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Opened 5 years ago
Last modified 5 years ago
#4454 assigned defect
Commands from newly installed bundles not available
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Cannot install SEQCROW to use the angle function
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\zeropin\Google Drive\Research\122320NextSeq\CTCF(Upstream)
> Analysis\Structural comparison.cxs" format session
Log from Fri Apr 2 11:49:26 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/zeropin/Google Drive/Research/122320NextSeq/CTCF(Upstream)
> Analysis/Structural analysis of methylation effect.cxs"
Log from Fri Apr 2 00:16:10 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5t00
Summary of feedback from opening 5t00 fetched from pdb
---
warnings | Atom HO5' is not in the residue template for DT /B:1
Atom HO5' is not in the residue template for DG /C:1
Atom HO5' is not in the residue template for DT /E:1
Atom HO5' is not in the residue template for DG /F:1
notes | Fetching compressed mmCIF 5t00 from
http://files.rcsb.org/download/5t00.cif
Fetching CCD 5CM from http://ligand-expo.rcsb.org/reports/5/5CM/5CM.cif
5t00 title:
Human CTCF ZnF3-7 and methylated DNA complex [more info...]
Chain information for 5t00 #1
---
Chain | Description
A D | Transcriptional repressor CTCF
B E | DNA (5'-tag(5CM)gccccctgctggc-3')
C F | DNA (5'-gccagcaggggg(5CM)GCTA-3')
Non-standard residues in 5t00 #1
---
ZN — zinc ion
5t00 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #1/D
2309 atoms, 2320 bonds, 19 pseudobonds, 163 residues, 2 models selected
> hide sel cartoons
> hide selatoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/D
> select #1/C
557 atoms, 588 bonds, 30 residues, 1 model selected
> select #1/B
557 atoms, 574 bonds, 39 residues, 1 model selected
> select #1/E
545 atoms, 574 bonds, 27 residues, 1 model selected
> hide #1/E
> hide #1/F
> select #1/A
2339 atoms, 2338 bonds, 20 pseudobonds, 176 residues, 2 models selected
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> select #1/B
557 atoms, 574 bonds, 39 residues, 1 model selected
> color sel bynucleotide
> color sel bynucleotide
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 535 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 535 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 535 atom styles
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 535 atom styles
> select #1/C
557 atoms, 588 bonds, 30 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 544 atom styles
> show sel atoms
Alignment identifier is 1/C
> ui mousemode right zoom
> ui mousemode right zoom
> ui mousemode right rotate
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> select #1/C
557 atoms, 588 bonds, 30 residues, 1 model selected
> select #1/A
2339 atoms, 2338 bonds, 20 pseudobonds, 176 residues, 2 models selected
Alignment identifier is 1/A
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> style sel stick
Changed 12 atom styles
> hide sel atoms
> style sel stick
Changed 12 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 12 atom styles
> style sel sphere
Changed 12 atom styles
> style sel ball
Changed 12 atom styles
> show sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> color sel bychain
> color sel bychain
> style sel ball
Changed 12 atom styles
> style sel ball
Changed 12 atom styles
> show sel atoms
> color sel byhetero
> select
6860 atoms, 6982 bonds, 131 pseudobonds, 461 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> hide sel atoms
> select #1/B
557 atoms, 574 bonds, 39 residues, 1 model selected
Alignment identifier is 1/B
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel atoms
> save "C:/Users/zeropin/Google Drive/Research/122320NextSeq/CTCF(Upstream)
> Analysis/Structural analysis of methylation effect.cxs"
> open 5kkq
Summary of feedback from opening 5kkq fetched from pdb
---
warnings | Atom HO5' is not in the residue template for DT /B:1
Atom HO5' is not in the residue template for DG /C:1
Atom HO5' is not in the residue template for DT /E:1
Atom HO5' is not in the residue template for DG /F:1
note | Fetching compressed mmCIF 5kkq from
http://files.rcsb.org/download/5kkq.cif
5kkq title:
Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure
[more info...]
Chain information for 5kkq #2
---
Chain | Description
A D | Transcriptional repressor CTCF
B E | DNA (5'-D(*TP*ap*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
C F | DNA (5'-D(*GP*CP*CP*ap*GP*CP*ap*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3')
Non-standard residues in 5kkq #2
---
ZN — zinc ion
5kkq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #2/A
2443 atoms, 2391 bonds, 20 pseudobonds, 232 residues, 2 models selected
> ui mousemode right zoom
> select #2/D
2433 atoms, 2373 bonds, 20 pseudobonds, 237 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #2/E
573 atoms, 571 bonds, 58 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> hide sel atoms
> select #2/D
2433 atoms, 2373 bonds, 20 pseudobonds, 237 residues, 2 models selected
> select #2/C
582 atoms, 585 bonds, 58 residues, 1 model selected
> select #2/A
2443 atoms, 2391 bonds, 20 pseudobonds, 232 residues, 2 models selected
> select #2/B
571 atoms, 571 bonds, 56 residues, 1 model selected
> select #2/F
580 atoms, 585 bonds, 56 residues, 1 model selected
> hide sel atoms
> select #2/A
2443 atoms, 2391 bonds, 20 pseudobonds, 232 residues, 2 models selected
> hide sel surfaces
> hide sel surfaces
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel cartoons
Alignment identifier is 2/A
> hide sel cartoons
> color #2/A red
> color #2/A blue
> color #1/A orange
> select #2/B
571 atoms, 571 bonds, 56 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> hide sel surfaces
> hide sel atoms
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 532 atom styles
Alignment identifier is 2/B
> hide sel atoms
> select #2/B
571 atoms, 571 bonds, 56 residues, 1 model selected
> select #2/orange
Nothing selected
> select #2/b
571 atoms, 571 bonds, 56 residues, 1 model selected
> color #2/b orange
> select clear
> color #1/b blue
> select #2/C
582 atoms, 585 bonds, 58 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> hide sel surfaces
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 541 atom styles
> show sel atoms
Alignment identifier is 2/C
> hide sel atoms
> hide sel atoms
> color #2/c orange
> color #1/c blue
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
Drag select of 28 atoms, 34 bonds
> select clear
> save "C:/Users/zeropin/Google Drive/Research/122320NextSeq/CTCF(Upstream)
> Analysis/Structural analysis of methylation effect.cxs"
opened ChimeraX session
> select #1
6860 atoms, 6982 bonds, 131 pseudobonds, 461 residues, 3 models selected
> hide #1
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 12 atom styles
> color sel byhetero
> select clear
> color #2/C blue
> select clear
> ui mousemode right distance
> distance #2/C:3@H5 #2/A:451@OD2
Distance between 5kkq #2/C DC 3 H5 and /A ASP 451 OD2: 2.635Å
> ui mousemode right translate
> hide #1.2 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> show #1.1 models
> show #1.2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select ::name="HOH"
424 atoms, 424 residues, 2 models selected
> hide sel & #!2 atoms
> close #1
> color sel byhetero
> color sel byhetero
> color sel byhetero
> color sel bynucleotide
> color sel bynucleotide
> select clear
> set bgColor white
> lighting simple
> lighting simple
> lighting soft
> lighting full
> set bgColor black
> open 5yel
5yel title:
Crystal structure of CTCF ZFs6-11-gb7CSE [more info...]
Chain information for 5yel #1
---
Chain | Description
A B | Transcriptional repressor CTCF
C E | DNA (26-mer)
D F | DNA (26-mer)
Non-standard residues in 5yel #1
---
ZN — zinc ion
5yel mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #1/B
1333 atoms, 1361 bonds, 27 pseudobonds, 174 residues, 3 models selected
> select #1/A
1321 atoms, 1349 bonds, 27 pseudobonds, 172 residues, 3 models selected
> show sel cartoons
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> ui mousemode right zoom
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel cartoons
Alignment identifier is 1/A
> hide sel cartoons
> show sel cartoons
> show sel surfaces
> color sel byhetero
> set bgColor white
> set bgColor black
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> show sel atoms
> select #1/B
1333 atoms, 1361 bonds, 27 pseudobonds, 174 residues, 3 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> close #1
> open 5yel
5yel title:
Crystal structure of CTCF ZFs6-11-gb7CSE [more info...]
Chain information for 5yel #1
---
Chain | Description
A B | Transcriptional repressor CTCF
C E | DNA (26-mer)
D F | DNA (26-mer)
Non-standard residues in 5yel #1
---
ZN — zinc ion
5yel mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> view #!1 clip false
> select #1/A
1321 atoms, 1349 bonds, 27 pseudobonds, 172 residues, 3 models selected
> select #1/B
1333 atoms, 1361 bonds, 27 pseudobonds, 174 residues, 3 models selected
> hide sel cartoons
> hide sel surfaces
> hide sel surfaces
> hide sel atoms
> select #1/C
533 atoms, 597 bonds, 26 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> select #1/D
526 atoms, 590 bonds, 26 residues, 1 model selected
> hide sel atoms
> select #1/A
1321 atoms, 1349 bonds, 27 pseudobonds, 172 residues, 3 models selected
> hide sel atoms
> show sel cartoons
Alignment identifier is 1/A
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel cartoons
> color sel byhetero
> style sel ball
Changed 8 atom styles
> select #1/E
533 atoms, 597 bonds, 26 residues, 1 model selected
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 533 atom styles
> show sel atoms
> select #1/F
526 atoms, 590 bonds, 26 residues, 1 model selected
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 526 atom styles
> show sel atoms
> hide sel cartoons
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> show sel atoms
> select #1/E
533 atoms, 597 bonds, 26 residues, 1 model selected
Alignment identifier is 1/E
> hide sel atoms
> hide sel atoms
> select #1/F
526 atoms, 590 bonds, 26 residues, 1 model selected
Alignment identifier is 1/F
> hide sel atoms
> hide sel atoms
> color sel bynucleotide
> color sel byhetero
> ui mousemode right translate
> select clear
> view #!2 clip false
> select #2
7182 atoms, 7076 bonds, 135 pseudobonds, 697 residues, 4 models selected
> select #1
4772 atoms, 5084 bonds, 176 pseudobonds, 450 residues, 4 models selected
> select #2
7182 atoms, 7076 bonds, 135 pseudobonds, 697 residues, 4 models selected
> view #!1-2 clip false
> ui mousemode right "translate selected atoms"
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> select clear
> mmaker #2/C #1/F matrix nucleic
> matchmaker #2/C #1/F matrix Nucleic
Missing required "to" argument
> mmaker #2/C to #1/F matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5yel, chain F (#1) with 5kkq, chain C (#2), sequence alignment
score = 27.1
RMSD between 8 pruned atom pairs is 0.798 angstroms; (across all 8 pairs:
0.798)
> mmaker #2/C DC 3 to #1/F DC 21 matrix nucleic
> matchmaker #2/C DC 3 to #1/F DC 21 matrix nucleic
Expected a keyword
> mmaker #2/C DC 3 to #1/F DC 21
> matchmaker #2/C DC 3 to #1/F DC 21
Expected a keyword
> select #1
4772 atoms, 5084 bonds, 176 pseudobonds, 450 residues, 4 models selected
> ui mousemode right "translate selected atoms"
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> select #1
4772 atoms, 5084 bonds, 176 pseudobonds, 450 residues, 4 models selected
> ui mousemode right zoom
> ui mousemode right "translate selected atoms"
> select clear
> undo
> undo
> select #1/A
1321 atoms, 1349 bonds, 27 pseudobonds, 172 residues, 3 models selected
Alignment identifier is 1/A
> hide sel atoms
> show sel atoms
> hide sel atoms
> undo
> ui mousemode right translate
> show sel atoms
> show sel atoms
> hide sel atoms
> select clear
> show sel atoms
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting full
> lighting simple
> ui tool show Distances
> select clear
> select #1/A 451
Expected a keyword
> select #1/A ASP 451
Expected a keyword
> ui mousemode right distance
> ui mousemode right select
> select #2/C:3@H5
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/C
582 atoms, 585 bonds, 58 residues, 1 model selected
> select #2/C 3
Expected a keyword
> select #2/C DC 3
Expected a keyword
> select #2/C:3
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #2/C:DC
150 atoms, 156 bonds, 5 residues, 1 model selected
> select #2/C:3
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #2/C:4
32 atoms, 34 bonds, 1 residue, 1 model selected
> select #2/C:3
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #1/F
526 atoms, 590 bonds, 26 residues, 1 model selected
> select #1/F:21
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/F:22
21 atoms, 23 bonds, 1 residue, 1 model selected
> mmaker #2/C:3 to #1/F:21 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5yel, chain F (#1) with 5kkq, chain C (#2), sequence alignment
score = 4
Fewer than 3 residues aligned; cannot match 5yel, chain F with 5kkq, chain C
> mmaker #2/C:2:4 to #1/F:20:22 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5yel, chain F (#1) with 5kkq, chain C (#2), sequence alignment
score = 8
Fewer than 3 residues aligned; cannot match 5yel, chain F with 5kkq, chain C
> mmaker #2/C to #1/F matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5yel, chain F (#1) with 5kkq, chain C (#2), sequence alignment
score = 27.1
RMSD between 8 pruned atom pairs is 0.798 angstroms; (across all 8 pairs:
0.798)
> select #1/F
526 atoms, 590 bonds, 26 residues, 1 model selected
Destroying pre-existing alignment with identifier 1/F
Alignment identifier is 1/F
> select #1/F:20-22
59 atoms, 65 bonds, 3 residues, 1 model selected
> mmaker #1/F:20-22 to #2/C:2-4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5kkq, chain A (#2) with 5yel, chain A (#1), sequence alignment
score = 0
Fewer than 3 residues aligned; cannot match 5kkq, chain A with 5yel, chain A
> mmaker #1/F:20-23 to #2/C:2-5
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 5kkq, chain A (#2) with 5yel, chain A (#1), sequence alignment
score = 0
Fewer than 3 residues aligned; cannot match 5kkq, chain A with 5yel, chain A
> mmaker #1/F:20-23 to #2/C:2-5 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5kkq, chain C (#2) with 5yel, chain F (#1), sequence alignment
score = 16
RMSD between 4 pruned atom pairs is 0.314 angstroms; (across all 4 pairs:
0.314)
> mmaker #1/F:20-22 to #2/C:2-4 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5kkq, chain C (#2) with 5yel, chain F (#1), sequence alignment
score = 12
RMSD between 3 pruned atom pairs is 0.128 angstroms; (across all 3 pairs:
0.128)
> mmaker #1/F:21 to #2/C:3 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5kkq, chain C (#2) with 5yel, chain F (#1), sequence alignment
score = 4
Fewer than 3 residues aligned; cannot match 5kkq, chain C with 5yel, chain F
> mmaker #1/F:20-21 to #2/C:3-4 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5kkq, chain C (#2) with 5yel, chain F (#1), sequence alignment
score = 4
Fewer than 3 residues aligned; cannot match 5kkq, chain C with 5yel, chain F
> mmaker #1/F:20-22 to #2/C:2-4 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5kkq, chain C (#2) with 5yel, chain F (#1), sequence alignment
score = 12
RMSD between 3 pruned atom pairs is 0.128 angstroms; (across all 3 pairs:
0.128)
Drag select of 1 bonds, 1 atoms
Drag select of 1 atoms, 2 pseudobonds
> select clear
> ui mousemode right translate
> hide #1
> select #2
7182 atoms, 7076 bonds, 135 pseudobonds, 697 residues, 4 models selected
> select #2/B
571 atoms, 571 bonds, 56 residues, 1 model selected
> color sel byhetero
> select clear
> select #1/A
1321 atoms, 1349 bonds, 27 pseudobonds, 172 residues, 3 models selected
> ui mousemode right zoom
> ui mousemode right translate
> color #1/A red
> color #1/A orange
> select clear
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> select clear
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> select clear
> show sel cartoons
Drag select of 2 residues
> select #2/A
2443 atoms, 2391 bonds, 20 pseudobonds, 232 residues, 2 models selected
Alignment identifier is 2/A
> ui mousemode right zoom
> show sel cartoons
> select clear
> hide sel cartoons
> hide sel cartoons
> hide sel atoms
> show sel atoms
> color sel byhetero
> show sel atoms
> hide sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select clear
> color #2/A green
> set bgColor white
> color sel bychain
> color sel byhetero
> select #2/C:3
30 atoms, 31 bonds, 1 residue, 1 model selected
> color sel bynucleotide
> color sel byhetero
> color #2/C:3 black
> color sel byhetero
> select clear
> color #2/B black
> color byhetero
> color #2/B green
> color #2/B black
> color sel byhetero
> select #2/B
571 atoms, 571 bonds, 56 residues, 1 model selected
> color sel byhetero
> select #2/A
2443 atoms, 2391 bonds, 20 pseudobonds, 232 residues, 2 models selected
> color #2/A green
> color #2/A:451
> select clear
> select #2/A:451
12 atoms, 11 bonds, 1 residue, 1 model selected
> select down
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save "C:/Users/zeropin/Google Drive/Research/122320NextSeq/CTCF(Upstream)
> Analysis/Structural comparison.cxs" includeMaps true
opened ChimeraX session
> select ::name="ZN"
22 atoms, 22 residues, 2 models selected
> show selatoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show selatoms atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select ::name="ZN"
22 atoms, 22 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select #2/A:505
1 atom, 1 residue, 1 model selected
> show sel atoms
> color selAtoms purple
> select clear
> select #2/A:451
12 atoms, 11 bonds, 1 residue, 1 model selected
> color #2/A:451 black
> undo
> color #2/A:451 black atoms
> color sel byhetero
> select clear
> ui mousemode right distance
> distance #2/A:451@OD1 #2/C:3@H41
Distance between 5kkq #2/A ASP 451 OD1 and /C DC 3 H41: 2.158Å
> ui mousemode right "move label"
> ui mousemode right zoom
> close #3
> select #2/A:4511
Nothing selected
> select #2/A:451
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:451
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:451
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:451
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right distance
> distance #2/A:451@OD2 #2/C:3@H5
Distance between 5kkq #2/A ASP 451 OD2 and /C DC 3 H5: 2.635Å
> distance #2/A:451@OD1 #2/C:3@H41
Distance between 5kkq #2/A ASP 451 OD1 and /C DC 3 H41: 2.158Å
> ui mousemode right "move label"
> select clear
> save "C:/Users/zeropin/Google Drive/Research/122320NextSeq/CTCF(Upstream)
> Analysis/Structural analysis of methylation effect.cxs" includeMaps true
> open 5t00
Summary of feedback from opening 5t00 fetched from pdb
---
warnings | Atom HO5' is not in the residue template for DT /B:1
Atom HO5' is not in the residue template for DG /C:1
Atom HO5' is not in the residue template for DT /E:1
Atom HO5' is not in the residue template for DG /F:1
5t00 title:
Human CTCF ZnF3-7 and methylated DNA complex [more info...]
Chain information for 5t00 #4
---
Chain | Description
A D | Transcriptional repressor CTCF
B E | DNA (5'-tag(5CM)gccccctgctggc-3')
C F | DNA (5'-gccagcaggggg(5CM)GCTA-3')
Non-standard residues in 5t00 #4
---
ZN — zinc ion
5t00 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #3/A
Nothing selected
> show cartoons
> ui mousemode right zoom
> undo
> select #4/A
2339 atoms, 2338 bonds, 20 pseudobonds, 176 residues, 2 models selected
> ui mousemode right translate
> select #4/D,E,F
3407 atoms, 3482 bonds, 66 pseudobonds, 216 residues, 3 models selected
> hide #4/D,E,F
> hide #4/A
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> select #4/A
2339 atoms, 2338 bonds, 20 pseudobonds, 176 residues, 2 models selected
> show sel cartoons
> select #4/B
557 atoms, 574 bonds, 39 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 535 atom styles
> show sel atoms
> select #4/C
557 atoms, 588 bonds, 30 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 544 atom styles
> show sel atoms
> select #4/A
2339 atoms, 2338 bonds, 20 pseudobonds, 176 residues, 2 models selected
Alignment identifier is 4/A
> hide sel cartoons
> select #4/B
557 atoms, 574 bonds, 39 residues, 1 model selected
Alignment identifier is 4/B
> hide sel atoms
> hide sel atoms
> select #4/C
557 atoms, 588 bonds, 30 residues, 1 model selected
Alignment identifier is 4/C
> hide sel atoms
> hide sel atoms
> select #1/F
526 atoms, 590 bonds, 26 residues, 1 model selected
Alignment identifier is 1/F
> select #1/E
533 atoms, 597 bonds, 26 residues, 1 model selected
Alignment identifier is 1/E
> mmaker #4/C:2-4 to #1/F:20-22 matrix nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 5yel, chain F (#1) with 5t00, chain C (#4), sequence alignment
score = 12
RMSD between 3 pruned atom pairs is 0.183 angstroms; (across all 3 pairs:
0.183)
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> select #4
6860 atoms, 6982 bonds, 131 pseudobonds, 461 residues, 3 models selected
> select ::name="HOH"
424 atoms, 424 residues, 2 models selected
> hide sel atoms
> ui mousemode right rotate
> select #4
6860 atoms, 6982 bonds, 131 pseudobonds, 461 residues, 3 models selected
> hide sel atoms
> close #4
> ui mousemode right rotate
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\zeropin\Desktop\movie2.mp4
Movie saved to \C:Users\\...\Desktop\movie2.mp4
> ui mousemode right pivot
> ui mousemode right translate
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\zeropin\Desktop\movie3.mp4
Movie saved to \C:Users\\...\Desktop\movie3.mp4
> ui mousemode right distance
> select #4/458
Nothing selected
> select #4/A:458
Nothing selected
> select #2/A:458
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> style sel stick
Changed 22 atom styles
> style sel ball
Changed 22 atom styles
> show sel atoms
> select #1/A:458
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel ball
Changed 9 atom styles
> show sel atoms
> select #2/A:458
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> style sel stick
Changed 22 atom styles
> show sel atoms
> hide sel atoms
> select #1/A:458
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2/B:15@OP2
1 atom, 1 residue, 1 model selected
> angle #2/B:15@OP2 #2/A:451@OD1 #2/A:463
angle is provided by the uninstalled bundle SEQCROW
> toolshed show
> angle #2/B:15@OP2 #2/A:451@OD1 #2/A:463
angle is provided by the uninstalled bundle SEQCROW
Downloading bundle SEQCROW-0.24.3-py3-none-any.whl
Bundle installation canceled
Downloading bundle SEQCROW-0.24.3-py3-none-any.whl
Successfully installed SEQCROW-0.24.3 Send2Trash-1.5.0
Installed SEQCROW (0.24.3)
resumed SEQCROW queue
> angle #2/B:15@OP2 #2/A:451@OD1 #2/A:463
angle is provided by the uninstalled bundle SEQCROW
Downloading bundle SEQCROW-0.24.3-py3-none-any.whl
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished
session=self.session)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
AttributeError: 'str' object has no attribute 'name'
AttributeError: 'str' object has no attribute 'name'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
See log for complete Python traceback.
Downloading bundle SEQCROW-0.24.3-py3-none-any.whl
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished
session=self.session)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
AttributeError: 'str' object has no attribute 'name'
AttributeError: 'str' object has no attribute 'name'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 452.66
OpenGL renderer: Quadro T1000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20QTS00W00
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 16,901,595,136
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
Send2Trash: 1.5.0
SEQCROW: 0.24.3
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (1)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Commands from newly installed bundles not available |
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