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Opened 5 years ago
Last modified 5 years ago
#4041 feedback defect
"sel" specifier vs. "select" keyword
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Hmm... not sure whether to call this a bug or not. I recently added the keyword "select" to the "isolde stepTo" command, to control whether or not the new focal residue becomes selected. Problem is, this breaks the command "isolde stepTo sel" because the keyword "select" overrides the built-in "sel". The question is, should it do so, or should "sel" take precedence here?
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7k0r
Summary of feedback from opening 7k0r fetched from pdb
---
notes | Fetching compressed mmCIF 7k0r from
http://files.rcsb.org/download/7k0r.cif
Fetching CCD U5P from http://ligand-expo.rcsb.org/reports/U/U5P/U5P.cif
7k0r title:
Nucleotide bound SARS-CoV-2 Nsp15 [more info...]
Chain information for 7k0r #1
---
Chain | Description
A B C D E F | ORF1ab polyprotein
Non-standard residues in 7k0r #1
---
PO4 — phosphate ion
U5P — uridine-5'-monophosphate
> open 22610 fromDatabase emdb
Summary of feedback from opening 22610 fetched from emdb
---
note | Fetching compressed map 22610 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22610/map/emd_22610.map.gz
Opened emd_22610.map, grid size 256,256,256, pixel 1.14, shown at level 0.638,
step 1, values float32
> clipper associate #2 toModel #1
7k0r title:
Nucleotide bound SARS-CoV-2 Nsp15 [more info...]
Chain information for 7k0r
---
Chain | Description
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | ORF1ab polyprotein
Non-standard residues in 7k0r #1.2
---
PO4 — phosphate ion
U5P — uridine-5'-monophosphate
> volume gaussian #1 bfactor 50
> clipper associate #2 toModel #1
> isolde start
> set selectionWidth 4
Done loading forcefield
> set bgColor white
> clipper set contourSensitivity 0.25
> addh
Summary of feedback from adding hydrogens to 7k0r #1.2
---
warnings | Not adding hydrogens to /A MET 1 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A LYS 13 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 20 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 22 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 35 CB because it is missing heavy-atom bond
partners
133 messages similar to the above omitted
notes | Termini for 7k0r (#1.2) chain A determined from SEQRES records
Termini for 7k0r (#1.2) chain B determined from SEQRES records
Termini for 7k0r (#1.2) chain C determined from SEQRES records
Termini for 7k0r (#1.2) chain D determined from SEQRES records
Termini for 7k0r (#1.2) chain E determined from SEQRES records
1 messages similar to the above omitted
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A MET 1, /B MET 1, /C
MET 1, /D MET 1, /E MET 1, /F MET 1
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A LYS 345, /B LYS 345, /C
LYS 345, /D LYS 345, /E LYS 345, /F LYS 345
1902 hydrogen bonds
Adding 'H' to /A MET 1
Adding 'H' to /B MET 1
Adding 'H' to /C MET 1
Adding 'H' to /D MET 1
Adding 'H' to /E MET 1
1 messages similar to the above omitted
15450 hydrogens added
> hide HC
Loading residue template for PO4 from internal database
Loading residue template for U5P from internal database
> select #1
31584 atoms, 31920 bonds, 2082 residues, 15 models selected
> select clear
> select clear
> select clear
> isolde stepto first
> alias st isolde step $*
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> alias sa swapaa mousemode sel $*
> sa LYS
Traceback (most recent call last):
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2724, in start_sim
main_sel = self._last_main_sel = self._get_main_sim_selection()
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection
raise TypeError('You must select at least one atom from the current '
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection
raise TypeError('You must select at least one atom from the current '
See log for complete Python traceback.
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> sa LYS
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> open 7k0r
7k0r title:
Nucleotide bound SARS-CoV-2 Nsp15 [more info...]
Chain information for 7k0r #2
---
Chain | Description
A B C D E F | ORF1ab polyprotein
Non-standard residues in 7k0r #2
---
PO4 — phosphate ion
U5P — uridine-5'-monophosphate
> style sel stick
Changed 7 atom styles
> style stick
Changed 47646 atom styles
> color #2 lightgreen
> close #2#1.3#1#1.1-2
> open 7cyq
Summary of feedback from opening 7cyq fetched from pdb
---
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 25254
note | Fetching compressed mmCIF 7cyq from
http://files.rcsb.org/download/7cyq.cif
7cyq title:
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription
complex reveals an intermediate state in cap synthesis [more info...]
Chain information for 7cyq #1
---
Chain | Description
A | Replicase polyprotein 1ab
B D | nsp8
C | nsp7
E F | Replicase polyprotein 1ab
G | Replicase polyprotein 1ab
I | Primer
J | Template
Non-standard residues in 7cyq #1
---
MG — magnesium ion
ZN — zinc ion
7cyq title:
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription
complex reveals an intermediate state in cap synthesis [more info...]
Chain information for 7cyq
---
Chain | Description
1.2/A | Replicase polyprotein 1ab
1.2/B 1.2/D | nsp8
1.2/C | nsp7
1.2/E 1.2/F | Replicase polyprotein 1ab
1.2/G | Replicase polyprotein 1ab
1.2/I | Primer
1.2/J | Template
Non-standard residues in 7cyq #1.2
---
MG — magnesium ion
ZN — zinc ion
> view
> open 30504 fromDatabase emdb
Summary of feedback from opening 30504 fetched from emdb
---
note | Fetching compressed map 30504 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30504/map/emd_30504.map.gz
Opened emd_30504.map, grid size 448,448,448, pixel 0.82, shown at level 0.121,
step 2, values float32
> volume gaussian #2 bfactor 50
> clipper associate #2,3 toModel #1
> addh
Summary of feedback from adding hydrogens to 7cyq #1.2
---
warnings | Not adding hydrogens to /A LYS 849 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /B PHE 6 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B GLU 20 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B TYR 22 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B GLN 24 CB because it is missing heavy-atom bond
partners
50 messages similar to the above omitted
notes | Termini for 7cyq (#1.2) chain A determined from SEQRES records
Termini for 7cyq (#1.2) chain B determined from SEQRES records
Termini for 7cyq (#1.2) chain C determined from SEQRES records
Termini for 7cyq (#1.2) chain D determined from SEQRES records
Termini for 7cyq (#1.2) chain I determined from SEQRES records
4 messages similar to the above omitted
Chain-initial residues that are actual N termini: /E ALA 1
Chain-initial residues that are not actual N termini: /A ALA 4, /B PHE 6, /C
LYS 2, /D PHE 6, /I G 9, /J U 24, /F VAL 2, /F ALA 208, /F VAL 340, /E ALA
208, /E VAL 340, /G ASN 1
Chain-final residues that are actual C termini: /I G 33, /G GLN 113
Chain-final residues that are not actual C termini: /A THR 929, /B ASN 192, /C
GLU 73, /D ALA 191, /J G 50, /F GLY 203, /F ALA 336, /F PRO 593, /E GLY 203,
/E ALA 336, /E PRO 593
Missing OXT added to C-terminal residue /G GLN 113
1980 hydrogen bonds
Adding 'H' to /A ALA 4
Adding 'H' to /B PHE 6
Adding 'H' to /C LYS 2
Adding 'H' to /D PHE 6
Adding 'H' to /F VAL 2
5 messages similar to the above omitted
/A THR 929 is not terminus, removing H atom from 'C'
/B ASN 192 is not terminus, removing H atom from 'C'
/C GLU 73 is not terminus, removing H atom from 'C'
/D ALA 191 is not terminus, removing H atom from 'C'
/F PRO 593 is not terminus, removing H atom from 'C'
1 messages similar to the above omitted
20881 hydrogens added
> clipper set contourSensitivity 025
> clipper set contourSensitivity 0.25
> cofr centerOfView
> select #1
42723 atoms, 43294 bonds, 95 pseudobonds, 2717 residues, 18 models selected
Deleted the following atoms from residue GDP A1003: H3
> select ~protein
1722 atoms, 1844 bonds, 91 pseudobonds, 62 residues, 23 models selected
> select ~protein&~nucleic
49 atoms, 42 bonds, 36 pseudobonds, 10 residues, 22 models selected
> delete sel
> select #1
42720 atoms, 43291 bonds, 95 pseudobonds, 2717 residues, 24 models selected
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
> select clear
> select clear
> select clear
> select clear
> select clear
> open 7kqw
Summary of feedback from opening 7kqw fetched from pdb
---
notes | Fetching compressed mmCIF 7kqw from
http://files.rcsb.org/download/7kqw.cif
Fetching CCD SNM from http://ligand-expo.rcsb.org/reports/S/SNM/SNM.cif
7kqw title:
Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, methylated)
[more info...]
Chain information for 7kqw #2
---
Chain | Description
A | NSP3
> matchmaker #2 to #1/E
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 7cyq, chain E (#1.2) with 7kqw, chain A (#2), sequence alignment
score = 51.6
RMSD between 20 pruned atom pairs is 1.321 angstroms; (across all 129 pairs:
28.174)
> matchmaker #2 to #1/F
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 7cyq, chain F (#1.2) with 7kqw, chain A (#2), sequence alignment
score = 69.4
RMSD between 5 pruned atom pairs is 0.709 angstroms; (across all 171 pairs:
24.194)
> close #2
> select clear
> dssp
> open 5rlf
Summary of feedback from opening 5rlf fetched from pdb
---
notes | Fetching compressed mmCIF 5rlf from
http://files.rcsb.org/download/5rlf.cif
Fetching CCD NY7 from http://ligand-expo.rcsb.org/reports/N/NY7/NY7.cif
5rlf title:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase
in complex with Z235341991 [more info...]
Chain information for 5rlf #2
---
Chain | Description
A B | Helicase
Non-standard residues in 5rlf #2
---
NY7 — N-(2-methoxy-5-methylphenyl)glycinamide
PO4 — phosphate ion
ZN — zinc ion
5rlf mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> matchmaker #2 to #1/F
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 7cyq, chain F (#1.2) with 5rlf, chain A (#2), sequence alignment
score = 2875.4
RMSD between 358 pruned atom pairs is 1.292 angstroms; (across all 567 pairs:
2.557)
> open 5rlj
Summary of feedback from opening 5rlj fetched from pdb
---
notes | Fetching compressed mmCIF 5rlj from
http://files.rcsb.org/download/5rlj.cif
Fetching CCD VW4 from http://ligand-expo.rcsb.org/reports/V/VW4/VW4.cif
5rlj title:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase
in complex with Z1407673036 [more info...]
Chain information for 5rlj #3
---
Chain | Description
A B | Helicase
Non-standard residues in 5rlj #3
---
PO4 — phosphate ion
VW4 — (2S)-2-phenylpropane-1-sulfonamide
ZN — zinc ion
5rlj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close #2
> matchmaker #3 to #1/F
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 7cyq, chain F (#1.2) with 5rlj, chain A (#3), sequence alignment
score = 2889.8
RMSD between 365 pruned atom pairs is 1.307 angstroms; (across all 567 pairs:
2.692)
> isolde restrain torsions #1/F templateResidues #3/A angleRange 120
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> isolde restrain torsions #1/E templateResidues #3/A angleRange 120
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> hide #!3 models
> select #1/E,F
17872 atoms, 18070 bonds, 28 pseudobonds, 1177 residues, 3 models selected
> select clear
> select clear
> select clear
> select clear
> isolde restrain distances #1/E templateAtoms #3/A
RMSD between 564 pruned atom pairs is 2.033 angstroms; (across all 568 pairs:
2.074)
RMSD between 4 pruned atom pairs is 1.940 angstroms; (across all 4 pairs:
1.940)
> isolde restrain distances #1/F templateAtoms #3/A
RMSD between 534 pruned atom pairs is 2.155 angstroms; (across all 567 pairs:
2.684)
RMSD between 7 pruned atom pairs is 3.571 angstroms; (across all 33 pairs:
22.541)
RMSD between 7 pruned atom pairs is 3.654 angstroms; (across all 26 pairs:
23.019)
RMSD between 5 pruned atom pairs is 3.266 angstroms; (across all 19 pairs:
22.203)
RMSD between 3 pruned atom pairs is 4.342 angstroms; (across all 14 pairs:
32.601)
RMSD between 3 pruned atom pairs is 1.233 angstroms; (across all 11 pairs:
34.459)
RMSD between 3 pruned atom pairs is 2.739 angstroms; (across all 8 pairs:
27.900)
No further alignments of 3 or more residues found.
> select clear
> select clear
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> isolde release distances sel
> isolde release torsions sel
> isolde adjust distances #1 displayThreshold 0.5
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde release distances sel
> isolde release torsions sel
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde release distances sel
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> isolde release distances sel
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde release distances sel
> select clear
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> isolde release distances sel
> select clear
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde release distances sel
> open 6xip
Summary of feedback from opening 6xip fetched from pdb
---
note | Fetching compressed mmCIF 6xip from
http://files.rcsb.org/download/6xip.cif
6xip title:
The 1.5 A Crystal Structure of the Co-factor Complex of NSP7 and the
C-terminal Domain of NSP8 from SARS CoV-2 [more info...]
Chain information for 6xip #2
---
Chain | Description
A C | Non-structural protein 7
B D | Non-structural protein 8
Non-standard residues in 6xip #2
---
EDO — 1,2-ethanediol (ethylene glycol)
6xip mmCIF Assemblies
---
1| author_and_software_defined_assembly
> matchmaker #2 to #1/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 7cyq, chain D (#1.2) with 6xip, chain B (#2), sequence alignment
score = 594.7
RMSD between 106 pruned atom pairs is 0.676 angstroms; (across all 114 pairs:
1.616)
> isolde restrain distances #1/D templateAtoms #2/B
RMSD between 110 pruned atom pairs is 0.796 angstroms; (across all 114 pairs:
1.612)
RMSD between 4 pruned atom pairs is 1.789 angstroms; (across all 4 pairs:
1.789)
> isolde restrain distances #1/B templateAtoms #2/B
RMSD between 51 pruned atom pairs is 1.123 angstroms; (across all 115 pairs:
18.041)
RMSD between 5 pruned atom pairs is 3.293 angstroms; (across all 64 pairs:
23.680)
RMSD between 6 pruned atom pairs is 4.045 angstroms; (across all 59 pairs:
23.042)
RMSD between 3 pruned atom pairs is 2.110 angstroms; (across all 53 pairs:
25.894)
RMSD between 5 pruned atom pairs is 2.839 angstroms; (across all 50 pairs:
28.321)
RMSD between 4 pruned atom pairs is 3.868 angstroms; (across all 45 pairs:
25.816)
RMSD between 4 pruned atom pairs is 3.895 angstroms; (across all 41 pairs:
25.895)
RMSD between 4 pruned atom pairs is 2.848 angstroms; (across all 37 pairs:
32.533)
RMSD between 4 pruned atom pairs is 2.637 angstroms; (across all 33 pairs:
25.857)
RMSD between 3 pruned atom pairs is 0.902 angstroms; (across all 29 pairs:
26.788)
RMSD between 3 pruned atom pairs is 3.417 angstroms; (across all 26 pairs:
26.729)
RMSD between 3 pruned atom pairs is 2.646 angstroms; (across all 23 pairs:
29.663)
RMSD between 3 pruned atom pairs is 3.179 angstroms; (across all 20 pairs:
31.107)
No further alignments of 3 or more residues found.
> isolde restrain torsions #1/B templateResidues #2/B
> isolde restrain torsions #1/D templateResidues #2/B
> select #1/B,D
5593 atoms, 5630 bonds, 373 residues, 1 model selected
> hide #2 models
> select clear
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde release torsions sel
> select clear
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde release distances sel
> select clear
> isolde release torsions sel
> isolde release distances sel
> view #1/B:79
> isolde release torsions sel
> select clear
> isolde release torsions sel
> isolde release distances sel
> select clear
> alias rt isolde rel tors sel
> alias rd isolde rel dist sel
> rt
> rt
> rt
> rt
> rd
> select clear
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> rd
> rd
> rd
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> rd
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> rd
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> rd
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> rd
> dssp
> select #1
42720 atoms, 43291 bonds, 95 pseudobonds, 2717 residues, 24 models selected
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
> select clear
> select clear
> select clear
> isolde release distances #1
> select clear
> isolde adjust distances #1 kappa 0
> select clear
> isolde adjust distances #1 kappa 1
> select clear
> isolde release distances #1 strainedOnly true
> isolde release distances #1 strainedOnly true str 1.1 comp 0.9
Expected keyword "strainedOnly" or "stretchLimit"
> isolde release distances #1 strainedOnly true stretchLimit 1.1
> compressionLimit 0.9
> select clear
> isolde adjust distances #1 displayThreshold 0.5
> select clear
> open 6wd
'6wd' has no suffix
> open 6wxd
Summary of feedback from opening 6wxd fetched from pdb
---
note | Fetching compressed mmCIF 6wxd from
http://files.rcsb.org/download/6wxd.cif
6wxd title:
SARS-CoV-2 Nsp9 RNA-replicase [more info...]
Chain information for 6wxd #4
---
Chain | Description
A B | Non-structural protein 9
Non-standard residues in 6wxd #4
---
SO4 — sulfate ion
> matchmaker #4 to #1/G
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 7cyq, chain G (#1.2) with 6wxd, chain A (#4), sequence alignment
score = 557.5
RMSD between 102 pruned atom pairs is 0.805 angstroms; (across all 113 pairs:
2.807)
> isolde restrain torsions #1/G:9-100 templateResidues #4/A
> isolde restrain distances #1/G:9-100 templateAtoms #4/A
RMSD between 92 pruned atom pairs is 0.923 angstroms; (across all 92 pairs:
0.923)
> hide #4 models
> select #1/G
1747 atoms, 1763 bonds, 113 residues, 1 model selected
> select clear
> select clear
> show #4 models
> isolde restrain distances #1/G:9-120 templateAtoms #4/A
RMSD between 105 pruned atom pairs is 0.364 angstroms; (across all 105 pairs:
0.364)
> isolde restrain torsions #1/G:9-120 templateResidues #4/A
> select clear
> hide #4 models
> rd
> rt
> select clear
> rd
> rt
> select clear
> select clear
> sa LYS
> show #2 models
> hide #2 models
> show #!3 models
> hide #!3 models
> show #4 models
> view #1/C
> view #1/AL846
No objects specified.
> hide #4 models
> view #1/A:846
> isolde stepto #1/A
Multiple residues selected! Going to the first...
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
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> select clear
> select clear
> select clear
> st
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> st
> st
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> st
> st
> st
> st
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> st
> st
> st
> st
> st
> select clear
> st
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> st
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> st
> st
> st
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
50 atoms, 49 bonds, 4 residues, 1 model selected
> select clear
> st
> st
> st
> st
> st
> st
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> select clear
> select clear
> st
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> st
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> st
> select clear
> st
> st
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> st
> st
> st
> select clear
> st
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> st
> st
> st
> select clear
> st
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> st
> select clear
> st
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> st
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> st
> select clear
> st
> st
> st
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> st
> st
> st
> st
> st
> st
> select clear
> select clear
> st
> st
> st
> st
> st
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> st
> st
> st
> st
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> st
> st
> select clear
> st
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> st
> st
> select clear
> st
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> st
> select clear
> st
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> st
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> st
> st
> st
> st
> select clear
> st
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> st
> select clear
> st
> st
> st
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> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> select clear
> st
> st
> st
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> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> delete sel
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
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> st
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> st
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> st
> st
> st
> st
> st
> st
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> st
> st
> st
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> st
> st
> st
> select clear
> st
> st
> st
> st
> st
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> st
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> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
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> st
> st
> st
> st
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> st
> st
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> st
> st
> select clear
> st
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> st
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> st
> st
> select clear
> st
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> select clear
> st
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> st
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> st
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> st
> st
> st
> st
> st
> st
> st
> st
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> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
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> st
> st
> st
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> st
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> st
> st
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> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
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> st
> st
> st
> st
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> st
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> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
155 atoms, 155 bonds, 10 residues, 1 model selected
> select up
176 atoms, 176 bonds, 11 residues, 1 model selected
> select up
480 atoms, 486 bonds, 31 residues, 1 model selected
> select up
497 atoms, 502 bonds, 32 residues, 1 model selected
> select up
850 atoms, 857 bonds, 56 residues, 1 model selected
> select clear
> select clear
> select clear
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> rd
> rt
> sa LYS
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
155 atoms, 155 bonds, 10 residues, 1 model selected
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> select up
26 atoms, 24 bonds, 2 residues, 1 model selected
> select up
48 atoms, 47 bonds, 4 residues, 1 model selected
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> show #2 models
> hide #2 models
> show #!3 models
> hide #!3 models
> show #2 models
> matchmaker #2 to #1/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 7cyq, chain B (#1.2) with 6xip, chain B (#2), sequence alignment
score = 567.1
RMSD between 44 pruned atom pairs is 0.704 angstroms; (across all 115 pairs:
18.303)
> st
> hide #2 models
> st
> open 6wtc
Summary of feedback from opening 6wtc fetched from pdb
---
note | Fetching compressed mmCIF 6wtc from
http://files.rcsb.org/download/6wtc.cif
6wtc title:
Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the
C-terminal Domain of NSP8 from SARS CoV-2 [more info...]
Chain information for 6wtc #5
---
Chain | Description
A C | SARS-CoV-2 NSP7
B D | SARS-CoV-2 NSP8
Non-standard residues in 6wtc #5
---
ACY — acetic acid
6wtc mmCIF Assemblies
---
1| author_and_software_defined_assembly
> matchmaker #5 to #1/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 7cyq, chain B (#1.2) with 6wtc, chain D (#5), sequence alignment
score = 564.1
RMSD between 44 pruned atom pairs is 0.698 angstroms; (across all 115 pairs:
18.091)
> matchmaker #5 to #1/B:1.50
Invalid "to" argument: only initial part "#1/B:1" of atom specifier valid
> matchmaker #5 to #1/B:1-50
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 7cyq, chain B (#1.2) with 6wtc, chain A (#5), sequence alignment
score = 62.5
RMSD between 13 pruned atom pairs is 1.033 angstroms; (across all 42 pairs:
4.823)
> close #5
> select #1/B:1-50
522 atoms, 525 bonds, 45 residues, 1 model selected
> select clear
> select clear
> sa GLU
> sa TYR
> sa GLN
> sa VAL
> sa ASN
> sa ASP
> sa GLU
> sa LEU
> sa LYS
> sa LYS
> sa LYS
> sa LYS
> sa ASN
> sa SER
> select #1/B
2906 atoms, 2925 bonds, 187 residues, 1 model selected
> select clear
> select clear
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> rt
> rt
> rd
> select clear
> st
> st
> st
> st
> st
> st
> st
> rt
> rd
> st
> st
> st
> st
> st
> st
> st
> rd
> rt
> select clear
> st
> st
> st
> st
> st
> #1/B
Expected fewer arguments
> isolde release torsions #1/B
> isolde release distances #1/B
> select clear
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> sequence chain #1/C
Alignment identifier is 1.2/C
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> save working.cxs
Taking snapshot of stepper: 7cyq
> save working.cif #1
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> isolde ignore sel
ISOLDE: currently ignoring 1 residues in model 1.2
> delete sel
> isolde ~ignore
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> select #1/C
1152 atoms, 1155 bonds, 73 residues, 1 model selected
> select clear
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select #1/D
2831 atoms, 2850 bonds, 186 residues, 1 model selected
> select clear
> st
> sa SER
> st
> sa SER
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> sa GLU
> st
> st
> st
> sa GLU
> st
> sa GLN
> st
> st
> st
> st
> sa ASN
> st
> st
> sa ASP
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> sa LYS
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> select #1/D
2892 atoms, 2911 bonds, 186 residues, 1 model selected
> select clear
> st sel
> isolde stepto select
Missing "select" keyword's argument
> isolde stepto select
Missing "select" keyword's argument
> isolde stepto select
Missing "select" keyword's argument
> isolde stepto #1/D:55
OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 62G 10G 39G 284M 12G 51G
Swap: 4.9G 0B 4.9G
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
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-Async: 0.1
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-Clipper: 0.15.0
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: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 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-Phenix: 0.1
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
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
graphviz: 0.14.1
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
numpydoc: 1.0.0
objgraph: 3.4.1
openvr: 1.12.501
packaging: 20.4
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
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
ptyprocess: 0.6.0
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
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: 0.20
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
versioneer: 0.18
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → "sel" specifier vs. "select" keyword |
comment:2 by , 5 years ago
| Status: | accepted → feedback |
|---|
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Hi Tristan,
--Eric