The following bug report has been submitted:
Platform: Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC)
Description
I swear this was working before... for the command registered by:
def register_write_phenix_rsr(logger):
desc = CmdDesc(
required=[
('model', StructureArg),
('volume', MapArg),
('resolution', FloatArg)
],
keyword=[
('file_name', FileNameArg),
('restrain_positions', BoolArg),
('include_hydrogens', BoolArg)
],
synopsis='Write input files for phenix.real_space_refine, restraining the model to its current geometry.'
)
register('isolde write phenixRsrInput', desc, write_rsr_cmd, logger=logger)
... I'm getting an error in argument parsing unless I quote the first argument, i.e.:
isolde write phenixRsrInput #1 #1 4.0
Missing or invalid "volume" argument: invalid density map specifier
isolde write phenixRsrInput "#1" #1 4.0
save rebuilt_2_real_space_refined.pdb_for_phenix.cif #1.2 selectedOnly true
The actual method was broken as well, which means I'll need to push out a patch release...
Log:
UCSF ChimeraX version: 1.2.3 (2021-05-13)
© 2016-2021 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Opened J225_J228_composite_map.ccp4 as #1.1.1.1, grid size 400,400,400, pixel
1.06, shown at level 15.8, step 1, values float32
Log from Fri May 14 20:09:53 2021
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available
> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color bychain; color byhet
cs clipper set contourSensitivity {arguments}
UCSF ChimeraX version: 1.2.3 (2021-05-13)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open J225_J228_03May2021.pdb
Chain information for J225_J228_03May2021.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
> open J225_J228_composite_map.ccp4
Opened J225_J228_composite_map.ccp4 as #2, grid size 400,400,400, pixel 1.06,
shown at level 1.55, step 2, values float32
> volume #2 step 1
> volume #2 level 4.631
> volume #2 level 9.549
> volume #2 level 9.163
> clipper associate #2 toModel #1
Opened J225_J228_composite_map.ccp4 as #1.1.1.1, grid size 400,400,400, pixel
1.06, shown at level 19, step 1, values float32
Chain information for J225_J228_03May2021.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/D | No description available
> dssp
> addh
Summary of feedback from adding hydrogens to J225_J228_03May2021.pdb #1.2
---
notes | No usable SEQRES records for J225_J228_03May2021.pdb (#1.2) chain A;
guessing termini instead
No usable SEQRES records for J225_J228_03May2021.pdb (#1.2) chain B; guessing
termini instead
No usable SEQRES records for J225_J228_03May2021.pdb (#1.2) chain D; guessing
termini instead
Chain-initial residues that are actual N termini: /A GLU 1, /B HIS 1, /D GLU 3
Chain-initial residues that are not actual N termini: /A LYS 159, /A SER 518,
/A CYS 670, /A GLU 742, /B ASN 168, /B ASN 527, /B CYS 683, /B HIS 768
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A LYS 897, /A MET 156, /A
TYR 508, /A GLU 660, /A PRO 705, /B ASP 922, /B THR 162, /B PHE 518, /B ARG
656, /B LYS 718, /D LEU 64
1421 hydrogen bonds
Adding 'H' to /A LYS 159
Adding 'H' to /A SER 518
Adding 'H' to /A CYS 670
Adding 'H' to /A GLU 742
Adding 'H' to /B ASN 168
3 messages similar to the above omitted
/A LYS 897 is not terminus, removing H atom from 'C'
/B ASP 922 is not terminus, removing H atom from 'C'
/D LEU 64 is not terminus, removing H atom from 'C'
14085 hydrogens added
> set bgColor white
> isolde start
> set selectionWidth 4
Done loading forcefield
> clipper spotlight radius 13.00
> clipper spotlight radius 14.00
> clipper spotlight radius 15.00
> clipper spotlight radius 16.00
Created disulfide bonds between the following residues:
D18-D61; B192-B201; B647-B872; B304-B308; A294-A298; A120-A148; A234-A246;
A776-A785; B196-B207; A277-A291; A633-A849; A201-A209; A3-A22; A152-A175;
B169-B188; A302-A323; A205-A218; B208-B216; A185-A194; A162-A181; B288-B301;
A221-A230; A189-A200; B435-B468; A252-A273; D47-D52; A425-A458; B212-B225;
B8-B26; D6-D48; B259-B284; B126-B155; B228-B237; B266-B274; B241-B253;
B798-B807; B159-B182; B312-B333
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.8/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")
> select helix
3703 atoms, 3702 bonds, 228 residues, 1 model selected
> select strand
7336 atoms, 7339 bonds, 425 residues, 1 model selected
> select clear
> select #1
28445 atoms, 28842 bonds, 8 pseudobonds, 1771 residues, 14 models selected
ISOLDE: stopped sim
> select clear
> delete sel
> bond sel
Created 1 bond
> delete sel
> bond sel
Created 0 bonds
> bond sel
Created 0 bonds
> delete sel
> bond sel
Created 1 bond
> delete sel
> bond sel
Created 0 bonds
> delete sel
> delete sel
> delete sel
> delete sel
> delete sel
> delete sel
> select #1
28436 atoms, 28843 bonds, 8 pseudobonds, 1771 residues, 19 models selected
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st first
> stsel #1
Unknown command: stsel #1
> select #1
28436 atoms, 28843 bonds, 8 pseudobonds, 1771 residues, 19 models selected
> select clear
> cs 0.25
> open
> /run/media/tic20/storage/structure_dump/aus/melb/lawrence/hybrid_receptor/RealSpaceRefine_2/rebuilt_2_real_space_refined.pdb
Chain information for rebuilt_2_real_space_refined.pdb #2
---
Chain | Description
A | No description available
B | No description available
D | No description available
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J225_J228_03May2021.pdb, chain B (#1.2) with
rebuilt_2_real_space_refined.pdb, chain B (#2), sequence alignment score =
4166.1
RMSD between 630 pruned atom pairs is 1.230 angstroms; (across all 829 pairs:
12.596)
> close #1
Chain information for rebuilt_2_real_space_refined.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/D | No description available
> open
> /run/media/tic20/storage/structure_dump/aus/melb/lawrence/hybrid_receptor/2021_05/J225_J228_composite_map.ccp4
Opened J225_J228_composite_map.ccp4 as #2, grid size 400,400,400, pixel 1.06,
shown at level 1.55, step 2, values float32
> matchmaker #2 to #1
No molecules/chains to match specified
> matchmaker #2 to #1.2
No molecules/chains to match specified
> matchmaker #2 to #1
No molecules/chains to match specified
> clipper associate #2 toModel #1
Opened J225_J228_composite_map.ccp4 as #1.1.1.1, grid size 400,400,400, pixel
1.06, shown at step 1, values float32
> isolde restrain distances #1
> addh
Summary of feedback from adding hydrogens to rebuilt_2_real_space_refined.pdb
#1.2
---
notes | No usable SEQRES records for rebuilt_2_real_space_refined.pdb (#1.2)
chain A; guessing termini instead
No usable SEQRES records for rebuilt_2_real_space_refined.pdb (#1.2) chain B;
guessing termini instead
No usable SEQRES records for rebuilt_2_real_space_refined.pdb (#1.2) chain D;
guessing termini instead
Chain-initial residues that are actual N termini: /A GLU 1, /B HIS 1
Chain-initial residues that are not actual N termini: /A LYS 159, /A SER 518,
/A CYS 671, /A GLU 739, /B ASN 168, /B ASN 527, /B CYS 683, /B PRO 770, /D GLU
3
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A LYS 897, /A MET 156, /A
TYR 508, /A GLU 660, /A PRO 704, /B ASP 922, /B THR 162, /B PHE 518, /B ARG
656, /B PRO 718, /D PRO 63
1263 hydrogen bonds
/A LYS 897 is not terminus, removing H atom from 'C'
/B ASP 922 is not terminus, removing H atom from 'C'
/D PRO 63 is not terminus, removing H atom from 'C'
2 hydrogens added
> select #1
28405 atoms, 28814 bonds, 9 pseudobonds, 1769 residues, 14 models selected
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> select #1
28405 atoms, 28814 bonds, 9 pseudobonds, 1769 residues, 19 models selected
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> rd #1
> isolde release distances sel #1
Expected a keyword
> close #1.2.6
> clipper spotlight radius 17.00
> clipper spotlight radius 18.00
> cs 0.25
> select #1
28405 atoms, 28814 bonds, 9 pseudobonds, 1769 residues, 18 models selected
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> select up
58 atoms, 56 bonds, 3 residues, 1 model selected
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: stopped sim
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> 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 up
28 atoms, 26 bonds, 2 residues, 1 model selected
> select up
660 atoms, 667 bonds, 46 residues, 1 model selected
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> ht NE
Set protonation of HIS #1.2/A:362 to NE
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> st
> st
> st
> st
> st
> st
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> 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 /A
Alignment identifier is 1.2/A
> aa ASP
> aa GLY
ISOLDE: started sim
ISOLDE: stopped sim
> aa GLN
ISOLDE: started sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: stopped sim
> aa ASP
ISOLDE: started sim
ISOLDE: stopped sim
> select :508-525
368 atoms, 371 bonds, 1 pseudobond, 24 residues, 2 models selected
> aa asn
ISOLDE: started sim
ISOLDE: stopped sim
> select clear
> aa asp
> aa gly
ISOLDE: started sim
ISOLDE: stopped sim
> select clear
> aa gln
ISOLDE: started sim
ISOLDE: stopped sim
> aa asp
> aa ala
ISOLDE: started sim
ISOLDE: stopped sim
> aa ala
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> aa cys
> aa cys
Created disulphide bond between B524 and A514.
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> aa gly
> aa ser
ISOLDE: started sim
ISOLDE: stopped sim
> aa gly
> aa ser
ISOLDE: started sim
ISOLDE: stopped sim
> sequence chain /B
Alignment identifier is 1.2/B
> save working.cxs
Taking snapshot of stepper: rebuilt_2_real_space_refined.pdb
FYI: command is replacing existing command: "build modify"
FYI: command is replacing existing command: "build start"
FYI: command is replacing existing command: "bond"
FYI: command is replacing existing command: "~bond"
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> select clear
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
Unable to flip peptide bond after 50 rounds. Giving up.
ISOLDE: stopped sim
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> delete sel
> save working.cxs
Taking snapshot of stepper: rebuilt_2_real_space_refined.pdb
> save working.cif #1
Not saving entity_poly_seq for non-authoritative sequences
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> aa arg
ISOLDE: started sim
ISOLDE: stopped sim
> aa pro
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> delete sel
> st sel
> isolde stepto select
Missing "select" keyword's argument
> st sel
> isolde stepto select
Missing "select" keyword's argument
> st sel sel
> isolde stepto select sel
Invalid "select" argument: Expected true or false (or 1 or 0)
> st selAtoms
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
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> save working.cxs
Taking snapshot of stepper: rebuilt_2_real_space_refined.pdb
ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
> select clear
ISOLDE: stopped sim
> st
> st
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ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
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> st
> st
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> st
> st
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> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
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> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
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> st
ISOLDE: started sim
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
ISOLDE: stopped sim
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
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ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
> st
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> st
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> delete sel
> st
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ISOLDE: stopped sim
Deleted the following atoms from residue CYS B308: H1
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
> st
> st
> st
> st
> st
ISOLDE: started sim
> select clear
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
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ISOLDE: started sim
ISOLDE: stopped sim
> st
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> save working.cxs
Taking snapshot of stepper: rebuilt_2_real_space_refined.pdb
> usage isolde write phenixrsr
isolde write phenixRefineInput model [fileName a file name] [includeHydrogens
true or false] [numProcessors an integer] [numMacrocycles an integer]
[nqhFlips true or false]
— Write input files for phenix.refine, restraining the model to its current
geometry.
isolde write phenixRsrInput model volume resolution [fileName a file name]
[restrainPositions true or false] [includeHydrogens true or false]
— Write input files for phenix.real_space_refine, restraining the model to its
current geometry.
resolution: a number
isolde write refmacRestraints model [distanceCutoff a number] [includeWaters
true or false] [fileName a file name]
— Write REFMAC input to restrain a model to its current geometry
> phenixrsr #1 #1 4.0
Unknown command: isolde write phenixrsr #1 #1 4.0
> isolde write phenixRsrInput #1 #1 4.0
Missing or invalid "volume" argument: invalid density map specifier
> isolde write phenixRsrInput #1 #1.1.1.1 4.0
Missing or invalid "volume" argument: invalid density map specifier
> isolde write phenixRsrInput #1 #1.1.1.1
Missing or invalid "volume" argument: empty atom specifier
> isolde write phenixRsrInput #1
Missing or invalid "volume" argument: empty atom specifier
> isolde write phenixRsrInput #1 #1 #1
Missing or invalid "volume" argument: empty atom specifier
> isolde write phenixRsrInput #1 #1.1.1.1 #1
Missing or invalid "volume" argument: empty atom specifier
> isolde write phenixRsrInput #1.2 #1.1.1.1
Missing or invalid "volume" argument: empty atom specifier
> open
> /run/media/tic20/storage/structure_dump/aus/melb/lawrence/hybrid_receptor/2021_05/J225_J228_composite_map.ccp4
Opened J225_J228_composite_map.ccp4 as #2, grid size 400,400,400, pixel 1.06,
shown at level 1.55, step 2, values float32
> isolde write phenixRsrInput #1.2 #2 4.0
Missing or invalid "volume" argument: invalid density map specifier
> isolde write phenixRsrInput #1.2 #2 #2
Missing or invalid "volume" argument: empty atom specifier
> isolde write phenixRsrInput #1 #2
Missing or invalid "volume" argument: empty atom specifier
> isolde write phenixRsrInput #1.2 #2
Missing or invalid "volume" argument: empty atom specifier
> isolde write phenixRsrInput #1.2 #2
Missing or invalid "volume" argument: empty atom specifier
> select #1.2
28404 atoms, 28816 bonds, 7 pseudobonds, 1774 residues, 12 models selected
> select clear
> isolde write phenixRsrInput "#1.2" #1.1.1.1
Missing or invalid "resolution" argument: Expected a number
> isolde write phenixRsrInput "#1.2" #1.1.1.1 4.0
/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/output/refinement/phenix/real_space_refine_input.py:21:
FutureWarning: elementwise comparison failed; returning scalar instead, but in
the future will perform elementwise comparison
model.atoms[model.atoms.element_numbers != 'H'].selecteds=True
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/output/refinement/phenix/cmd.py", line 18, in
write_rsr_cmd
write_real_space_refine_defaults(
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/output/refinement/phenix/real_space_refine_input.py",
line 21, in write_real_space_refine_defaults
model.atoms[model.atoms.element_numbers != 'H'].selecteds=True
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])
File "atomic_cpp/cymol.pyx", line 755, in
chimerax.atomic.cymol.CyAtom.c_ptr_to_py_inst
TypeError: only size-1 arrays can be converted to Python scalars
TypeError: only size-1 arrays can be converted to Python scalars
File "atomic_cpp/cymol.pyx", line 755, in
chimerax.atomic.cymol.CyAtom.c_ptr_to_py_inst
See log for complete Python traceback.
> close #2
> save working.cxs
Taking snapshot of stepper: rebuilt_2_real_space_refined.pdb
——— End of log from Fri May 14 20:09:53 2021 ———
opened ChimeraX session
> isolde write phenixRsrInput #1 #1 4.0
Missing or invalid "volume" argument: invalid density map specifier
> usage isolde write phenixRsr
isolde write phenixRsrInput model volume resolution [fileName a file name]
[restrainPositions true or false] [includeHydrogens true or false]
— Write input files for phenix.real_space_refine, restraining the model to its
current geometry.
resolution: a number
> isolde write phenixRsrInput "#1" #1 4.0
> save rebuilt_2_real_space_refined.pdb_for_phenix.cif #1.2 selectedOnly true
Not saving entity_poly_seq for non-authoritative sequences
A phenix.real_space_refine input file real_space_refine.eff with settings
recommended for ISOLDE models has been written to
/run/media/tic20/storage/structure_dump/aus/melb/lawrence/hybrid_receptor/2021_05
along with a current snapshot of your model
(rebuilt_2_real_space_refined.pdb_for_phenix.cif). You can start a refinement
job by running the following command in the working directory:
phenix.real_space_refine real_space_refine.eff.
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
Virutal Machine: none
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 9G 28G 1.3G 23G 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
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.3
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-DevelExtras: 0.4.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.2
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: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
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: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-Phenix: 0.2
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
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: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.4
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
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: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.0
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Tristan,
--Eric