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Opened 4 years ago
Closed 4 years ago
#6448 closed defect (limitation)
Crash in lx4/session saving
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19043
ChimeraX Version: 1.4.dev202201150102 (2022-01-15 01:02:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x800706ba
Thread 0x00004084 (most recent call first):
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-packages\lz4\frame\__init__.py", line 416 in decompress
Windows fatal exception: access violation
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202201150102 (2022-01-15)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/PDB-
> GluK2/apo.pdb
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/PDB-
> GluK2/cls1.pdb
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/PDB-
> GluK2/cls2.pdb
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/PDB-
> GluK2/cls4.pdb
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/PDB-
> GluK2/cls5.pdb
Chain information for apo.pdb #1
---
Chain | Description
A B C D | No description available
Chain information for cls1.pdb #2
---
Chain | Description
A B C D | No description available
Chain information for cls2.pdb #3
---
Chain | Description
A B C D | No description available
Chain information for cls4.pdb #4
---
Chain | Description
A B C D | No description available
Chain information for cls5.pdb #5
---
Chain | Description
A B C D | No description available
> lighting soft
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> open 4uqq
Summary of feedback from opening 4uqq fetched from pdb
---
warnings | Unknown polymer entity '2' near line 24060
Atom OXT is not in the residue template for GLU /A:999
Atom OXT is not in the residue template for GLU /B:999
Atom OXT is not in the residue template for GLU /C:999
Atom OXT is not in the residue template for GLU /D:999
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
4uqq title:
Electron density map of GluK2 desensitized state in complex with
2S,4R-4-methylglutamate [more info...]
Chain information for 4uqq #6
---
Chain | Description | UniProt
A B C D | glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
> matchmaker #6 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 apo.pdb, chain A (#1) with 4uqq, chain A (#6), sequence alignment
score = 3588.2
RMSD between 362 pruned atom pairs is 1.014 angstroms; (across all 693 pairs:
2.371)
> hide #!3 models
> ui tool show "Side View"
> open 5kuf
5kuf title:
GluK2EM with 2S,4R-4-methylglutamate [more info...]
Chain information for 5kuf #7
---
Chain | Description | UniProt
A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
Non-standard residues in 5kuf #7
---
SYM — 2S,4R-4-methylglutamate
> matchmaker #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 apo.pdb, chain C (#1) with 5kuf, chain A (#7), sequence alignment
score = 3605.9
RMSD between 702 pruned atom pairs is 0.883 angstroms; (across all 747 pairs:
1.153)
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!3 models
> show #!5 models
> cartoon style #3,5 modeHelix tube sides 20
> show #!4 models
> cartoon style #3-5 modeHelix tube sides 20
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 target m
> show #!1 models
> show #!2 models
> cartoon style #1-2,4-5 modeHelix tube sides 20
> hide #!1 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!2 models
> show #!3 models
> color #2-5 cornflower blue
> morph #3,4,5,2 same true
Computed 151 frame morph #8
> coordset #8 1,151
> show #8 target ab
> cartoon hide #8
> style #8 ball
Changed 23920 atom styles
> style #8 sphere
Changed 23920 atom styles
> select #3,4,5,2:431-546
15064 atoms, 15368 bonds, 1856 residues, 4 models selected
> select #8:431-546
3760 atoms, 3836 bonds, 464 residues, 1 model selected
> color sel hot pink
> select #8:668-810
4504 atoms, 4580 bonds, 572 residues, 1 model selected
> color sel purple
> color sel orange
> color sel lime
> color sel cyan
> color sel yellow
> select clear
> hide #!8 models
> show #!7 models
> hide #!7 models
> open 5kuh
5kuh title:
GluK2EM with LY466195 [more info...]
Chain information for 5kuh #9
---
Chain | Description | UniProt
A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
Non-standard residues in 5kuh #9
---
LY5 —
(3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic
acid (LY466195)
> matchmaker #9 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 apo.pdb, chain A (#1) with 5kuh, chain B (#9), sequence alignment
score = 3232.3
RMSD between 352 pruned atom pairs is 0.962 angstroms; (across all 636 pairs:
34.008)
> matchmaker #9/A to #1/A
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 apo.pdb, chain A (#1) with 5kuh, chain A (#9), sequence alignment
score = 3228.7
RMSD between 357 pruned atom pairs is 0.955 angstroms; (across all 636 pairs:
13.413)
> morph #3,4,5,2,9 same true
Computed 201 frame morph #10
> coordset #10 1,201
> select #10
11772 atoms, 11756 bonds, 12 pseudobonds, 2416 residues, 2 models selected
> cartoon hide (#!10 & sel)
> show (#!10 & sel) target ab
> style (#!10 & sel) sphere
Changed 11772 atom styles
> select #8:668-810
4504 atoms, 4580 bonds, 572 residues, 1 model selected
> select #10:668-810
1992 atoms, 1988 bonds, 412 residues, 1 model selected
> color sel orange
> select #10:431-546
1648 atoms, 1640 bonds, 4 pseudobonds, 340 residues, 2 models selected
> color (#!10 & sel) hot pink
> close #10
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> show #!9 models
> show #!7 models
> hide #!7 models
> hide #!9 models
> morph #7, 9 same true
Computed 51 frame morph #10
> coordset #10 1,51
> hide #!10 models
> show #!10 models
> close #10
> matchmaker #9 to #7
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 5kuf, chain A (#7) with 5kuh, chain B (#9), sequence alignment
score = 3408.1
RMSD between 360 pruned atom pairs is 0.988 angstroms; (across all 636 pairs:
33.818)
> show #!7 models
> show #!9 models
> matchmaker #9/A to #7/A
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 5kuf, chain A (#7) with 5kuh, chain A (#9), sequence alignment
score = 3404.5
RMSD between 364 pruned atom pairs is 0.967 angstroms; (across all 636 pairs:
13.205)
> show #!2 models
> cartoon style #2,7,9 modeHelix tube sides 20
> hide #!9 models
> show #!9 models
> hide #!2 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> color #9 #ffaa00 transparency 0
> show #!2 models
> open 6jfy
Summary of feedback from opening 6jfy fetched from pdb
---
note | Fetching compressed mmCIF 6jfy from
http://files.rcsb.org/download/6jfy.cif
6jfy title:
GluK3 receptor trapped in Desensitized state [more info...]
Chain information for 6jfy #10
---
Chain | Description | UniProt
A B C D | Glutamate receptor ionotropic, kainate 3 | GRIK3_RAT
> open 6jfz
6jfz title:
GluK3 receptor complex with UBP310 [more info...]
Chain information for 6jfz #11
---
Chain | Description | UniProt
A B C D | Glutamate receptor ionotropic, kainate 3 | GRIK3_RAT
> matchmaker #10/A to #7/A
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 5kuf, chain A (#7) with 6jfy, chain A (#10), sequence alignment
score = 3217.4
RMSD between 488 pruned atom pairs is 1.307 angstroms; (across all 715 pairs:
2.230)
> matchmaker #10/A to #7/A bring #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 5kuf, chain A (#7) with 6jfy, chain A (#10), sequence alignment
score = 3217.4
RMSD between 488 pruned atom pairs is 1.307 angstroms; (across all 715 pairs:
2.230)
> matchmaker #11/A to #7/A
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 5kuf, chain A (#7) with 6jfz, chain A (#11), sequence alignment
score = 3199.6
RMSD between 260 pruned atom pairs is 1.317 angstroms; (across all 714 pairs:
6.017)
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/All-
> states-all-KARS.cxs
> hide #!9 models
> hide #!2 models
> hide #!10 models
> hide #!11 models
> morph #10,11 same true
Computed 51 frame morph #12
> coordset #12 1,51
> hide #!12 models
> show #!12 models
> cartoon hide #12
> show #12 target ab
> style #12 sphere
Changed 22788 atom styles
> color #12 magenta
> color #12 #ffaa7fff
> hide #!12 models
> morph #10,11 same true warp true
Expected a keyword
> morph #10,11 same true warp true
Expected a keyword
> morph #10,11 same true wrap true
Computed 101 frame morph #13
> coordset #13 1,101
> hide #!13 models
> show #!13 models
> cartoon hide #13
> show #13 target ab
> style #13 sphere
Changed 22788 atom styles
> color #13 blue
> hide #!13 models
> morph #3,4,5,2 same true wrap true
Computed 201 frame morph #14
> coordset #14 1,201
> hide #!14 models
> show #!14 models
> cartoon hide #14
> show #14 target ab
> style #14 sphere
Changed 23920 atom styles
> hide #!14 models
> show #!5 models
> hide #!5 models
> open 7ks0
7ks0 title:
GluK2/K5 with 6-Cyano-7-nitroquinoxaline-2,3-dione (CNQX) [more info...]
Chain information for 7ks0 #15
---
Chain | Description | UniProt
A C | Glutamate receptor ionotropic, kainate 5,Green fluorescent protein
chimera | GFP_AEQVI
B D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
> open 7ks3
7ks3 title:
GluK2/K5 with L-Glu [more info...]
Chain information for 7ks3 #16
---
Chain | Description | UniProt
A C | Glutamate receptor ionotropic, kainate 5,Green fluorescent protein
chimera | GFP_AEQVI
B D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
> matchmaker #16 to #15
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 7ks0, chain A (#15) with 7ks3, chain C (#16), sequence alignment
score = 4896.9
RMSD between 374 pruned atom pairs is 0.607 angstroms; (across all 724 pairs:
8.832)
> color #16 #ff5500 transparency 0
> color #15 #0055ff transparency 0
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> hide #!15 models
> show #!7 models
> hide #!7 models
> matchmaker #16 to #7
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 5kuf, chain B (#7) with 7ks3, chain D (#16), sequence alignment
score = 4002.8
RMSD between 478 pruned atom pairs is 1.087 angstroms; (across all 721 pairs:
2.565)
> show #!7 models
> cartoon style #7,16 modeHelix tube sides 20
> color #16 #00aa7f transparency 0
> set bgColor black
> set bgColor transparent
> matchmaker #15 to #7
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 5kuf, chain A (#7) with 7ks0, chain D (#15), sequence alignment
score = 3961.4
RMSD between 298 pruned atom pairs is 0.929 angstroms; (across all 730 pairs:
42.202)
> show #!15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> matchmaker #15 to #16
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 7ks3, chain C (#16) with 7ks0, chain A (#15), sequence alignment
score = 4896.9
RMSD between 374 pruned atom pairs is 0.607 angstroms; (across all 724 pairs:
8.832)
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> hide #!15 models
> show #!15 models
> show #!9 models
> cartoon style #9,15 modeHelix tube sides 20
> matchmaker #15/A:668-810 to #9/A:668-810
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 5kuh, chain A (#9) with 7ks0, chain A (#15), sequence alignment
score = 364.7
RMSD between 97 pruned atom pairs is 0.883 angstroms; (across all 103 pairs:
1.080)
> hide #!9 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/All-
> states-all-KARS.cxs
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!2 models
> select #2/D:521
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select add #2/D:776
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #2/A:776
28 atoms, 26 bonds, 3 residues, 1 model selected
> select add #2/A:783
36 atoms, 33 bonds, 4 residues, 1 model selected
> show sel target ab
> select add #2/A:787
45 atoms, 41 bonds, 5 residues, 1 model selected
> select add #2/D:696
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel target ab
> color sel byhetero
> open 3g3f
Summary of feedback from opening 3g3f fetched from pdb
---
warnings | Unknown polymer entity '2' near line 9940
Atom OXT is not in the residue template for GLU /A:260
Atom OXT is not in the residue template for GLU /B:260
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
notes | Fetching compressed mmCIF 3g3f from
http://files.rcsb.org/download/3g3f.cif
Fetching CCD IPA from http://ligand-expo.rcsb.org/reports/I/IPA/IPA.cif
3g3f title:
Crystal structure of the GluR6 ligand binding domain dimer with glutamate and
NaCl at 1.38 Angstrom resolution [more info...]
Chain information for 3g3f #17
---
Chain | Description | UniProt
A B | Glutamate receptor, ionotropic kainate 2 | GRIK2_RAT
Non-standard residues in 3g3f #17
---
CL — chloride ion
IPA — isopropyl alcohol (2-propanol)
NA — sodium ion
> hide #!2 models
> view #17
> mathc #17/A to #2/A
Unknown command: mathc #17/A to #2/A
> matchmaker #17/A to #2/A
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 cls1.pdb, chain A (#2) with 3g3f, chain A (#17), sequence alignment
score = 1142.2
RMSD between 206 pruned atom pairs is 1.062 angstroms; (across all 251 pairs:
1.715)
> view #2
> show #!2 models
> cartoon style sel modeHelix tube sides 20
> select #17
8745 atoms, 8231 bonds, 17 pseudobonds, 1095 residues, 3 models selected
> cartoon style (#!17 & sel) modeHelix tube sides 20
> select clear
> hide #!2 models
> show #!2 models
> hide #!17 models
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dynameomics
cls1.pdb #2/A ASP 776: phi -62.6, psi -44.1 trans
Changed 486 bond radii
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Class_comparison/All-
> states-all-KARS.cxs
> show #!17 models
> hide #!17 models
> hide #!2 models
> show #!17 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #17:229
24 atoms, 22 bonds, 2 residues, 1 model selected
> show sel target ab
> show #!2 models
> hide #!17 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom-glyc2.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4.dev202201150102 (2022-01-15)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\nxb318\\\Documents\\\EM_related\\\rGluK2-3m-domoic_acid_processing\\\FROM_EXX\\\cls1_relion\\\cls1_mutations-a.cxs
Opened run_class001-zflip.mrc gaussian as #4, grid size 420,420,420, pixel
1.06, shown at level 0.00815, step 1, values float32
Opened map_wide_target-zflip.mrc as #5, grid size 420,420,420, pixel 1.06,
shown at level 0.227, step 1, values float32
Opened run_class001.mrc as #7, grid size 420,420,420, pixel 1.06, shown at
level 0.00856, step 1, values float32
Opened emdb 8289 as #15, grid size 300,300,300, pixel 1.32, shown at level
0.0337, step 1, values float32
Opened postprocess-zlfip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.0135, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #18, grid size 420,420,420, pixel
1.06, shown at level 0.0143, step 1, values float32
Opened model_real_space_refined_006.pdb map 3.5 as #19, grid size 118,134,190,
pixel 1.17, shown at level 0.1, step 1, values float32
Opened postprocess-zlfip_bfactor-100.mrc as #20, grid size 420,420,420, pixel
1.06, shown at level 0.0121, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #26, grid size 420,420,420, pixel
1.06, shown at level 0.00862, step 1, values float32
Log from Fri Mar 11 14:53:36 2022UCSF ChimeraX version: 1.4.dev202201150102
(2022-01-15)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\nxb318\\\Documents\\\EM_related\\\rGluK2-3m-domoic_acid_processing\\\FROM_EXX\\\cls1_relion\\\cls1_model-
> map-corr-hotspots_dom-glyc2.cxs
Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.0103, step 1, values float32
Opened run_class001-zflip.mrc as #2, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32
Opened run_class001-zflip.mrc gaussian as #4, grid size 420,420,420, pixel
1.06, shown at level 0.00815, step 1, values float32
Opened map_wide_target-zflip.mrc as #5, grid size 420,420,420, pixel 1.06,
shown at level 0.227, step 1, values float32
Opened mask.mrc as #6, grid size 420,420,420, pixel 1.06, shown at level
0.995, step 1, values float32
Opened run_class001.mrc as #7, grid size 420,420,420, pixel 1.06, shown at
level 0.00856, step 1, values float32
Opened run_class001_region_4511.mrc as #9, grid size 106,134,133, pixel 1.06,
shown at level 0.028, step 1, values float32
Opened run_class001_region_4508.mrc as #10, grid size 58,55,70, pixel 1.06,
shown at level 0.0175, step 1, values float32
Opened run_class001_region_4496.mrc as #11, grid size 101,98,112, pixel 1.06,
shown at level 0.0157, step 1, values float32
Opened run_class001_region_4510.mrc as #12, grid size 59,52,70, pixel 1.06,
shown at level 0.0174, step 1, values float32
Opened emdb 8289 as #15, grid size 300,300,300, pixel 1.32, shown at level
0.0337, step 1, values float32
Opened postprocess-zlfip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.0135, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #18, grid size 420,420,420, pixel
1.06, shown at level 0.013, step 1, values float32
Opened model_real_space_refined_006.pdb map 3.5 as #19, grid size 118,134,190,
pixel 1.17, shown at level 0.1, step 1, values float32
Opened postprocess-zlfip_bfactor-100.mrc as #20, grid size 420,420,420, pixel
1.06, shown at level 0.0121, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #26, grid size 420,420,420, pixel
1.06, shown at level 0.00862, step 1, values float32
Log from Wed Mar 2 11:50:47 2022UCSF ChimeraX version: 1.4.dev202201150102
(2022-01-15)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\nxb318\\\Documents\\\EM_related\\\rGluK2-3m-domoic_acid_processing\\\FROM_EXX\\\cls1_relion\\\cls1_model-
> map-corr-hotspots_dom-glyc1.cxs
Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.0103, step 1, values float32
Opened run_class001-zflip.mrc as #2, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32
Opened run_class001-zflip.mrc gaussian as #4, grid size 420,420,420, pixel
1.06, shown at level 0.00815, step 1, values float32
Opened map_wide_target-zflip.mrc as #5, grid size 420,420,420, pixel 1.06,
shown at level 0.227, step 1, values float32
Opened mask.mrc as #6, grid size 420,420,420, pixel 1.06, shown at level
0.995, step 1, values float32
Opened run_class001.mrc as #7, grid size 420,420,420, pixel 1.06, shown at
level 0.00856, step 1, values float32
Opened run_class001_region_4511.mrc as #9, grid size 106,134,133, pixel 1.06,
shown at level 0.028, step 1, values float32
Opened run_class001_region_4508.mrc as #10, grid size 58,55,70, pixel 1.06,
shown at level 0.0175, step 1, values float32
Opened run_class001_region_4496.mrc as #11, grid size 101,98,112, pixel 1.06,
shown at level 0.0157, step 1, values float32
Opened run_class001_region_4510.mrc as #12, grid size 59,52,70, pixel 1.06,
shown at level 0.0174, step 1, values float32
Opened emdb 8289 as #15, grid size 300,300,300, pixel 1.32, shown at level
0.0337, step 1, values float32
Opened postprocess-zlfip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.0135, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #18, grid size 420,420,420, pixel
1.06, shown at level 0.013, step 1, values float32
Opened model_real_space_refined_006.pdb map 3.5 as #19, grid size 118,134,190,
pixel 1.17, shown at level 0.1, step 1, values float32
Opened postprocess-zlfip_bfactor-100.mrc as #20, grid size 420,420,420, pixel
1.06, shown at level 0.0121, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #26, grid size 420,420,420, pixel
1.06, shown at level 0.00862, step 1, values float32
Log from Fri Dec 17 13:58:26 2021UCSF ChimeraX version: 1.3.dev202109080319
(2021-09-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom.cxs
Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.0103, step 1, values float32
Opened run_class001-zflip.mrc as #2, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32
Opened run_class001-zflip.mrc gaussian as #4, grid size 420,420,420, pixel
1.06, shown at level 0.00815, step 1, values float32
Opened map_wide_target-zflip.mrc as #5, grid size 420,420,420, pixel 1.06,
shown at level 0.227, step 1, values float32
Opened mask.mrc as #6, grid size 420,420,420, pixel 1.06, shown at level
0.995, step 1, values float32
Opened run_class001.mrc as #7, grid size 420,420,420, pixel 1.06, shown at
level 0.00856, step 1, values float32
Opened run_class001_region_4511.mrc as #9, grid size 106,134,133, pixel 1.06,
shown at level 0.028, step 1, values float32
Opened run_class001_region_4508.mrc as #10, grid size 58,55,70, pixel 1.06,
shown at level 0.0175, step 1, values float32
Opened run_class001_region_4496.mrc as #11, grid size 101,98,112, pixel 1.06,
shown at level 0.0157, step 1, values float32
Opened run_class001_region_4510.mrc as #12, grid size 59,52,70, pixel 1.06,
shown at level 0.0174, step 1, values float32
Opened emdb 8289 as #15, grid size 300,300,300, pixel 1.32, shown at level
0.0337, step 1, values float32
Opened postprocess-zlfip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.0135, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #18, grid size 420,420,420, pixel
1.06, shown at level 0.0133, step 1, values float32
Opened model_real_space_refined_006.pdb map 3.5 as #19, grid size 118,134,190,
pixel 1.17, shown at level 0.1, step 1, values float32
Opened postprocess-zlfip_bfactor-100.mrc as #20, grid size 420,420,420, pixel
1.06, shown at level 0.0121, step 1, values float32
Opened postprocess-zlfip.mrc gaussian as #26, grid size 420,420,420, pixel
1.06, shown at level 0.00862, step 1, values float32
Log from Wed Dec 15 15:42:50 2021UCSF ChimeraX version: 1.3.dev202109080319
(2021-09-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> KNISRKPGNVLKTLDPILITIIAMSALGVLLGAVCGVVLYCACWHNGMSERNLSALENYNFELVDGVKLKKDKLNTQSTYSEA
Running AlphaFold prediction
[Repeated 5 time(s)]
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001.mrc
Opened run_class001.mrc as #1, grid size 420,420,420, pixel 1.06, shown at
level 0.0073, step 2, values float32
> lighting soft
> volume #1 step 1
> volume #1 level 0.01378
> close
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001-zflip.mrc
Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J069/run_class001-zflip.mrc
Opened run_class001-zflip.mrc as #2, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32
> volume #1 step 1
> volume #1 level 0.01385
> open 5kuf
5kuf title:
GluK2EM with 2S,4R-4-methylglutamate [more info...]
Chain information for 5kuf #3
---
Chain | Description | UniProt
A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
Non-standard residues in 5kuf #3
---
SYM — 2S,4R-4-methylglutamate
> select /D:257
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,1.828,0,1,0,3.2622,0,0,1,36.727
> view matrix models #3,1,0,0,25.225,0,1,0,17.775,0,0,1,36.252
> view matrix models #3,1,0,0,26.83,0,1,0,27.253,0,0,1,35.153
> volume gaussian #0 sDev3
Expected a keyword
> volume gaussian #0 sDev 3
[Repeated 1 time(s)]
> volume gaussian #0 sDev3
Expected a keyword
> volume gaussian #0 sDev2
Expected a keyword
> volume gaussian #0 sDev 2
> volume gaussian #1 sDev 3
Opened run_class001-zflip.mrc gaussian as #4, grid size 420,420,420, pixel
1.06, shown at step 1, values float32
> ui tool show "Fit in Map"
Fit molecule 5kuf (#3) to map run_class001-zflip.mrc gaussian (#4) using 23728
atoms
average map value = 0.01334, steps = 140
shifted from previous position = 1.95
rotated from previous position = 16.4 degrees
atoms outside contour = 943, contour level = 0.0081455
Position of 5kuf (#3) relative to run_class001-zflip.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.96348453 0.26449551 0.04170951 -27.69856620
-0.26719499 0.95985080 0.08540068 70.25952441
-0.01744681 -0.09342681 0.99547327 60.04897916
Axis -0.31703139 0.10487430 -0.94259879
Axis point 250.60948183 187.80794280 0.00000000
Rotation angle (degrees) 16.38165949
Shift along axis -40.45236161
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/map_wide_target-
> zflip.mrc
Opened map_wide_target-zflip.mrc as #5, grid size 420,420,420, pixel 1.06,
shown at level -0.00608, step 2, values float32
> volume #5 step 1
> volume #5 level 0.326
> volume #5 level 0.3019
> ui tool show "Hide Dust"
> surface dust #5 size 6.36
> select ligand
44 atoms, 40 bonds, 4 residues, 1 model selected
> select ::name="ASN"
928 atoms, 812 bonds, 116 residues, 1 model selected
> select ::name="SER"
1392 atoms, 1192 bonds, 232 residues, 1 model selected
> volume #5 level 0.2273
> hide #!3 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/mask.mrc
Opened mask.mrc as #6, grid size 420,420,420, pixel 1.06, shown at level 1,
step 2, values float32
> volume #6 level 0.9948
> volume #6 step 1
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001.mrc
Opened run_class001.mrc as #7, grid size 420,420,420, pixel 1.06, shown at
level 0.0073, step 2, values float32
> volume #7 step 1
> ui tool show "Segment Map"
Segmenting run_class001.mrc, density threshold 0.007301
Only showing 60 of 77 regions.
Showing 60 of 77 region surfaces
4410 watershed regions, grouped to 77 regions
Showing run_class001.seg - 77 regions, 60 surfaces
Segmenting run_class001.mrc, density threshold 0.007301
Showing 19 region surfaces
4410 watershed regions, grouped to 19 regions
Showing run_class001.seg - 19 regions, 19 surfaces
> volume #7 level 0.008563
Segmenting run_class001.mrc, density threshold 0.008563
Only showing 60 of 508 regions.
Showing 60 of 508 region surfaces
3986 watershed regions, grouped to 508 regions
Showing run_class001.seg - 508 regions, 60 surfaces
Segmenting run_class001.mrc, density threshold 0.008563
Showing 19 region surfaces
3986 watershed regions, grouped to 19 regions
Showing run_class001.seg - 19 regions, 19 surfaces
Segmenting run_class001.mrc, density threshold 0.008563
Showing 4 region surfaces
3986 watershed regions, grouped to 4 regions
Showing run_class001.seg - 4 regions, 4 surfaces
Segmenting run_class001.mrc, density threshold 0.008563
Only showing 60 of 3803 regions.
Showing 60 of 3803 region surfaces
Showing 4 region surfaces
3803 watershed regions, grouped to 4 regions
Showing run_class001.seg - 4 regions, 4 surfaces
> select clear
Segmenting run_class001.mrc, density threshold 0.008563
Showing 4 region surfaces
3986 watershed regions, grouped to 4 regions
Showing run_class001.seg - 4 regions, 4 surfaces
Ungrouped to 4 regions
> select clear
Ungrouped to 5 regions
Ungrouped to 2 regions
Grouped 2 regions
[Repeated 1 time(s)]Grouped 3 regions
> select clear
Grouped 2 regions
> select clear
Grouped 4 regions
> select clear
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001.seg
> models #8
Saving 1 regions to mrc file...
Opened run_class001_region_4511.mrc as #9, grid size 106,134,133, pixel 1.06,
shown at step 1, values float32
Wrote run_class001_region_4511.mrc
Saving 1 regions to mrc file...
Opened run_class001_region_4508.mrc as #10, grid size 58,55,70, pixel 1.06,
shown at step 1, values float32
Wrote run_class001_region_4508.mrc
Saving 1 regions to mrc file...
Opened run_class001_region_4496.mrc as #11, grid size 101,98,112, pixel 1.06,
shown at step 1, values float32
Wrote run_class001_region_4496.mrc
Saving 1 regions to mrc file...
Opened run_class001_region_4510.mrc as #12, grid size 59,52,70, pixel 1.06,
shown at step 1, values float32
Wrote run_class001_region_4510.mrc
Segmenting run_class001.mrc, density threshold 0.008563
Showing 4 region surfaces
3986 watershed regions, grouped to 4 regions
Showing run_class001.seg - 4 regions, 4 surfaces
Segmenting mask.mrc, density threshold 0.994821
Showing 4 region surfaces
1521906 watershed regions, grouped to 4 regions
Showing mask.seg - 4 regions, 4 surfaces
Chain information for best_model.pdb #13
---
Chain | Description
A | No description available
AlphaFold prediction finished
Results in C:\Users\nxb318/Downloads\ChimeraX\AlphaFold\prediction_7
> ui tool show "Volume Viewer"
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> hide #13 models
> close #13
> hide #!8 models
> show #!8 models
> hide #8.1 models
> show #8.1 models
> hide #8.1 models
> show #8.1 models
> hide #8.1 models
> show #8.1 models
> hide #8.1 models
> show #8.1 models
> close #8
> hide #!6 models
> show #!1 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> 5kuf
Unknown command: 5kuf
> open 5kuf
5kuf title:
GluK2EM with 2S,4R-4-methylglutamate [more info...]
Chain information for 5kuf #8
---
Chain | Description | UniProt
A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT
Non-standard residues in 5kuf #8
---
SYM — 2S,4R-4-methylglutamate
> hide #!8 models
> color #8 white
> color #3 yellow
> show #!3 models
> select #1
2 models selected
> transparency sel 50
> select clear
> hide #!1 models
> select #3/B:397
8 atoms, 7 bonds, 1 residue, 1 model selected
> select B:356
Expected an objects specifier or a keyword
> interfaces sel /A,B contacting /C,D
Expected a keyword
> interfaces sel /A,B contacting /C,D
Expected a keyword
> interfaces sel #3 /A,B contacting /C,D
Expected a keyword
> select sequence AACA
Nothing selected
> select B:396
Expected an objects specifier or a keyword
> select B/396
Expected an objects specifier or a keyword
> select #3
23728 atoms, 24248 bonds, 8 pseudobonds, 3004 residues, 2 models selected
> ~select:/isHelix
Unknown command: ~select:/isHelix
> ~select :/isHelix
> select subtract :/isHelix
Expected an objects specifier or a keyword
> select :/isHelix
Expected an objects specifier or a keyword
> select #3 :/isHelix
Expected a keyword
> ~select #3 :/isHelix
> select subtract #3 :/isHelix
Expected a keyword
> select clear
> show #!1 models
> material transparentCastShadows true
> help select
> select #3
23728 atoms, 24248 bonds, 8 pseudobonds, 3004 residues, 2 models selected
> select clear
> select #3/A
5932 atoms, 6062 bonds, 2 pseudobonds, 751 residues, 2 models selected
> select clear
> select #3/A:422
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:396-514
962 atoms, 981 bonds, 119 residues, 1 model selected
> select #3/B:400-514
934 atoms, 953 bonds, 115 residues, 1 model selected
> select #3/B:696
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:696
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #3/B:400-514
934 atoms, 953 bonds, 115 residues, 1 model selected
> select add #3/B:692
943 atoms, 961 bonds, 116 residues, 1 model selected
> select add #3/B:637-775
2029 atoms, 2067 bonds, 254 residues, 1 model selected
> color sel blue
> color sel orange
> color sel red
> select #3/B:400-514
934 atoms, 953 bonds, 115 residues, 1 model selected
> 637-775
Unknown command: 637-775
> select #3/B:400-514,637-775
2029 atoms, 2067 bonds, 254 residues, 1 model selected
> select clear
> select #3/C:400-514,637-775
2029 atoms, 2067 bonds, 254 residues, 1 model selected
> select #3/B:400-514,637-775
2029 atoms, 2067 bonds, 254 residues, 1 model selected
> select #3/B,D:400-514,637-775
4058 atoms, 4134 bonds, 508 residues, 1 model selected
> hide #!3 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/RealSpaceRefine_3/aligned_model_real_space_refined_003a.pdb
Chain information for aligned_model_real_space_refined_003a.pdb #13
---
Chain | Description
A B C D | No description available
> select #13/D:805
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.53992,0.83534,0.10343,-119.76,0.84119,-0.53983,-0.031232,183.76,0.029747,0.10387,-0.99415,450.85
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.53992,0.83534,0.10343,-151.14,0.84119,-0.53983,-0.031232,159.45,0.029747,0.10387,-0.99415,458.24
> view matrix models
> #13,0.53992,0.83534,0.10343,-149.85,0.84119,-0.53983,-0.031232,154.59,0.029747,0.10387,-0.99415,434.55
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.91977,0.37983,0.098752,-130.11,0.38833,-0.91721,-0.08898,380.38,0.056779,0.12019,-0.99113,422.76
> view matrix models
> #13,0.96031,0.27126,0.06504,-104.69,0.27316,-0.96171,-0.022211,404.92,0.056525,0.039095,-0.99764,445.01
> view matrix models
> #13,0.93847,0.3383,0.06954,-117.24,0.34099,-0.93956,-0.031006,384.08,0.054847,0.05281,-0.9971,441.83
> view matrix models
> #13,0.93908,0.34151,-0.038785,-91.871,0.33724,-0.93731,-0.087859,398.29,-0.066358,0.069427,-0.99538,468.19
> show #!4 models
> ui tool show "Fit in Map"
Fit molecule aligned_model_real_space_refined_003a.pdb (#13) to map
run_class001-zflip.mrc gaussian (#4) using 23660 atoms
average map value = 0.01329, steps = 84
shifted from previous position = 7.06
rotated from previous position = 2.82 degrees
atoms outside contour = 1017, contour level = 0.0081455
Position of aligned_model_real_space_refined_003a.pdb (#13) relative to
run_class001-zflip.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.92482441 0.37323340 -0.07346162 -88.15314091
0.36673559 -0.92611813 -0.08837530 388.57975343
-0.10101875 0.05479065 -0.99337463 487.28837345
Axis 0.98100053 0.18882679 -0.04452423
Axis point 0.00000000 193.72922142 249.00159772
Rotation angle (degrees) 175.81544494
Shift along axis -34.80015073
> hide #!4 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/RealSpaceRefine_14/aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb
Chain information for
aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb #14
---
Chain | Description
A B C D | No description available
> color #14 #636073
> color #14 #734830
Fit molecule
aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb (#14)
to map run_class001-zflip.mrc gaussian (#4) using 23660 atoms
average map value = 0.01326, steps = 60
shifted from previous position = 0.992
rotated from previous position = 1.58 degrees
atoms outside contour = 961, contour level = 0.0081455
Position of
aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb (#14)
relative to run_class001-zflip.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.99986415 0.01546082 0.00571314 -4.27698970
-0.01558334 0.99963513 0.02206286 -1.69477296
-0.00536995 -0.02214889 0.99974026 5.55607469
Axis -0.80169906 0.20097158 -0.56292899
Axis point -0.00000000 248.90445133 80.57293940
Rotation angle (degrees) 1.58006147
Shift along axis -0.03941810
> hide #!13 models
> set bgColor white
> set bgColor black
> select #14/A:657
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #14/A:456
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #14/A:656
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #14/A:456
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #14/A:689
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #14/A:459
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #14/A:409
37 atoms, 32 bonds, 5 residues, 1 model selected
> select add #14/A:491
44 atoms, 38 bonds, 6 residues, 1 model selected
> select add #14/A:458
48 atoms, 41 bonds, 7 residues, 1 model selected
> select add #14/A:457
60 atoms, 53 bonds, 8 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> set bgColor white
> show #!3 models
> hide #!14 models
> show #!14 models
> ui tool show "Side View"
> hide #!3 models
> show #!3 models
> hide #!14 models
> select ligand
88 atoms, 80 bonds, 8 residues, 2 models selected
> volume #1 level 0.01719
> set bgColor black
> color (#!3 & sel) blue
> color (#!3 & sel) hot pink
> color (#!3 & sel) white
> lighting soft
[Repeated 1 time(s)]
> open 8289 from EMDB
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 71, in cmd_open
provider_args = mgr.fetch_args(fetches[0][1], format_name=fetches[0][2])
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\open_command\manager.py", line 170, in fetch_args
args.update(provider_info.bundle_info.run_provider(self.session,
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1287, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\map\\__init__.py", line 147, in run_provider
class Info(OpenerInfo):
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\map\\__init__.py", line 149, in Info
_name=session.data_formats[name].nicknames[0], **kw):
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\data_formats\manager.py", line 140, in __getitem__
raise KeyError("No known data format '%s'" % key)
KeyError: "No known data format 'EMDB'"
KeyError: "No known data format 'EMDB'"
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\data_formats\manager.py", line 140, in __getitem__
raise KeyError("No known data format '%s'" % key)
See log for complete Python traceback.
> open 8289 fromDatabase emdb
Summary of feedback from opening 8289 fetched from emdb
---
note | Fetching compressed map 8289 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-8289/map/emd_8289.map.gz
Opened emdb 8289 as #15, grid size 300,300,300, pixel 1.32, shown at level
0.0211, step 2, values float32
> hide #!3 models
> hide #!1 models
> volume #15 step 1
> ui tool show "Hide Dust"
> surface dust #15 size 7.94
> volume #15 level 0.03371
> lighting soft
Fit map emdb 8289 in map run_class001-zflip.mrc gaussian using 83452 points
correlation = 0.9636, correlation about mean = 0.4287, overlap = 53.61
steps = 356, shift = 52.8, angle = 16.7 degrees
Position of emdb 8289 (#15) relative to run_class001-zflip.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.96208415 0.26912308 0.04434923 -28.98690147
-0.27206070 0.95844814 0.08579124 71.42727634
-0.01941803 -0.09460407 0.99532558 60.83184094
Axis -0.31427152 0.11109065 -0.94281084
Axis point 249.98231173 189.99831084 0.00000000
Rotation angle (degrees) 16.67876411
Shift along axis -40.30825871
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!3 models
> select #15
3 models selected
> transparency sel 50
> select clear
> select ligand
88 atoms, 80 bonds, 8 residues, 2 models selected
> show #!14 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!15 models
> show #!1 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!15 models
> hide #!1 models
> show #!1 models
> show #!3 models
> select clear
> hide #!15 models
> volume #1 level 0.01311
> volume #1 level 0.01367
> show #!8 models
> hide #!8 models
> show #!15 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> volume #1 level 0.01459
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!3 models
> hide #!1 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/run_class001-zflip.mrc
Opened run_class001-zflip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.00802, step 2, values float32
> volume #16 step 1
> volume #16 level 0.01418
> close #16
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/postprocess-
> zlfip.mrc
Opened postprocess-zlfip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.00798, step 2, values float32
> volume #16 step 1
> volume #16 color #fcff4e
> volume #16 level 0.01342
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/Swissprot/swissmodel/cls1_LBDdimer/model_real_space_refined_006.pdb
Chain information for model_real_space_refined_006.pdb #17
---
Chain | Description
A B C D | No description available
> select #16
2 models selected
> transparency sel 50
> select clear
> volume #16 level 0.0135
> volume gaussian #16 bfactor-50
Expected a keyword
> volume gaussian #16 Bfactor-50
Expected a keyword
> volume gaussian #16 bFactor-50
Expected a keyword
> select #16
2 models selected
> volume gaussian #16 bFactor-50
Expected a keyword
> volume gaussian #16 bactor-50
Expected a keyword
> volume gaussian #16 bfactor-50
Expected a keyword
> volume gaussian #16 bfactor -50
Opened postprocess-zlfip.mrc gaussian as #18, grid size 420,420,420, pixel
1.06, shown at step 1, values float32
> select #18
2 models selected
> transparency sel 50
> volume #18 level 0.01392
> select #17/D:723
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> slect #17:721-730
Unknown command: slect #17:721-730
> select #17:721-730
320 atoms, 316 bonds, 40 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> volume #18 level 0.01531
> molmap #17
Missing or invalid "resolution" argument: Expected a number
> molmap #17 3.5A
Missing or invalid "resolution" argument: Expected a number
> molmap #17 3.5 A
Expected a keyword
> molmap #17 3.5
Opened model_real_space_refined_006.pdb map 3.5 as #19, grid size 118,134,190,
pixel 1.17, shown at level 0.1, step 1, values float32
> hide #17 models
> select #19
2 models selected
> hide #!18 models
> show #17 models
> show #!18 models
> hide #!19 models
> select #17
25552 atoms, 26152 bonds, 3224 residues, 1 model selected
> style sel sphere
Changed 25552 atom styles
> undo
> cartoon style sel modeHelix tube sides 20
> hide #!18 models
> select clear
> select #17:424-427
116 atoms, 112 bonds, 16 residues, 1 model selected
> color sel hot pink
> show #!19 models
> hide #!19 models
> show #!18 models
> volume #18 level 0.01297
> hide #!18 models
> show #!18 models
> select clear
> select #17/A:379
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #17/A:380
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #17/C:380
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #17:380
28 atoms, 24 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> color sel red
> style sel ball
Changed 28 atom styles
> volume #18 level 0.01392
> select #17/C:275
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17:275
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel red
> style sel ball
Changed 32 atom styles
> show (sel-residues & sidechain) target ab
> volume #18 level 0.00976
> volume #18 level 0.0134
> show #!16 models
> hide #!18 models
> select #17:492-496
140 atoms, 136 bonds, 20 residues, 1 model selected
> color sel red
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 140 atom styles
> select #17/D:771
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #17/D:772
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #17/D:771
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #17/D:770
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #17/D:769
25 atoms, 22 bonds, 4 residues, 1 model selected
> color sel red
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 25 atom styles
> select #17:769-772
100 atoms, 100 bonds, 16 residues, 1 model selected
> hide #!16 models
> show #!18 models
> volume #18 level 0.01644
> style sel ball
Changed 100 atom styles
> show (sel-residues & sidechain) target ab
> color sel yellow
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots.cxs includeMaps true
> volume #18 level 0.01418
> volume gaussian #16 bfactor -150
Opened postprocess-zlfip.mrc gaussian as #20, grid size 420,420,420, pixel
1.06, shown at step 1, values float32
> select #20
2 models selected
> transparency sel 50
> volume #20 level 0.01406
> hide #!18 models
> select #17/A:715
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #17/B:760
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #17/A:715
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide #!20 models
> show #!20 models
> ui tool show "Hide Dust"
> surface dust #20 size 6.36
> help help:user/tools/modelpanel.html
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/postprocess-
> zlfip_bfactor-100.mrc models #20
> select #17/D:531
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 9 atom styles
> select #17/D:523
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 11 atom styles
> volume #20 level 0.01211
> hide #!20 models
> show #!19 models
> hide #!19 models
> show #!18 models
> show #!12 models
> hide #!12 models
> select #17:771
16 atoms, 12 bonds, 4 residues, 1 model selected
> select clear
> select #17/D:771
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel ball
Changed 4 atom styles
> view matrix models
> #17,0.99675,-0.01814,-0.078475,22.218,0.021101,0.99909,0.037074,-12.723,0.077731,-0.03861,0.99623,-7.9766
> hide #!18 models
> hide #17 models
> show #17 models
> show #!18 models
> ui tool show "Fit in Map"
Fit molecule model_real_space_refined_006.pdb (#17) to map postprocess-
zlfip.mrc gaussian (#18) using 25552 atoms
average map value = 0.01868, steps = 148
shifted from previous position = 1.95
rotated from previous position = 5.12 degrees
atoms outside contour = 7479, contour level = 0.014184
Position of model_real_space_refined_006.pdb (#17) relative to postprocess-
zlfip.mrc gaussian (#18) coordinates:
Matrix rotation and translation
0.99999993 -0.00019749 0.00032083 -0.04514043
0.00019754 0.99999997 -0.00015763 -0.00363414
-0.00032080 0.00015769 0.99999994 -0.01422802
Axis 0.38603990 0.78554480 0.48362441
Axis point -3.42520476 0.00000000 108.01509991
Rotation angle (degrees) 0.02339956
Shift along axis -0.02716181
> select #17:777
36 atoms, 32 bonds, 4 residues, 1 model selected
> color sel cyan
> style sel ball
Changed 36 atom styles
> show sel target ab
> hide #!18 models
> select #17:423-426
124 atoms, 120 bonds, 16 residues, 1 model selected
> show sel target ab
> select clear
> select #17:776
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel cyan
> show sel target ab
> style sel ball
Changed 32 atom styles
> show #!20 models
> hide #!20 models
> show #!18 models
> select clear
> ui tool show "Side View"
> hide #17 models
> show #17 models
> hide #!18 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots.cxs includeMaps true
> open 1YAE
Summary of feedback from opening 1YAE fetched from pdb
---
notes | Fetching compressed mmCIF 1yae from
http://files.rcsb.org/download/1yae.cif
Fetching CCD FUC from http://ligand-expo.rcsb.org/reports/F/FUC/FUC.cif
Fetching CCD DOQ from http://ligand-expo.rcsb.org/reports/D/DOQ/DOQ.cif
1yae title:
Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain
Complexed with Domoic Acid [more info...]
Chain information for 1yae #21
---
Chain | Description
A B C D E F | Glutamate receptor, ionotropic kainate 2
Non-standard residues in 1yae #21
---
DOQ —
(2S,3S,4S)-2-carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadienyl]-3-pyrrolidineacetic
acid ((2S,3S,4S)-3-carboxymethyl-4-[(1Z,3E,5R)-5-carboxy-1-methyl-
hexa-1,3-dienyl]-pyrrolidine-2-carboxylic acid; domoic acid)
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
1yae mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
6| author_and_software_defined_assembly
7| software_defined_assembly
8| software_defined_assembly
9| software_defined_assembly
> view #21
> select #21/B:543@CG
1 atom, 1 residue, 1 model selected
> select #21
12512 atoms, 12663 bonds, 10 pseudobonds, 1616 residues, 2 models selected
> hide (#!21 & sel) target a
> style (#!21 & sel) ball
Changed 12512 atom styles
> show (#!21 & sel) target ab
> cartoon (#!21 & sel)
> hide (#!21 & sel) target a
> select ligand
370 atoms, 363 bonds, 25 residues, 3 models selected
> select #21
12512 atoms, 12663 bonds, 10 pseudobonds, 1616 residues, 2 models selected
> hide (#!21 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!21 & sel-residues)
> show (#!21 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> show (#!21 & sel-residues & sidechain) target ab
> cartoon (#!21 & sel)
> hide (#!21 & sel) target a
> ui tool show "Show Sequence Viewer"
> sequence chain #21/A
Alignment identifier is 21/A
> select clear
> select
> #21/A:454-457,461-475,500-507,520-526,670-676,688-697,699-717,720-731,739-747,774-800
962 atoms, 968 bonds, 118 residues, 1 model selected
> close #21
> view #17
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb
Chain information for G2-LBD-domoat-xray-1YAE.pdb #21
---
Chain | Description
F | No description available
> matchmaker #21 to #17/B
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 model_real_space_refined_006.pdb, chain B (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 845.8
RMSD between 193 pruned atom pairs is 1.055 angstroms; (across all 226 pairs:
3.524)
> show #!1 models
> hide #17 models
> hide #!1 models
> show #17 models
> matchmaker #21 to #17/C
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 model_real_space_refined_006.pdb, chain C (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 883.6
RMSD between 210 pruned atom pairs is 1.121 angstroms; (across all 226 pairs:
1.340)
> hide #17 models
> show #17 models
> select #21/F:1603@CAS
1 atom, 1 residue, 1 model selected
> select ligand
110 atoms, 102 bonds, 9 residues, 3 models selected
> color (#!21 & sel) yellow
> color (#!21 & sel) byelement
> hide #17 models
> show #!1 models
> transparency #1.1 0
> view matrix models
> #3,0.9505,0.30702,0.047804,-33.515,-0.31035,0.94553,0.098206,78.621,-0.015049,-0.10818,0.99402,62.281,#8,0.99899,0.044806,0.0023207,-9.1322,-0.044836,0.99888,0.014838,6.3071,-0.0016533,-0.014927,0.99989,3.2421,#21,0.97221,0.23269,-0.025747,-11.035,-0.22439,0.95756,0.18093,39.791,0.066755,-0.17013,0.98316,55.135
> hide #!1 models
> show #17 models
> matchmaker #21 to #17/C
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 model_real_space_refined_006.pdb, chain C (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 883.6
RMSD between 210 pruned atom pairs is 1.121 angstroms; (across all 226 pairs:
1.340)
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/domoat.pdb
> matchmaker #22 to #21
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align #22 toAtoms #21
Unequal number of atoms to pair, 22 and 1837
> align #22 toAtoms sele
Invalid "toAtoms" argument: invalid atoms specifier
> align #22 toAtoms #21/F DOQ
Expected a keyword
> align #22 toAtoms #21/F
Unequal number of atoms to pair, 22 and 1837
> select #17/C:488
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #!1 models
> hide #!1 models
> show #!18 models
> hide #!18 models
> show #!18 models
> select #18
3 models selected
> transparency sel 0
> select clear
> transparency #18.1 50
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb
Chain information for G2-LBD-domoat-xray-1YAE.pdb #23
---
Chain | Description
F | No description available
> color #21 #565711
> color #21 #a9ab21
> color #21 #b3b523
> color #21 #a8b515
> color #21 #b5aa14
> color #21 #d3c617
> color #23 #d3c617
> matchmaker #23 to #17/D
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 model_real_space_refined_006.pdb, chain D (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#23), sequence alignment score = 838
RMSD between 158 pruned atom pairs is 1.348 angstroms; (across all 226 pairs:
4.630)
> volume #18 level 0.0133
> hide #!18 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom.cxs includeMaps true
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb
Chain information for G2-LBD-domoat-xray-1YAE.pdb #24
---
Chain | Description
F | No description available
> color #24 #d3c617
> matchmaker #24 to #17/B
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 model_real_space_refined_006.pdb, chain B (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#24), sequence alignment score = 845.8
RMSD between 193 pruned atom pairs is 1.055 angstroms; (across all 226 pairs:
3.524)
> show #!8 models
> hide #17 models
> show #17 models
> matchmaker #8 to #17
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 model_real_space_refined_006.pdb, chain C (#17) with 5kuf, chain A
(#8), sequence alignment score = 3831.8
RMSD between 523 pruned atom pairs is 1.112 angstroms; (across all 749 pairs:
2.536)
> hide #17 models
> hide #!21 models
> show #!21 models
> hide #!23 models
> show #!23 models
> show #17 models
> hide #!8 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb
Chain information for G2-LBD-domoat-xray-1YAE.pdb #25
---
Chain | Description
F | No description available
> color #25 #d3c617
> matchmaker #25 to #17/A
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 model_real_space_refined_006.pdb, chain A (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#25), sequence alignment score = 869.8
RMSD between 219 pruned atom pairs is 0.920 angstroms; (across all 226 pairs:
1.106)
> matchmaker #24 to #17/B
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 model_real_space_refined_006.pdb, chain B (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#24), sequence alignment score = 845.8
RMSD between 193 pruned atom pairs is 1.055 angstroms; (across all 226 pairs:
3.524)
> matchmaker #21 to #17/C
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 model_real_space_refined_006.pdb, chain C (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 883.6
RMSD between 210 pruned atom pairs is 1.121 angstroms; (across all 226 pairs:
1.340)
> matchmaker #23 to #17/D
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 model_real_space_refined_006.pdb, chain D (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#23), sequence alignment score = 838
RMSD between 158 pruned atom pairs is 1.348 angstroms; (across all 226 pairs:
4.630)
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-win_amd64.whl
> show #!15 models
> hide #17 models
> hide #!15 models
> hide #!24 models
> hide #!25 models
> hide #!23 models
> hide #22 models
> hide #!21 models
> show #!1 models
> hide #!1 models
> show #!8 models
> show #!15 models
> select ligand
176 atoms, 168 bonds, 12 residues, 6 models selected
> volume #1 level 0.01477
> view matrix models
> #3,0.96314,0.26892,0.0066141,-21.211,-0.26899,0.96303,0.014993,82.446,-0.0023377,-0.016219,0.99987,40.665,#8,0.98287,0.18433,-0.0004728,-9.2607,-0.18432,0.98284,0.0069539,62.021,0.0017465,-0.0067476,0.99998,37.748,#21,0.98512,0.15259,-0.079136,11.159,-0.14642,0.98609,0.078714,38.684,0.090046,-0.065956,0.99375,28.177,#23,0.80596,0.22886,-0.54594,84.525,0.033016,0.90343,0.42746,-17.357,0.59105,-0.36254,0.72057,25.781,#24,0.1117,-0.99345,0.024262,396.54,0.99374,0.11167,-0.002869,-1.7422,0.00014099,0.02443,0.9997,31.465,#25,-0.98568,-0.16861,-0.0037711,456.76,0.16678,-0.97784,0.12657,358.64,-0.025028,0.12413,0.99195,23.062
> select clear
> volume gaussian #16 sDev 2
Opened postprocess-zlfip.mrc gaussian as #26, grid size 420,420,420, pixel
1.06, shown at step 1, values float32
> ui tool show "Fit in Map"
Fit molecule 5kuf (#8) to map postprocess-zlfip.mrc gaussian (#26) using 23728
atoms
average map value = 0.01479, steps = 116
shifted from previous position = 4.4
rotated from previous position = 7.36 degrees
atoms outside contour = 1936, contour level = 0.0086179
Position of 5kuf (#8) relative to postprocess-zlfip.mrc gaussian (#26)
coordinates:
Matrix rotation and translation
0.96460927 0.25873376 0.05085074 -28.87980803
-0.26254876 0.96030068 0.09429080 66.90198132
-0.02443579 -0.10430458 0.99424516 63.57505245
Axis -0.35281467 0.13375031 -0.92608459
Axis point 244.92423035 199.30981971 0.00000000
Rotation angle (degrees) 16.34642612
Shift along axis -39.73849567
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_cryosparc/cls2_highRes-
> zflip.mrc
Opened cls2_highRes-zflip.mrc as #27, grid size 420,420,420, pixel 1.06, shown
at level -0.026, step 2, values float32
> volume #27 step 1
> volume #27 level 0.006917
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!15 models
> hide #!8 models
> show #17 models
> close #27
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_cryosparc/cryosparc_P1_J3_004_volume_map-
> zflip.mrc
Opened cryosparc_P1_J3_004_volume_map-zflip.mrc as #27, grid size 420,420,420,
pixel 1.06, shown at level 0.154, step 2, values float32
> volume #27 level 0.4581
> volume #27 step 1
> volume #27 level 0.3595
> ui tool show "Hide Dust"
> surface dust #27 size 6.36
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/model-
> coot-1-glycans.pdb
model-coot-1-glycans.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) cls1_LBD-dimer [more
info...]
Chain information for model-coot-1-glycans.pdb #28
---
Chain | Description
A B C D | No description available
Non-standard residues in model-coot-1-glycans.pdb #28
---
BMA — (BMA)
NAG — (NAG)
> hide #17 models
> hide #!27 models
> show #!27 models
> transparency #27.1 50
> hide #!27 models
> close #27
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/G2-3m-dom-
> cls1_glyc.pdb
Chain information for G2-3m-dom-cls1_glyc.pdb #27
---
Chain | Description
A B C D | No description available
> hide #!28 models
> show #!1 models
> volume #1 level 0.01035
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #27/A
Alignment identifier is 27/A
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select
> #27/A:2-11,42-51,96-98,113-115,138-143,165-170,192-196,220-223,242-247,335-337,340-342,356-361,366-372,399-404,444-449,503-510,648-651,700-705,719-721,727-729
1820 atoms, 1824 bonds, 108 residues, 1 model selected
> select
> #27/A:19-33,55-67,79-92,120-134,146-151,153-156,158-160,176-188,199-212,228-230,234-239,254-269,285-302,323-332,422-425,429-441,467-473,488-491,520-523,528-549,573-575,598-626,628-630,638-643,656-662,667-679,688-697,706-715,742-755,757-766,773-775,777-779,788-802
5325 atoms, 5342 bonds, 330 residues, 1 model selected
> select
> #27/A:2-11,42-51,96-98,113-115,138-143,165-170,192-196,220-223,242-247,335-337,340-342,356-361,366-372,399-404,444-449,503-510,648-651,700-705,719-721,727-729
1820 atoms, 1824 bonds, 108 residues, 1 model selected
> select clear
> open "C:/Users/nxb318/Downloads/output_merged_1 (1).pdb"
Chain information for output_merged_1 (1).pdb #29
---
Chain | Description
A B C D | No description available
> hide #27 models
> open C:/Users/nxb318/Downloads/output_merged_1.pdb
Chain information for output_merged_1.pdb #30
---
Chain | Description
A B C D | No description available
> hide #29 models
> close #29
> show #!3 models
> hide #!3 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> close #3
> show #17 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #30 models
> show #30 models
> hide #17 models
> cartoon style #30 modeHelix tube sides 20
> show #!25 models
> show #!24 models
> show #!23 models
> show #!21 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/G2-3m-dom-
> cls1_glyc.pdb
Chain information for G2-3m-dom-cls1_glyc.pdb #3
---
Chain | Description
A B C D | No description available
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!21 models
> hide #30 models
> show #30 models
> hide #30 models
> show #30 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #30 models
> show #30 models
> close #3
> hide #30 models
> show #17 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom.cxs includeMaps true
——— End of log from Wed Dec 15 15:42:50 2021 ———
opened ChimeraX session
> show #!18 models
> show #!2 models
> show #30 models
> hide #30 models
> hide #!2 models
> hide #!18 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_dimer-
> model_real_space_refined_006_real_space_refined_018.pdb
Chain information for cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb #3
---
Chain | Description
A B C D | No description available
> matchmaker #3 to #17
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 model_real_space_refined_006.pdb, chain B (#17) with cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb, chain B (#3),
sequence alignment score = 4048.9
RMSD between 737 pruned atom pairs is 0.774 angstroms; (across all 806 pairs:
1.116)
> hide #17 models
> show #!23 models
> show #!24 models
> show #!25 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #22 models
Drag select of 22 atoms, 22 bonds
> ui mousemode right "translate selected models"
> view matrix models #22,1,0,0,13.901,0,1,0,30.176,0,0,1,65.768
> view matrix models #22,1,0,0,37.309,0,1,0,14.102,0,0,1,62.052
> view matrix models #22,1,0,0,39.347,0,1,0,20.372,0,0,1,63.319
> select #3/C:275
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> hide #3 models
Drag select of 22 atoms, 22 bonds
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.45669,-0.85218,-0.2554,541.76,0.88768,-0.45549,-0.067509,98.108,-0.0588,-0.25754,0.96448,126.98
> view matrix models
> #22,-0.74933,0.6599,-0.055107,303.69,-0.6518,-0.7497,-0.11448,481.59,-0.11686,-0.049862,0.9919,98.053
> view matrix models
> #22,-0.23005,0.97317,0.0050809,128.87,-0.97298,-0.22989,-0.021529,441.5,-0.019783,-0.0098964,0.99976,69.234
> view matrix models
> #22,-0.066942,0.92462,0.37497,32.06,-0.96205,-0.15946,0.22145,380.46,0.26455,-0.34591,0.9002,86.584
> view matrix models
> #22,-0.51137,0.85898,0.025836,203.76,-0.85143,-0.50234,-0.15075,487.78,-0.11651,-0.099086,0.98823,107.19
> view matrix models
> #22,0.99937,0.035159,-0.0038077,34.135,0.034921,-0.96409,0.26327,301.83,0.0055853,-0.26324,-0.96472,484.24
> view matrix models
> #22,-0.18355,-0.79507,-0.57807,536.32,-0.72995,-0.28363,0.62188,276.35,-0.6584,0.53611,-0.5283,402.1
> view matrix models
> #22,-0.38817,-0.22247,-0.89433,541.06,-0.90259,-0.10423,0.41768,320.8,-0.18614,0.96935,-0.16034,157.44
> view matrix models
> #22,-0.61171,-0.2895,-0.7362,569.32,-0.70023,0.63117,0.33362,167.34,0.36809,0.71959,-0.58881,166.2
> show #3 models
> show #!18 models
> select #3/D:698
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:793
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:789
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #3/A:793
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #3/D:698
21 atoms, 18 bonds, 3 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> select #3/A:792
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #18
3 models selected
> select #3/D:699
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #3/D:522
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:783
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/D:522
15 atoms, 13 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> select #3:698
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #3:275
32 atoms, 28 bonds, 4 residues, 1 model selected
> hide #22 models
> show #22 models
> hide #3 models
> show #3 models
> hide #!18 models
> hide #22 models
> hide #3 models
> show #17 models
> show #!18 models
> select #3:412
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #17:412
32 atoms, 28 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> color sel red
> select #17:275
32 atoms, 28 bonds, 4 residues, 1 model selected
> hide #!18 models
> show #!18 models
> select #17:430
32 atoms, 28 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> color sel red
> volume #18 level 0.0109
> hide #17 models
> volume #18 level 0.009118
> show #17 models
> volume #18 level 0.01372
> hide #!18 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/4ogg/structure.pdb
structure.pdb title:
Generated by GMML [more info...]
Non-standard residues in structure.pdb #29
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
> view #29
> view matrix models
> #17,0.52814,0.0903,0.84434,-99.512,-0.40742,0.89935,0.15866,81.049,-0.74503,-0.42779,0.51178,375.95
> view matrix models
> #17,0.50396,0.2505,0.8266,-126.63,-0.46418,0.88562,0.014614,129.03,-0.72839,-0.39106,0.5626,352.52
Drag select of 120 atoms, 124 bonds
> ui mousemode right "translate selected models"
> view matrix models #29,1,0,0,205.55,0,1,0,190.22,0,0,1,286.8
> ui tool show "Side View"
> view matrix models #29,1,0,0,259.34,0,1,0,207.41,0,0,1,235.98
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.39617,-0.91805,-0.01525,271.86,0.67151,0.30103,-0.6771,196,0.6262,0.25801,0.73574,224.01
> view matrix models
> #29,-0.10393,-0.95078,0.29192,281.45,0.50691,-0.30316,-0.80693,200.12,0.85571,0.06411,0.51347,219.94
> view matrix models
> #29,-0.011717,-0.97702,-0.21284,275.07,0.75114,0.1319,-0.64683,196.33,0.66004,-0.16745,0.73233,226.02
> view matrix models
> #29,-0.13375,-0.96864,-0.20941,276.55,0.7708,0.031131,-0.63632,196.79,0.62288,-0.24652,0.74246,227.04
> ui mousemode right "translate selected models"
> view matrix models
> #29,-0.13375,-0.96864,-0.20941,279.41,0.7708,0.031131,-0.63632,179.9,0.62288,-0.24652,0.74246,227.16
> view matrix models
> #29,-0.13375,-0.96864,-0.20941,269.19,0.7708,0.031131,-0.63632,178.58,0.62288,-0.24652,0.74246,221.44
> view matrix models
> #29,-0.13375,-0.96864,-0.20941,273.48,0.7708,0.031131,-0.63632,177.83,0.62288,-0.24652,0.74246,230.02
> view matrix models
> #29,-0.13375,-0.96864,-0.20941,269.79,0.7708,0.031131,-0.63632,172.99,0.62288,-0.24652,0.74246,232.64
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.012259,-0.99272,0.11985,271.67,0.8392,-0.054955,-0.54103,173.67,0.54368,0.10721,0.83242,232.52
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.012259,-0.99272,0.11985,272.51,0.8392,-0.054955,-0.54103,177.37,0.54368,0.10721,0.83242,234.86
> view matrix models
> #29,0.012259,-0.99272,0.11985,265.88,0.8392,-0.054955,-0.54103,174.59,0.54368,0.10721,0.83242,235.08
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.53516,-0.84294,-0.055321,256.75,0.73164,0.49524,-0.46846,173.5,0.42228,0.21022,0.88175,236.5
> view matrix models
> #29,0.48472,-0.87446,0.019195,258.35,0.80235,0.4358,-0.40782,173.63,0.34826,0.21308,0.91286,237.72
> view matrix models
> #29,0.38085,-0.92133,0.078162,260.52,0.78746,0.27889,-0.54966,173.2,0.48462,0.27089,0.83172,234.85
> view matrix models
> #29,0.32554,-0.93165,0.16141,262.14,0.85226,0.21519,-0.47681,173.55,0.40949,0.29279,0.86406,235.98
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.32554,-0.93165,0.16141,261.56,0.85226,0.21519,-0.47681,173.48,0.40949,0.29279,0.86406,235.8
> select clear
> hide HC
> select #17/C:275@CA
1 atom, 1 residue, 1 model selected
> select #17/C:275@CB
1 atom, 1 residue, 1 model selected
> select #17/C:275
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> show #!18 models
> select #17 #27
76680 atoms, 77877 bonds, 6453 residues, 2 models selected
> show #!23 models
> show #!16 models
> hide #!16 models
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.80244,-0.29952,0.51611,-0.63872,0.48034,0.8374,-0.26085,-15.011,-0.35406,0.45722,0.81584,17.255,#27,0.75599,-0.6302,-0.177,238.8,0.23622,0.51484,-0.8241,238.98,0.61048,0.5812,0.53808,-170.12
> view matrix models
> #17,0.82901,0.30822,0.46663,-134.5,-0.22317,0.94743,-0.2293,113.77,-0.51277,0.085957,0.85421,129.81,#27,0.88072,-0.10503,-0.46185,153.39,-0.064681,0.9393,-0.33695,103.16,0.46921,0.32663,0.82046,-142.15
> view matrix models
> #17,0.97481,0.2221,0.020189,-49.428,-0.22123,0.97447,-0.038376,64.914,-0.028197,0.032944,0.99906,-0.93718,#27,0.56359,-0.2555,-0.78555,331.83,0.10089,0.96514,-0.24152,38.3,0.81987,0.056864,0.56972,-105.29
> view matrix models
> #17,0.99913,-0.02301,0.034695,-2.2434,0.022233,0.9995,0.022609,-9.9638,-0.035198,-0.021818,0.99914,13.146,#27,0.52644,-0.48365,-0.69925,373.32,0.28027,0.87518,-0.39434,51.613,0.80269,0.011618,0.59628,-96.911
> show #!26 models
> hide #!26 models
> ui tool show "Fit in Map"
Fit molecules model_real_space_refined_006.pdb (#17), G2-3m-dom-cls1_glyc.pdb
(#27) to map postprocess-zlfip.mrc gaussian (#26) using 76680 atoms
average map value = 0.008275, steps = 112
shifted from previous position = 0.783
rotated from previous position = 2.11 degrees
atoms outside contour = 37703, contour level = 0.0086179
Position of model_real_space_refined_006.pdb (#17) relative to postprocess-
zlfip.mrc gaussian (#26) coordinates:
Matrix rotation and translation
0.99995206 0.00021586 0.00978935 -2.29360096
-0.00029680 0.99996578 0.00826768 -2.04255583
-0.00978723 -0.00827019 0.99991791 4.10109578
Axis -0.64520055 0.76375142 -0.02000069
Axis point 416.62156911 0.00000000 247.02591872
Rotation angle (degrees) 0.73432681
Shift along axis -0.16219707
Position of G2-3m-dom-cls1_glyc.pdb (#27) relative to postprocess-zlfip.mrc
gaussian (#26) coordinates:
Matrix rotation and translation
0.51208268 -0.46382513 -0.72293677 377.24893591
0.25717798 0.88584777 -0.38617771 52.35828887
0.81953085 0.01183149 0.57291290 -95.61320455
Axis 0.22762109 -0.88213578 0.41234100
Axis point 287.55889679 0.00000000 327.67093327
Rotation angle (degrees) 60.95989697
Shift along axis 0.25744824
> select clear
> hide #!18 models
> select #27
51128 atoms, 51725 bonds, 3229 residues, 1 model selected
> show #27 models
> hide #27 models
> show #!26 models
> hide #!26 models
> select #29
120 atoms, 124 bonds, 6 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.32554,-0.93165,0.16141,260.62,0.85226,0.21519,-0.47681,180.67,0.40949,0.29279,0.86406,251.55
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.13536,0.87001,0.47408,256.36,-0.77577,0.39071,-0.4955,199.64,-0.61632,-0.30071,0.72782,266.07
> view matrix models
> #29,0.52892,0.69178,-0.49162,242.4,-0.5451,-0.16707,-0.82156,196.45,-0.65047,0.70252,0.28872,256.41
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.52892,0.69178,-0.49162,240.69,-0.5451,-0.16707,-0.82156,193.63,-0.65047,0.70252,0.28872,257.67
> view matrix models
> #29,0.52892,0.69178,-0.49162,240.22,-0.5451,-0.16707,-0.82156,194.16,-0.65047,0.70252,0.28872,258.11
> show #!18 models
> volume #18 level 0.01079
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.91199,0.41016,-0.0070817,242.08,-0.11613,0.24158,-0.96341,185.14,-0.39344,0.87944,0.26795,253.74
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.91199,0.41016,-0.0070817,239.74,-0.11613,0.24158,-0.96341,187.65,-0.39344,0.87944,0.26795,253.7
> hide #!18 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Asn275.pdb models #29 relModel #18
> show #!18 models
> hide #!18 models
> select #29 #17
25672 atoms, 26276 bonds, 3230 residues, 2 models selected
> combine sele
Expected a keyword
> ui tool show "Build Structure"
> hide #29 models
> hide #17 models
> hide #!23 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Asn275.pdb
Glyc-C-Asn275.pdb title:
Generated by GMML [more info...]
Non-standard residues in Glyc-C-Asn275.pdb #31
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
> show #17 models
> hide #17 models
> close #29
> color #31 #5b42cd
Drag select of 111 atoms, 117 bonds
Drag select of 120 atoms, 124 bonds
> color sel byhetero
> hide HC
> show #17 models
> style sel ball
Changed 120 atom styles
> select clear
> select #17/C
6388 atoms, 6538 bonds, 806 residues, 1 model selected
> select add #31
6508 atoms, 6662 bonds, 812 residues, 2 models selected
> show #3 models
> hide #17 models
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Asn275.pdb
Glyc-C-Asn275.pdb title:
Generated by GMML [more info...]
Non-standard residues in Glyc-C-Asn275.pdb #29
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
> hide #31 models
> select #3/C #29
6508 atoms, 6662 bonds, 812 residues, 2 models selected
> matchmaker sele to #3/A
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> name frozen C+glyc sel
> matchmaker C+glyc to #3/A
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match
match_items = (refs[0], matches)
IndexError: list index out of range
IndexError: list index out of range
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match
match_items = (refs[0], matches)
See log for complete Python traceback.
> help help:user/menu.html#named-selections
> name frozen Cglyc sel
> matchmaker Cglyc sel to #3/A
Expected a keyword
> matchmaker Cglyc to #3/A
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match
match_items = (refs[0], matches)
IndexError: list index out of range
IndexError: list index out of range
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match
match_items = (refs[0], matches)
See log for complete Python traceback.
> matchmaker #3C to 17/A bring #29
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker #3/C to 17/A bring #29
Invalid "to" argument: invalid atoms specifier
> matchmaker #3/C to #3/A bring #29
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match
match_items = (refs[0], matches)
IndexError: list index out of range
IndexError: list index out of range
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match
match_items = (refs[0], matches)
See log for complete Python traceback.
> matchmaker #3/C to #17/A bring #29
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 model_real_space_refined_006.pdb, chain A (#17) with cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb, chain C (#3),
sequence alignment score = 3961.9
RMSD between 396 pruned atom pairs is 0.715 angstroms; (across all 806 pairs:
8.247)
> hide #3 models
> show #31 models
> show #17 models
> show #!18 models
> volume #18 level 0.01341
> hide #!18 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.99651,0.031498,0.077363,424,-0.015715,-0.98033,0.19671,401.16,0.082038,0.19481,0.9774,-55.548,#29,-0.99631,0.02943,0.080667,423.57,-0.012879,-0.98002,0.19847,399.94,0.084896,0.1967,0.97678,-56.529
> view matrix models
> #3,-0.99641,0.031641,0.078568,423.68,-0.01511,-0.97913,0.20268,399.45,0.083341,0.20077,0.97609,-56.835,#29,-0.9962,0.029575,0.081871,423.25,-0.012257,-0.9788,0.20443,398.22,0.086182,0.20265,0.97545,-57.808
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.99641,0.031641,0.078568,423.76,-0.01511,-0.97913,0.20268,399.86,0.083341,0.20077,0.97609,-56.16,#29,-0.9962,0.029575,0.081871,423.33,-0.012257,-0.9788,0.20443,398.63,0.086182,0.20265,0.97545,-57.133
> show #!18 models
> hide #17 models
> show #17 models
> hide #!18 models
> hide HC
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom-glyc.cxs includeMaps true
> hide #29 models
> show #29 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> A-Asn275.pdb models #29 relModel #18
> close #29,31
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> A-Asn275.pdb
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Asn275.pdb
Glyc-A-Asn275.pdb title:
Generated by GMML [more info...]
Non-standard residues in Glyc-A-Asn275.pdb #29
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
Glyc-C-Asn275.pdb title:
Generated by GMML [more info...]
Non-standard residues in Glyc-C-Asn275.pdb #31
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
> show #!18 models
> volume #18 level 0.009536
> volume #18 level 0.01403
> volume #18 level 0.01424
> hide #31 models
> show #31 models
> select #31
120 atoms, 124 bonds, 6 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.99931,-0.0015523,0.037142,-8.871,-0.0028536,0.99298,0.11827,-27.672,-0.037065,-0.1183,0.99229,34.749
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.99931,-0.0015523,0.037142,-8.9037,-0.0028536,0.99298,0.11827,-27.766,-0.037065,-0.1183,0.99229,35.277
> volume #18 level 0.01058
> volume #18 level 0.01299
> select clear
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> A-Asn275.pdb
Glyc-A-Asn275.pdb title:
Generated by GMML [more info...]
Non-standard residues in Glyc-A-Asn275.pdb #32
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
> hide #31 models
> hide #29 models
> hide #!18 models
> select #32
120 atoms, 124 bonds, 6 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #32,1,0,0,14.687,0,1,0,-47.998,0,0,1,0.72631
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.75997,-0.36,-0.54115,590.43,0.47632,-0.87497,-0.086852,353.76,-0.44223,-0.32376,0.83643,211.35
> view matrix models
> #32,-0.96375,-0.02178,-0.2659,476.28,-0.030636,-0.98103,0.1914,411.42,-0.26503,0.19261,0.94481,18.377
> view matrix models
> #32,0.56795,-0.74817,-0.34305,375.65,-0.80177,-0.5971,-0.025173,521.47,-0.186,0.28934,-0.93898,450.25
> ui mousemode right "translate selected models"
> view matrix models
> #32,0.56795,-0.74817,-0.34305,382.94,-0.80177,-0.5971,-0.025173,526.32,-0.186,0.28934,-0.93898,434.54
> view matrix models
> #32,0.56795,-0.74817,-0.34305,388.58,-0.80177,-0.5971,-0.025173,537.22,-0.186,0.28934,-0.93898,454.89
> view matrix models
> #32,0.56795,-0.74817,-0.34305,403.21,-0.80177,-0.5971,-0.025173,524.81,-0.186,0.28934,-0.93898,448.19
> view matrix models
> #32,0.56795,-0.74817,-0.34305,404.37,-0.80177,-0.5971,-0.025173,526.15,-0.186,0.28934,-0.93898,465.61
> view matrix models
> #32,0.56795,-0.74817,-0.34305,409.38,-0.80177,-0.5971,-0.025173,526.69,-0.186,0.28934,-0.93898,480.84
> view matrix models
> #32,0.56795,-0.74817,-0.34305,418.57,-0.80177,-0.5971,-0.025173,528.63,-0.186,0.28934,-0.93898,476.9
> ui mousemode right "rotate selected models"
> view matrix models
> #32,0.59161,-0.74862,-0.29927,403.02,-0.79216,-0.60878,-0.043136,534.18,-0.1499,0.26259,-0.95319,480.07
> view matrix models
> #32,0.74618,-0.15555,-0.64732,309.51,-0.64332,-0.4187,-0.64096,606.36,-0.17133,0.8947,-0.41249,188.88
> ui mousemode right "translate selected models"
> view matrix models
> #32,0.74618,-0.15555,-0.64732,307.7,-0.64332,-0.4187,-0.64096,603.86,-0.17133,0.8947,-0.41249,193.52
> show #!18 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #32,0.74618,-0.15555,-0.64732,305.98,-0.64332,-0.4187,-0.64096,603.52,-0.17133,0.8947,-0.41249,191.39
> view matrix models
> #32,0.74618,-0.15555,-0.64732,305.2,-0.64332,-0.4187,-0.64096,601.79,-0.17133,0.8947,-0.41249,193.63
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.58917,-0.49893,0.63558,335.46,0.76652,-0.096282,0.63497,-79.112,-0.25561,0.86128,0.43916,5.4033
> view matrix models
> #32,-0.6618,-0.66268,0.35053,462.73,0.55408,-0.1174,0.82414,-79.039,-0.50499,0.73964,0.44487,84.211
> view matrix models
> #32,-0.93278,0.36022,-0.013091,348.74,-0.32153,-0.81506,0.48197,356.9,0.16294,0.45378,0.87609,-83.969
> view matrix models
> #32,-0.7982,0.48626,0.35557,197.78,0.02521,-0.56277,0.82623,138.03,0.60187,0.66846,0.43695,-115.3
> view matrix models
> #32,-0.77475,0.50181,0.38464,181.91,0.075215,-0.53088,0.8441,115.56,0.62778,0.6829,0.37356,-108.21
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.77475,0.50181,0.38464,182.21,0.075215,-0.53088,0.8441,115.51,0.62778,0.6829,0.37356,-107.2
> view matrix models
> #32,-0.77475,0.50181,0.38464,183.5,0.075215,-0.53088,0.8441,116.77,0.62778,0.6829,0.37356,-105.92
> view matrix models
> #32,-0.77475,0.50181,0.38464,183.11,0.075215,-0.53088,0.8441,116.78,0.62778,0.6829,0.37356,-106.64
> view matrix models
> #32,-0.77475,0.50181,0.38464,183.28,0.075215,-0.53088,0.8441,116.78,0.62778,0.6829,0.37356,-107.32
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.76976,0.4717,0.43008,178.52,0.12185,-0.55279,0.82436,118.02,0.6266,0.68697,0.36804,-106.73
> view matrix models
> #32,-0.80337,0.39177,0.44844,200.81,0.096299,-0.6577,0.7471,169,0.58764,0.64339,0.49065,-118.7
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.80337,0.39177,0.44844,200.96,0.096299,-0.6577,0.7471,169.4,0.58764,0.64339,0.49065,-119.07
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/4ogt/structure.pdb
structure.pdb title:
Generated by GMML [more info...]
Non-standard residues in structure.pdb #33
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
> hide #32 models
> show #32 models
> matchmaker #33 to #32
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align #33 toAtoms #32
RMSD between 120 atom pairs is 2.523 angstroms
> hide #32 models
> select #33
120 atoms, 124 bonds, 6 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #33,-0.057156,0.86746,-0.49421,243.74,-0.98138,-0.13973,-0.13177,219.72,-0.18336,0.47748,0.8593,290.48
> view matrix models
> #33,-0.54869,-0.7684,-0.3294,261.02,0.65632,-0.63997,0.39961,209.15,-0.51787,0.0030705,0.85545,297.19
> view matrix models
> #33,-0.99044,-0.0075634,-0.13774,263.4,0.031117,-0.98501,-0.16966,212.79,-0.1344,-0.17232,0.97583,295.03
> view matrix models
> #33,-0.98616,-0.10755,-0.12621,264.07,0.11329,-0.99279,-0.039213,213.19,-0.12108,-0.052969,0.99123,294.3
> view matrix models
> #33,-0.58456,-0.34692,0.73344,269.47,-0.079488,-0.87514,-0.4773,210.33,0.80745,-0.33731,0.484,280.25
> view matrix models
> #33,-0.4808,-0.45043,0.75229,269.09,0.17557,-0.89005,-0.4207,208.04,0.85907,-0.070195,0.50701,278.25
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.4808,-0.45043,0.75229,268.48,0.17557,-0.89005,-0.4207,206.64,0.85907,-0.070195,0.50701,276.98
> select up
258008 atoms, 262690 bonds, 26082 residues, 49 models selected
> select up
258008 atoms, 262690 bonds, 26082 residues, 49 models selected
> select down
120 atoms, 124 bonds, 6 residues, 1 model selected
> align #33 toAtoms #32
RMSD between 120 atom pairs is 2.523 angstroms
> show #32 models
> hide #33 models
> show #33 models
> hide #32 models
> hide #33 models
> show #32 models
> close #33
> show #31 models
> show #29 models
> show #30 models
> hide #30 models
> show #30 models
> hide #31 models
> show #31 models
> hide #31 models
> hide #32 models
> show #32 models
> show #31 models
> hide #31 models
> show #31 models
> hide #30 models
> show #3 models
> hide #!18 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> matchmaker #3 to #17
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 model_real_space_refined_006.pdb, chain B (#17) with cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb, chain B (#3),
sequence alignment score = 4048.9
RMSD between 737 pruned atom pairs is 0.774 angstroms; (across all 806 pairs:
1.116)
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Thr380.pdb models #32 relModel #18
> matchmaker #3/C to #17/A bring #32
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 model_real_space_refined_006.pdb, chain A (#17) with cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb, chain C (#3),
sequence alignment score = 3961.9
RMSD between 396 pruned atom pairs is 0.715 angstroms; (across all 806 pairs:
8.247)
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Thr380.pdb
Glyc-C-Thr380.pdb title:
Generated by GMML [more info...]
Non-standard residues in Glyc-C-Thr380.pdb #33
---
0MA — (0MA)
4YA — (4YA)
4YB — (4YB)
ROH — (ROH)
VMB — (VMB)
> matchmaker #3 to #17
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 model_real_space_refined_006.pdb, chain B (#17) with cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb, chain B (#3),
sequence alignment score = 4048.9
RMSD between 737 pruned atom pairs is 0.774 angstroms; (across all 806 pairs:
1.116)
> hide #3 models
> show #!18 models
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom-glyc1.cxs includeMaps true
——— End of log from Fri Dec 17 13:58:26 2021 ———
opened ChimeraX session
> ui tool show "Side View"
> hide #17 models
> show #17 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #17 models
> show #17 models
> select #17/A:776
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/A:776@CG
1 atom, 1 residue, 1 model selected
> select #17/A:776@CG
1 atom, 1 residue, 1 model selected
> select #17/A:776@CG
1 atom, 1 residue, 1 model selected
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!23 models
> show #!25 models
> show #!24 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> open 1yae
1yae title:
Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain
Complexed with Domoic Acid [more info...]
Chain information for 1yae #34
---
Chain | Description
A B C D E F | Glutamate receptor, ionotropic kainate 2
Non-standard residues in 1yae #34
---
DOQ —
(2S,3S,4S)-2-carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadienyl]-3-pyrrolidineacetic
acid ((2S,3S,4S)-3-carboxymethyl-4-[(1Z,3E,5R)-5-carboxy-1-methyl-
hexa-1,3-dienyl]-pyrrolidine-2-carboxylic acid; domoic acid)
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
1yae mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
6| author_and_software_defined_assembly
7| software_defined_assembly
8| software_defined_assembly
9| software_defined_assembly
> matchmaker #34/A to #17/A
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 model_real_space_refined_006.pdb, chain A (#17) with 1yae, chain A
(#34), sequence alignment score = 1262.6
RMSD between 252 pruned atom pairs is 0.924 angstroms; (across all 261 pairs:
1.262)
> matchmaker #34/A to #17/D
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 model_real_space_refined_006.pdb, chain D (#17) with 1yae, chain A
(#34), sequence alignment score = 1214.6
RMSD between 178 pruned atom pairs is 1.278 angstroms; (across all 261 pairs:
5.607)
> select #34/A,B,C,D
8515 atoms, 8609 bonds, 4 pseudobonds, 1110 residues, 2 models selected
> select #34/B,C,D
6401 atoms, 6470 bonds, 3 pseudobonds, 835 residues, 2 models selected
> delete atoms (#!34 & sel)
> delete bonds (#!34 & sel)
> select #34/E
2115 atoms, 2145 bonds, 1 pseudobond, 269 residues, 2 models selected
> delete atoms (#!34 & sel)
> delete bonds (#!34 & sel)
> matchmaker #34/A to #17/A
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 model_real_space_refined_006.pdb, chain A (#17) with 1yae, chain A
(#34), sequence alignment score = 1262.6
RMSD between 252 pruned atom pairs is 0.924 angstroms; (across all 261 pairs:
1.262)
> matchmaker #34/F to #17/A
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 model_real_space_refined_006.pdb, chain A (#17) with 1yae, chain F
(#34), sequence alignment score = 1208
RMSD between 219 pruned atom pairs is 0.920 angstroms; (across all 226 pairs:
1.106)
> hide #17,29,31-34 target a
> cartoon #17,29,31-34
> hide #31 models
> show #31 models
> show #17,29,31-34 target ab
> hide #17,29,31-34 target a
> hide #!34 models
> select
> ::name="0MA"::name="4YA"::name="4YB"::name="BMA"::name="DOQ"::name="FUC"::name="HOH"::name="NAG"::name="ROH"::name="SYM"::name="VMB"
1177 atoms, 1185 bonds, 83 residues, 14 models selected
> show (#29,31-33 & sel) target ab
> select clear
> hide HC
> select #17/A:776
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
model_real_space_refined_006.pdb #17/A ASP 776: phi -62.6, psi -44.1 trans
Changed 438 bond radii
> swapaa #!17/A:776 LYS criteria 1 rotLib Dunbrack
Using Dunbrack library
model_real_space_refined_006.pdb #!17/A ASP 776: phi -62.6, psi -44.1 trans
Applying LYS rotamer (chi angles: -70.5 179.2 -179.5 178.4) to
model_real_space_refined_006.pdb #!17/A LYS 776
> swapaa interactive sel LYS rotLib Dynameomics
model_real_space_refined_006.pdb #17/A LYS 776: phi -62.6, psi -44.1 trans
Changed 486 bond radii
> swapaa #!17/A:776 LYS criteria 1 rotLib Dynameomics retain false
Using Dynameomics library
model_real_space_refined_006.pdb #!17/A LYS 776: phi -62.6, psi -44.1 trans
Applying LYS rotamer (chi angles: -68.4 -176.1 -171.6 -61.7) to
model_real_space_refined_006.pdb #!17/A LYS 776
> hide #29 models
> show #29 models
> show #30 models
> hide #30 models
> hide #17 models
> show #17 models
> select #17/B
6388 atoms, 6538 bonds, 806 residues, 1 model selected
> select #17/B:776
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/B,C,D:776
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel target ab
> swapaa interactive sel LYS rotLib Dynameomics
model_real_space_refined_006.pdb #17/B ASP 776: phi -62.5, psi -41.0 trans
Changed 486 bond radii
model_real_space_refined_006.pdb #!17/C ASP 776: phi -67.8, psi -42.2 trans
Changed 486 bond radii
model_real_space_refined_006.pdb #!17/D ASP 776: phi -59.4, psi -39.1 trans
Changed 486 bond radii
> swapaa #!17/D:776 LYS criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/D ASP 776: phi -59.4, psi -39.1 trans
Applying LYS rotamer (chi angles: -68.4 -176.1 -171.6 -61.7) to
model_real_space_refined_006.pdb #!17/D LYS 776
> swapaa #!17/C:776 LYS criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/C ASP 776: phi -67.8, psi -42.2 trans
Applying LYS rotamer (chi angles: -68.4 -176.1 -171.6 -61.7) to
model_real_space_refined_006.pdb #!17/C LYS 776
> swapaa #!17/B:776 LYS criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/B ASP 776: phi -62.5, psi -41.0 trans
Applying LYS rotamer (chi angles: -68.4 -176.1 -171.6 -61.7) to
model_real_space_refined_006.pdb #!17/B LYS 776
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dynameomics
model_real_space_refined_006.pdb #17/B LYS 776: phi -62.5, psi -41.0 trans
Changed 648 bond radii
model_real_space_refined_006.pdb #!17/C LYS 776: phi -67.8, psi -42.2 trans
Changed 648 bond radii
model_real_space_refined_006.pdb #!17/D LYS 776: phi -59.4, psi -39.1 trans
Changed 648 bond radii
> swapaa #!17/D:776 ARG criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/D LYS 776: phi -59.4, psi -39.1 trans
Applying ARG rotamer (chi angles: -70.3 179.7 67.7 -173.9) to
model_real_space_refined_006.pdb #!17/D ARG 776
> swapaa #!17/C:776 ARG criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/C LYS 776: phi -67.8, psi -42.2 trans
Applying ARG rotamer (chi angles: -70.3 179.7 67.7 -173.9) to
model_real_space_refined_006.pdb #!17/C ARG 776
> swapaa #!17/B:776 ARG criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/B LYS 776: phi -62.5, psi -41.0 trans
Applying ARG rotamer (chi angles: -70.3 179.7 67.7 -173.9) to
model_real_space_refined_006.pdb #!17/B ARG 776
> swapaa interactive sel ARG rotLib Dynameomics
model_real_space_refined_006.pdb #17/B ARG 776: phi -62.5, psi -41.0 trans
Changed 648 bond radii
model_real_space_refined_006.pdb #!17/C ARG 776: phi -67.8, psi -42.2 trans
Changed 648 bond radii
model_real_space_refined_006.pdb #!17/D ARG 776: phi -59.4, psi -39.1 trans
Changed 648 bond radii
> select #17/B:886
Nothing selected
> select #17/B:856
Nothing selected
> select #17/A:776
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17:776
42 atoms, 38 bonds, 4 residues, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dynameomics
model_real_space_refined_006.pdb #17/A LYS 776: phi -62.6, psi -44.1 trans
Changed 45 bond radii
model_real_space_refined_006.pdb #!17/B ARG 776: phi -62.5, psi -41.0 trans
Changed 45 bond radii
model_real_space_refined_006.pdb #!17/C ARG 776: phi -67.8, psi -42.2 trans
Changed 45 bond radii
model_real_space_refined_006.pdb #!17/D ARG 776: phi -59.4, psi -39.1 trans
Changed 45 bond radii
> swapaa #!17/D:776 ASP criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/D ARG 776: phi -59.4, psi -39.1 trans
Applying ASP rotamer (chi angles: -178.1 62.8) to
model_real_space_refined_006.pdb #!17/D ASP 776
> swapaa #!17/B:776 ASP criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/B ARG 776: phi -62.5, psi -41.0 trans
Applying ASP rotamer (chi angles: -178.1 62.8) to
model_real_space_refined_006.pdb #!17/B ASP 776
> swapaa interactive sel ASP rotLib Dynameomics
model_real_space_refined_006.pdb #17/A LYS 776: phi -62.6, psi -44.1 trans
Changed 45 bond radii
model_real_space_refined_006.pdb #!17/B ASP 776: phi -62.5, psi -41.0 trans
Changed 45 bond radii
model_real_space_refined_006.pdb #!17/C ARG 776: phi -67.8, psi -42.2 trans
Changed 45 bond radii
model_real_space_refined_006.pdb #!17/D ASP 776: phi -59.4, psi -39.1 trans
Changed 45 bond radii
> swapaa #!17/D:776 ASP criteria 1 rotLib Dynameomics retain false
Using Dynameomics library
model_real_space_refined_006.pdb #!17/D ASP 776: phi -59.4, psi -39.1 trans
Applying ASP rotamer (chi angles: -178.1 62.8) to
model_real_space_refined_006.pdb #!17/D ASP 776
> swapaa #!17/C:776 ASP criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/C ARG 776: phi -67.8, psi -42.2 trans
Applying ASP rotamer (chi angles: -178.1 62.8) to
model_real_space_refined_006.pdb #!17/C ASP 776
> swapaa #!17/A:776 ASP criteria 1 rotLib Dynameomics
Using Dynameomics library
model_real_space_refined_006.pdb #!17/A LYS 776: phi -62.6, psi -44.1 trans
Applying ASP rotamer (chi angles: -178.1 62.8) to
model_real_space_refined_006.pdb #!17/A ASP 776
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> select clear
> select #17/A:776
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dynameomics
model_real_space_refined_006.pdb #17/A ASP 776: phi -62.6, psi -44.1 trans
Changed 45 bond radii
> swapaa #!17/A:776 ASP criteria 4 rotLib Dynameomics retain false
Using Dynameomics library
model_real_space_refined_006.pdb #!17/A ASP 776: phi -62.6, psi -44.1 trans
Applying ASP rotamer (chi angles: -75.6 116.8) to
model_real_space_refined_006.pdb #!17/A ASP 776
> swapaa interactive sel ASP rotLib Dynameomics
model_real_space_refined_006.pdb #17/A ASP 776: phi -62.6, psi -44.1 trans
Changed 45 bond radii
> select #17/C:776@CG
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dynameomics
model_real_space_refined_006.pdb #17/C ASP 776: phi -67.8, psi -42.2 trans
Changed 45 bond radii
> swapaa #!17/C:776 ASP criteria 4 rotLib Dynameomics retain false
Using Dynameomics library
model_real_space_refined_006.pdb #!17/C ASP 776: phi -67.8, psi -42.2 trans
Applying ASP rotamer (chi angles: -75.6 116.8) to
model_real_space_refined_006.pdb #!17/C ASP 776
No residues selected
> ui mousemode right distance
> distance #17/A:776@CG #29/A:4@H2O
Distance between model_real_space_refined_006.pdb #17/A ASP 776 CG and Glyc-A-
Asn275.pdb #29/A VMB 4 H2O: 5.432Å
> distance #17/C:776@CG #31/A:4@O2
Distance between model_real_space_refined_006.pdb #17/C ASP 776 CG and Glyc-C-
Asn275.pdb #31/A VMB 4 O2: 6.313Å
> show #3 models
> hide #3 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #27 models
> hide #29 models
> show #29 models
> show #30 models
> hide #30 models
> show #30 models
> hide #30 models
> show #30 models
> hide #27 models
> hide #!16 models
> show #27 models
> hide #27 models
> hide #30 models
> hide #17 models
> show #17 models
> select #17:737
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #17:738
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel target ab
> color sel yellow
> color sel byelement
> color sel yellow
> color sel byhetero
> select #17:776
32 atoms, 28 bonds, 4 residues, 1 model selected
> select clear
> select #17:486-490
136 atoms, 136 bonds, 20 residues, 1 model selected
> select #17:486-490, 516-519
248 atoms, 248 bonds, 36 residues, 1 model selected
> select #17:486-490, 516-519, 523
292 atoms, 288 bonds, 40 residues, 1 model selected
> show #22 models
> show #!23 models
> color sel #55aaffff
> color sel #ffaaffff
> color sel #55aaffff
> color sel #55ff7fff
> color sel #ffffffff
> color sel #55aaffff
> color sel #55ff7fff
> select clear
> hide #17 models
> select #23/F:1603@CAI
1 atom, 1 residue, 1 model selected
> hide #!23 models
> show #17 models
> select #17:486-490, 516-519, 523
292 atoms, 288 bonds, 40 residues, 1 model selected
> select #17:440, 486-490, 516-519, 523, 721, 738
396 atoms, 380 bonds, 52 residues, 1 model selected
> select #17:440, 486-490, 516-519, 523, 688, 721, 738
412 atoms, 392 bonds, 56 residues, 1 model selected
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #17 models
> hide #29 models
> hide #31 models
> hide #32 models
> hide #33 models
> show #17 models
> hide #22 models
> select #17:696
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #17:696,787
72 atoms, 64 bonds, 8 residues, 1 model selected
> show sel target ab
> color sel magenta
> color sel byhetero
> select clear
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom-glyc2.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\session.py", line 894, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\session.py", line 628, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\session.py", line 894, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\session.py", line 628, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.4.dev202201150102\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom-glyc2.cxs
——— End of log from Wed Mar 2 11:50:47 2022 ———
opened ChimeraX session
> show #33 models
> show #32 models
> show #31 models
> show #30 models
> hide #30 models
> show #30 models
> hide #30 models
> show #29 models
> show #27 models
> hide #27 models
> show #!16 models
> show #!2 models
> hide #!2 models
> hide #!16 models
> show #!18 models
> volume #18 level 0.01508
> show #30 models
> hide #30 models
> show #!28 models
> hide #33 models
> hide #32 models
> hide #31 models
> select #28
25753 atoms, 26356 bonds, 3239 residues, 1 model selected
> cartoon hide sel
> select clear
> hide #!18 models
> show #!18 models
> hide #29 models
> show #29 models
> hide #29 models
> show #31 models
> hide #31 models
> show #32 models
> hide #32 models
> show #33 models
> show #27 models
> hide #17 models
> show #17 models
> hide #!18 models
> show #!18 models
> hide #27 models
> volume #18 level 0.01431
> select
> ::name="0MA"::name="4YA"::name="4YB"::name="BMA"::name="DOQ"::name="FUC"::name="HOH"::name="NAG"::name="ROH"::name="SYM"::name="VMB"
1177 atoms, 1185 bonds, 83 residues, 14 models selected
> color zone #18 near sele distance 10
Invalid "near" argument: invalid atoms specifier
> color zone #18 near selection distance 10
Invalid "near" argument: invalid atoms specifier
> ui tool show "Color Zone"
> color (#33#!28 & sel) orange
> color (#33#!28 & sel) byhetero
> color zone #18 near sel distance 10.03
> color single #18
> color (#33#!28 & sel) orange
> color zone #18 near sel distance 6.77
> color single #18
> transparency #18.1 0
> color zone #18 near sel distance 5
> hide #!28 models
> show #!28 models
> show #27 models
> hide #27 models
> show #29 models
> hide #29 models
> show #29 models
> show #30 models
> hide #30 models
> show #30 models
> hide #30 models
> show #30 models
> hide #29 models
> hide #30 models
> show #32 models
> show #31 models
> show #29 models
> hide #17 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> color (#29,31-33 & sel) orange
> show #17 models
> show #!18 models
> color single #18
> color zone #18 near sel distance 5
> color single #18
> color zone #18 near sel distance 5
> color single #18
[Repeated 1 time(s)]
> close #9-12
> close #6
> close #1
> close #2
> color zone #18 near sel distance 5
[Repeated 1 time(s)]
> color single #18
> select clear
> select #33
120 atoms, 124 bonds, 6 residues, 1 model selected
> select #32
120 atoms, 124 bonds, 6 residues, 1 model selected
> ~select #32
Nothing selected
> select
> ::name="0MA"::name="4YA"::name="4YB"::name="BMA"::name="DOQ"::name="FUC"::name="HOH"::name="NAG"::name="ROH"::name="SYM"::name="VMB"
1177 atoms, 1185 bonds, 83 residues, 14 models selected
> color zone #18 near sel distance 5
> color single #18
> select clear
> select #33,32,31,29
480 atoms, 496 bonds, 24 residues, 4 models selected
> color sel black
> color zone #18 near sel distance 5
> color single #18
> color sel orange
> color zone #18 near sel distance 5
> hide #17 models
> select clear
> hide #29 models
> hide #31 models
> hide #32 models
> show #!28 models
> hide #!18 models
Drag select of 564 atoms, 566 bonds
> select clear
Drag select of 79 atoms, 83 bonds
> select clear
Drag select of 21 atoms, 21 bonds
> select clear
> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_dimer-
> model_real_space_refined_006_real_space_refined_018-glyc6-TEST.pdb
Chain information for cls1_dimer-
model_real_space_refined_006_real_space_refined_018-glyc6-TEST.pdb #1
---
Chain | Description
A B C D | No description available
> hide #!28 models
> select #1
26272 atoms, 26940 bonds, 3260 residues, 1 model selected
> cartoon hide sel
> select clear
Drag select of 4 atoms, 1 bonds
Drag select of 26 atoms, 22 bonds
> select clear
Drag select of 25 atoms, 22 bonds
Drag select of 12 atoms, 12 bonds
> hide sel target a
Drag select of 22 atoms, 23 bonds
Drag select of 4 atoms, 3 bonds
Drag select of 18 atoms, 17 bonds
Drag select of 22 atoms, 23 bonds
> hide sel target a
Drag select of 8 atoms, 7 bonds
> hide sel target a
> select protein
286379 atoms, 291691 bonds, 50 pseudobonds, 29735 residues, 22 models selected
> hide (#1 & sel) target a
> show #17 models
> hide #17 models
Drag select of 548 atoms, 576 bonds
> color (#1,33 & sel) black
> color (#1,33 & sel) orange
> show #17 models
> select clear
> show #!18 models
> hide #17 models
> hide #!18 models
Drag select of 548 atoms, 576 bonds
> show #!18 models
> color zone #18 near sel distance 5
> color zone #18 near sel distance 4.4
> color single #18
> color zone #18 near sel distance 4.4
> show #17 models
> hide #17 models
> hide #1 models
> hide #!18 models
> show #17 models
> hide #33 models
> show #33 models
> hide #33 models
> show #32 models
> hide #32 models
> show #31 models
> hide #31 models
> show #29 models
> show #!28 models
> hide #!28 models
> show #32 models
> show #33 models
> hide #33 models
> show #33 models
> show #31 models
> ui tool show "Side View"
> select #17/D:769
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #17/D:770
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #17/D:771
19 atoms, 17 bonds, 3 residues, 1 model selected
> select add #17/D:772
25 atoms, 22 bonds, 4 residues, 1 model selected
> show sel target ab
> select clear
> cd
> C:\Users\nxb318\Documents\EM_related\rGluK2-3m-domoic_acid_processing\FROM_EXX\Glycans
Current working directory is:
C:\Users\nxb318\Documents\EM_related\rGluK2-3m-domoic_acid_processing\FROM_EXX\Glycans
> save cls1-side1_glyc.tif width 2400 height 2400 supersample 4
> transparentBackground true
[Repeated 1 time(s)]
> save cls1-side2_glyc.tif width 2400 height 2400 supersample 4
> transparentBackground true
> hide #29 models
> hide #33 models
> hide #32 models
> hide #31 models
> show #30 models
> hide #30 models
> show #27 models
> hide #27 models
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> show #29 models
> show #31 models
> show #32 models
> show #33 models
> ui tool show "Show Sequence Viewer"
> sequence chain #17/A
Alignment identifier is 17/A
> select #17/A:839
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/A:828-839
81 atoms, 81 bonds, 12 residues, 1 model selected
> select #17/A:828-839
81 atoms, 81 bonds, 12 residues, 1 model selected
> select
> #17/A:35-44,75-84,129-131,146-148,171-176,198-203,225-229,253-256,275-280,368-370,373-375,389-394,399-405,432-437,477-482,513-518,536-543,681-684,733-738,752-755,760-762,764-767
976 atoms, 978 bonds, 119 residues, 1 model selected
> select
> #17/A:52-66,88-101,112-125,153-167,179-184,186-189,191-193,209-221,232-245,261-263,267-272,287-301,318-336,356-365,455-458,462-474,500-506,521-524,553-556,561-582,606-608,631-659,661-663,671-676,689-695,700-710,721-730,739-748,775-788,790-799,806-808,810-812,821-835
2622 atoms, 2639 bonds, 329 residues, 1 model selected
> select
> #17/A:35-44,75-84,129-131,146-148,171-176,198-203,225-229,253-256,275-280,368-370,373-375,389-394,399-405,432-437,477-482,513-518,536-543,681-684,733-738,752-755,760-762,764-767
976 atoms, 978 bonds, 119 residues, 1 model selected
> select
> #17/A:52-66,88-101,112-125,153-167,179-184,186-189,191-193,209-221,232-245,261-263,267-272,287-301,318-336,356-365,455-458,462-474,500-506,521-524,553-556,561-582,606-608,631-659,661-663,671-676,689-695,700-710,721-730,739-748,775-788,790-799,806-808,810-812,821-835
2622 atoms, 2639 bonds, 329 residues, 1 model selected
> color zone #18 near sel distance 4.41
> color zone #18 near sel distance 4.43
> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_mutations-a.cxs
——— End of log from Fri Mar 11 14:53:36 2022 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 496.49
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Locale: en_US.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7071
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 34,140,291,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.10
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.32.2
ChimeraX-AtomicLibrary: 5.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202201150102
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.1
ChimeraX-ModelPanel: 1.3.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.7.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.3
filelock: 3.4.2
fonttools: 4.28.5
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.25
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.0.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.0
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.0
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.24
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 303
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.8
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (3)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in lx4/session saving |
comment:2 by , 4 years ago
I see near the end of the Log that the there were MemoryError messages trying to save a session. I guess the opening of a session that caused the crash was because ChimeraX was out of memory.
comment:3 by , 4 years ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
There are several tracebacks in the log:
- KeyError: "No known data format 'EMDB'"
- IndexError: list index out of range
- MemoryError
Not much we can do about running out of memory.
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Reported by Nebojsa Bogdanovic