1 model selected
> select up
1513 atoms, 1521 bonds, 94 residues, 1 model selected
> select up
1723 atoms, 1731 bonds, 115 residues, 1 model selected
> select up
35079 atoms, 35421 bonds, 2181 residues, 1 model selected
> select down
1723 atoms, 1731 bonds, 115 residues, 1 model selected
> select #11/X
126 atoms, 126 bonds, 8 residues, 1 model selected
> color sel lime
> select #11/Z
126 atoms, 126 bonds, 8 residues, 1 model selected
> color sel lime
> select #11/W
16791 atoms, 16991 bonds, 5 pseudobonds, 1052 residues, 2 models selected
> select clear
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 86 atom styles
> select clear
[Repeated 1 time(s)]
> select #11/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
213 atoms, 216 bonds, 13 residues, 1 model selected
> select up
237 atoms, 242 bonds, 14 residues, 1 model selected
> select up
35079 atoms, 35421 bonds, 2181 residues, 1 model selected
> select down
237 atoms, 242 bonds, 14 residues, 1 model selected
> select up
35079 atoms, 35421 bonds, 2181 residues, 1 model selected
> ui tool show "Color Actions"
> color sel olive drab target acs
> select #11/B:581
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
210 atoms, 210 bonds, 14 residues, 1 model selected
> select up
264 atoms, 265 bonds, 18 residues, 1 model selected
> select up
283 atoms, 283 bonds, 19 residues, 1 model selected
> select up
833 atoms, 839 bonds, 53 residues, 1 model selected
> select up
877 atoms, 882 bonds, 56 residues, 1 model selected
> select up
3131 atoms, 3154 bonds, 196 residues, 1 model selected
> select up
3145 atoms, 3167 bonds, 197 residues, 1 model selected
> select up
4961 atoms, 4998 bonds, 309 residues, 1 model selected
> select up
35079 atoms, 35421 bonds, 2181 residues, 1 model selected
> color sel olive drab target acs
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> color sel magenta target acs
[Repeated 1 time(s)]
> color sel byhetero
> select #11/A:2036
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
311 atoms, 318 bonds, 18 residues, 1 model selected
> select add #11/A:2113
333 atoms, 339 bonds, 19 residues, 1 model selected
> select up
722 atoms, 734 bonds, 41 residues, 1 model selected
> select add #11/A:2116
736 atoms, 748 bonds, 42 residues, 1 model selected
> select up
772 atoms, 785 bonds, 44 residues, 1 model selected
> select add #11/A:2076
796 atoms, 808 bonds, 45 residues, 1 model selected
> select up
1070 atoms, 1086 bonds, 61 residues, 1 model selected
> select add #11/A:2054
1089 atoms, 1104 bonds, 62 residues, 1 model selected
> select up
1341 atoms, 1359 bonds, 78 residues, 1 model selected
> select add #11/A:2072
1358 atoms, 1375 bonds, 79 residues, 1 model selected
> select up
1497 atoms, 1516 bonds, 88 residues, 1 model selected
> color sel cornflower blue target acs
> select #11/A:2092
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #11/A:2063
24 atoms, 22 bonds, 2 residues, 1 model selected
> select up
80 atoms, 79 bonds, 6 residues, 1 model selected
> color sel cornflower blue target acs
> select clear
> select #11/A:970
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
336 atoms, 340 bonds, 21 residues, 1 model selected
> select up
4789 atoms, 4841 bonds, 290 residues, 1 model selected
> color sel hot pink target acs
> select #11/B:993
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
270 atoms, 273 bonds, 16 residues, 1 model selected
> select up
4789 atoms, 4841 bonds, 290 residues, 1 model selected
> color sel hot pink target acs
> hide #9 models
> hide #!3 models
> select clear
> select #11/A:1308
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
101 atoms, 102 bonds, 7 residues, 1 model selected
> select up
8931 atoms, 9036 bonds, 554 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale turquoise target acs
> select #11/B:1297
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
90 atoms, 90 bonds, 6 residues, 1 model selected
> select up
8931 atoms, 9036 bonds, 554 residues, 1 model selected
> color sel pale turquoise target acs
> select clear
> turn 90 x
Expected an axis vector or a keyword
> turn x 90
[Repeated 3 time(s)]
> turn x 45
> select clear
> select #11/A:2040
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
46 atoms, 45 bonds, 3 residues, 1 model selected
> color sel cornflower blue
> select clear
> show #9 models
> select #11/A:3000@O2B
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 45 bonds, 1 residue, 1 model selected
> style sel ball
Changed 43 atom styles
> select clear
> show #!7 models
> hide #!7 models
> show #!3 models
> select clear
> hide #!3 models
> hide #9 models
> show #!3 models
> select #3/A:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
80 atoms, 81 bonds, 10 residues, 2 models selected
> select up
832 atoms, 851 bonds, 107 residues, 2 models selected
> hide sel cartoons
> select clear
> select #3/A:402@O9
1 atom, 1 residue, 1 model selected
> select add #11/A:3000@O3B
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #3/A:402@O9 #11/A:3000@O3B
Distance between 3fap (2).pdb #3/A ARD 402 O9 and 6bcx.cif #11/A ATP 3000 O3B:
20.911Å
> distance style color black
[Repeated 2 time(s)]
> select clear
> ~distance #3/A:402@O9 #11/A:3000@O3B
> select #11/A:2165
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
202 atoms, 202 bonds, 11 residues, 1 model selected
> select up
9327 atoms, 9428 bonds, 570 residues, 1 model selected
> show sel surfaces
> mlp sel
Map values for surface "6bcx.cif_A SES surface": minimum -28.47, mean -3.145,
maximum 27.31
To also show corresponding color key, enter the above mlp command and add key
true
> transparency (#!11 & sel) 80
> transparency (#!11 & sel) 60
> select clear
> select #3/A:402@O8
1 atom, 1 residue, 1 model selected
> select clear
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #9 models
> show #!8 models
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> show #!3 models
> hide #9 models
> hide #!11 models
> select #3/A
1006 atoms, 924 bonds, 213 residues, 1 model selected
> show sel cartoons
> select clear
> open "/Users/katinaj/Downloads/3fap (2).pdb"
3fap (2).pdb title:
Atomic structures of the rapamycin analogs In complex with both human FKBP12
and FRB domain of frap [more info...]
Chain information for 3fap (2).pdb #12
---
Chain | Description | UniProt
A | FKBP12 | FKB1A_HUMAN 1-107
B | FRAP | FRAP_HUMAN 108-201
Non-standard residues in 3fap (2).pdb #12
---
ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug)
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #12 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fap (2).pdb, chain A (#3) with 3fap (2).pdb, chain A (#12),
sequence alignment score = 559.6
RMSD between 107 pruned atom pairs is 0.000 angstroms; (across all 107 pairs:
0.000)
> select clear
> hide #!3 models
> select #12/A:23
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
49 atoms, 50 bonds, 6 residues, 1 model selected
> select up
832 atoms, 851 bonds, 107 residues, 1 model selected
> select up
1006 atoms, 924 bonds, 213 residues, 1 model selected
> select down
832 atoms, 851 bonds, 107 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/ProteinDocking/FRB-
> Rapamycin.pdb
> open "/Users/katinaj/Downloads/3fap (2).pdb"
3fap (2).pdb title:
Atomic structures of the rapamycin analogs In complex with both human FKBP12
and FRB domain of frap [more info...]
Chain information for 3fap (2).pdb #13
---
Chain | Description | UniProt
A | FKBP12 | FKB1A_HUMAN 1-107
B | FRAP | FRAP_HUMAN 108-201
Non-standard residues in 3fap (2).pdb #13
---
ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug)
> hide #12 models
> show #12 models
> ui tool show Matchmaker
> matchmaker #13 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fap (2).pdb, chain A (#3) with 3fap (2).pdb, chain A (#13),
sequence alignment score = 559.6
RMSD between 107 pruned atom pairs is 0.000 angstroms; (across all 107 pairs:
0.000)
> hide #12 models
> select #13/A:101
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
93 atoms, 93 bonds, 11 residues, 1 model selected
> select up
832 atoms, 851 bonds, 107 residues, 1 model selected
> select up
1006 atoms, 924 bonds, 213 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> close #13
> open "/Users/katinaj/Downloads/3fap (2).pdb"
3fap (2).pdb title:
Atomic structures of the rapamycin analogs In complex with both human FKBP12
and FRB domain of frap [more info...]
Chain information for 3fap (2).pdb #13
---
Chain | Description | UniProt
A | FKBP12 | FKB1A_HUMAN 1-107
B | FRAP | FRAP_HUMAN 108-201
Non-standard residues in 3fap (2).pdb #13
---
ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug)
> ui tool show Matchmaker
> matchmaker #13 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fap (2).pdb, chain A (#3) with 3fap (2).pdb, chain A (#13),
sequence alignment score = 559.6
RMSD between 107 pruned atom pairs is 0.000 angstroms; (across all 107 pairs:
0.000)
> select #13/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
93 atoms, 93 bonds, 11 residues, 1 model selected
> select up
832 atoms, 851 bonds, 107 residues, 1 model selected
> select up
1006 atoms, 924 bonds, 213 residues, 1 model selected
> select down
832 atoms, 851 bonds, 107 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #13/B:199
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
180 atoms, 185 bonds, 20 residues, 1 model selected
> select up
796 atoms, 818 bonds, 94 residues, 1 model selected
> select down
180 atoms, 185 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #13/B:166
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
241 atoms, 245 bonds, 29 residues, 1 model selected
> select up
616 atoms, 632 bonds, 74 residues, 1 model selected
> select up
704 atoms, 632 bonds, 162 residues, 1 model selected
> select up
878 atoms, 705 bonds, 268 residues, 1 model selected
> select up
209526 atoms, 211739 bonds, 19922 residues, 13 models selected
> select down
878 atoms, 705 bonds, 268 residues, 4 models selected
> select down
704 atoms, 632 bonds, 162 residues, 1 model selected
> select up
878 atoms, 705 bonds, 268 residues, 1 model selected
> select down
704 atoms, 632 bonds, 162 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="HOH"
942 atoms, 942 residues, 7 models selected
> delete atoms (#13 & sel)
> delete bonds (#13 & sel)
> save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Rapamycin.pdb
> show #12 models
> hide #13 models
> save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/FRB-rap.pdb
No model chosen to save relative to
[Repeated 1 time(s)]
> save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/FRB-Rap.cif models
> #12 displayedOnly true
Fetching CCD ARD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/ARD/ARD.cif
> hide #12 models
> show #13 models
> save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Rap.cif models #13
> displayedOnly true
> show #12 models
> hide #13 models
> save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/FRB-Rap_Full.cif
> models #12
> open /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Avogadro/Rapamycin-
> EMin.pdb
> /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Avogadro/Rapamaycin_boundconformation.pdb
Rapamaycin_boundconformation.pdb title:
Rap [more info...]
Non-standard residues in Rapamaycin_boundconformation.pdb #15
---
ARD — (ARD)
> hide #12 models
> show #14-15 atoms
> select
208930 atoms, 211327 bonds, 131 pseudobonds, 19657 residues, 25 models
selected
> show sel & #14-15 atoms
> ui tool show Matchmaker
> matchmaker #14 to #15
No matrix compatible with both reference structure and all match structures
> close #14-15
> show #!4 models
> show #!3 models
> show #9 models
> open
> /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/ProteinDocking/FRB-S6K1Dock.pdb
FRB-S6K1Dock.pdb title:
Human PIK3C3 crystal structure [more info...]
Chain information for FRB-S6K1Dock.pdb #14
---
Chain | Description
A | No description available
D | No description available
> ui tool show Matchmaker
> matchmaker #!14 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wbh.pdb, chain D (#9) with FRB-S6K1Dock.pdb, chain D (#14),
sequence alignment score = 513.9
RMSD between 92 pruned atom pairs is 0.157 angstroms; (across all 92 pairs:
0.157)
> select clear
> hide #!14 models
> open
> /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/ProteinDocking/FRB-S6K1Dock2.pdb
FRB-S6K1Dock2.pdb title:
Human PIK3C3 crystal structure [more info...]
Chain information for FRB-S6K1Dock2.pdb #15
---
Chain | Description
A | No description available
D | No description available
> ui tool show Matchmaker
> matchmaker #!15 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wbh.pdb, chain D (#9) with FRB-S6K1Dock2.pdb, chain D (#15),
sequence alignment score = 513.9
RMSD between 92 pruned atom pairs is 0.157 angstroms; (across all 92 pairs:
0.157)
> select #15/A
8757 atoms, 8842 bonds, 1 pseudobond, 536 residues, 2 models selected
> select ::name="THR"
9831 atoms, 8871 bonds, 994 residues, 14 models selected
> show sel & #9#!3-4,15 atoms
> hide #!3 models
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> show #9#!4,15 atoms
> hide #9#!4,15 atoms
> select #15/A
8757 atoms, 8842 bonds, 1 pseudobond, 536 residues, 2 models selected
> select clear
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> show #9#!4,15 atoms
> hide #9#!4,15 atoms
> show #!10 models
> show #!11 models
> hide #!10 models
> select ::name="THR"
9831 atoms, 8871 bonds, 994 residues, 14 models selected
> show sel & #9#!4,11,15 atoms
> select clear
> close #14-15
> show #!7 models
> hide #!4 models
> ui tool show Matchmaker
> matchmaker #!7,11 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7pea.pdb, chain E (#4) with 5wbk (1).pdb, chain A (#7), sequence
alignment score = 2918.1
RMSD between 589 pruned atom pairs is 1.039 angstroms; (across all 1006 pairs:
3.430)
Matchmaker 7pea.pdb, chain A (#4) with 6bcx.cif, chain A (#11), sequence
alignment score = 12420.3
RMSD between 2107 pruned atom pairs is 0.865 angstroms; (across all 2178
pairs: 0.969)
> hide #9 models
> ui tool show Matchmaker
> matchmaker #!7 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6bcx.cif, chain W (#11) with 5wbk (1).pdb, chain A (#7), sequence
alignment score = 2885.7
RMSD between 599 pruned atom pairs is 1.051 angstroms; (across all 1002 pairs:
4.010)
> select
208717 atoms, 211107 bonds, 131 pseudobonds, 19655 residues, 23 models
selected
> hide sel & #!7,11 atoms
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> show #!3 models
> select #11/W:104
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
293 atoms, 294 bonds, 19 residues, 1 model selected
> select up
3272 atoms, 3311 bonds, 202 residues, 1 model selected
> select up
3336 atoms, 3374 bonds, 206 residues, 1 model selected
> select up
10473 atoms, 10600 bonds, 653 residues, 1 model selected
> show sel surfaces
> mlp sel
Map values for surface "6bcx.cif_W SES surface": minimum -28.2, mean -3.189,
maximum 28.24
To also show corresponding color key, enter the above mlp command and add key
true
> select #3/A
1006 atoms, 924 bonds, 213 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select ::name="RAP"
130 atoms, 136 bonds, 2 residues, 2 models selected
> show #!3,7,11 atoms
> hide #!3,7,11 atoms
> select #3/A
1006 atoms, 924 bonds, 213 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select #3/A:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
53 atoms, 52 bonds, 7 residues, 2 models selected
> select up
832 atoms, 851 bonds, 107 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #11/A:2359@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
101 atoms, 102 bonds, 7 residues, 2 models selected
> select up
9327 atoms, 9428 bonds, 570 residues, 2 models selected
> transparency (#!11 & sel) 30
> select #3/A:242@O
1 atom, 1 residue, 1 model selected
> select ::name="HOH"
837 atoms, 837 residues, 6 models selected
> hide sel & #!3 atoms
> select ::name="ATP"
86 atoms, 90 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select #3/A:402@O8
1 atom, 1 residue, 1 model selected
> select add #11/A:3000@O2B
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #3/A:402@O8 #11/A:3000@O2B
Distance between 3fap (2).pdb #3/A ARD 402 O8 and 6bcx.cif #11/A ATP 3000 O2B:
21.123Å
> select clear
> ~distance #3/A:402@O8 #11/A:3000@O2B
> show #!10 models
> hide #!10 models
> show #9 models
> hide #9#!3,7,11 surfaces
> show #9#!3,7,11 surfaces
> select #3/A:15@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
92 atoms, 94 bonds, 12 residues, 2 models selected
> hide sel surfaces
> select #3/A:65@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
80 atoms, 81 bonds, 10 residues, 2 models selected
> select up
832 atoms, 851 bonds, 107 residues, 2 models selected
> select up
1006 atoms, 924 bonds, 213 residues, 2 models selected
> hide sel surfaces
> hide #!7 models
> hide #!3 models
> select #9/D:2109@NH1
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> select up
352 atoms, 357 bonds, 20 residues, 2 models selected
> select up
1532 atoms, 1554 bonds, 92 residues, 2 models selected
> select up
1619 atoms, 1554 bonds, 179 residues, 2 models selected
> select up
1934 atoms, 1857 bonds, 213 residues, 2 models selected
> mlp sel
Map values for surface "5wbh.pdb_D SES surface": minimum -27.37, mean -3.145,
maximum 23.9
Map values for surface "5wbh.pdb_W SES surface": minimum -20.12, mean -1.559,
maximum 22.79
To also show corresponding color key, enter the above mlp command and add key
true
> select #9/W:401@CD
1 atom, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 2 models selected
> select up
90 atoms, 90 bonds, 5 residues, 2 models selected
> select up
300 atoms, 303 bonds, 19 residues, 2 models selected
> transparency (#!9 & sel) 60
> show sel atoms
> style sel stick
Changed 300 atom styles
> select clear
> select #9/W:406@OE1
1 atom, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 5 residues, 2 models selected
> select up
300 atoms, 303 bonds, 19 residues, 2 models selected
> color sel byhetero
> mlp sel
Map values for surface "5wbh.pdb_W SES surface": minimum -20.12, mean -1.559,
maximum 22.79
To also show corresponding color key, enter the above mlp command and add key
true
> transparency (#!9 & sel) 80
> select clear
> open /Users/katinaj/Downloads/EBP1_rank_1.pdb
Chain information for EBP1_rank_1.pdb #14
---
Chain | Description
A | No description available
> hide #14 models
> show #14 models
> hide #!11 models
> ui tool show Matchmaker
> matchmaker #14 to #9/W pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wbh.pdb, chain W (#9) with EBP1_rank_1.pdb, chain A (#14),
sequence alignment score = 19.4
RMSD between 10 pruned atom pairs is 1.508 angstroms; (across all 17 pairs:
4.785)
> select #14/A:67
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select #9/W:401@O
1 atom, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 2 models selected
> select up
90 atoms, 90 bonds, 5 residues, 2 models selected
> select up
300 atoms, 303 bonds, 19 residues, 2 models selected
> hide sel surfaces
> select #14/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> select #14/A:65
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #14/A:62
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #14/A:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 4 residues, 1 model selected
> select #14/A:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 5 residues, 1 model selected
> show sel atoms
> hide sel surfaces
> select #9/D:2039@O
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 2 models selected
> select up
336 atoms, 343 bonds, 20 residues, 2 models selected
> select up
1532 atoms, 1554 bonds, 92 residues, 2 models selected
> select up
1619 atoms, 1554 bonds, 179 residues, 2 models selected
> hide sel surfaces
> style sel stick
Changed 1619 atom styles
> color sel byhetero
> select clear
> show #13 models
> hide #13 models
> show #12 models
> hide #12 models
> show #!11 models
> hide #!9 models
> hide #!11 models
> select ::name="THR"
9103 atoms, 8191 bonds, 948 residues, 13 models selected
> show sel & #14 atoms
> show #!11 models
> select #14/A:37
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
390 atoms, 398 bonds, 55 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #14/A:46
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
390 atoms, 398 bonds, 55 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> show #!3 models
> select #3/A
1006 atoms, 924 bonds, 213 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!11 models
> select #14/A:112
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #14/A:113
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #14/A:114
26 atoms, 24 bonds, 3 residues, 1 model selected
> select add #14/A:115
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add #14/A:116
43 atoms, 39 bonds, 5 residues, 1 model selected
> select add #14/A:118
51 atoms, 46 bonds, 6 residues, 1 model selected
> select add #14/A:117
59 atoms, 53 bonds, 7 residues, 1 model selected
> color sel purple
> select clear
> hide #!3 models
> select #14/A:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium blue
> ui tool show "Color Actions"
> color sel light blue target acs
> color sel byhetero
> select #14/A:55
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel light blue target acs
> color sel byhetero
> select #14/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel light blue target acs
> color sel byhetero target acs
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select #14/A:70@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> ui tool show AlphaFold
> alphafold search #14
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Webservices job id: INTDN15CQKO6V8UL
BlastProtein failed: failed
BlastProtein failed: 'bytes' object has no attribute 'items'
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
> alphafold predict #14 minimize true
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> ui tool show "Modeller Comparative"
Populating font family aliases took 69 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> toolshed show
> swapaa /14:A:46 TPO
No amino acid residues specified for swapping
> swapaa #14/A:46 TPO
Using Dunbrack library
EBP1_rank_1.pdb #14/A THR 46: phi -164.3, psi 140.7 trans
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/swap_res/cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
See log for complete Python traceback.
> swapaa #14/A:46 TPO
Using Dunbrack library
EBP1_rank_1.pdb #14/A THR 46: phi -164.3, psi 140.7 trans
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/swap_res/cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: Z12Q000VBLL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 39 days, 23 hours, 1 minute
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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-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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
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: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Jade,
--Eric