id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4642 consecutive atom specs Tristan Croll Eric Pettersen "{{{ 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 > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > save working.cxs Taking snapshot of stepper: rebuilt_2_real_space_refined.pdb 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 > 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 ISOLDE: started sim ISOLDE: stopped sim > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st ISOLDE: started sim ISOLDE: stopped sim > st > st > st 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 > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > 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 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 > 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 > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > 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 ISOLDE: started sim ISOLDE: stopped sim > 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 ISOLDE: started sim ISOLDE: stopped sim 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 ISOLDE: started sim > select clear ISOLDE: stopped sim > st > st > st > st > st > st > st > st > st > st > st > st > st > delete sel > st > st > st > st > st > st > st > st > 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: 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 > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > 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 > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > 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 > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > 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 }}} " defect closed normal Command Line limitation chimera-programmers all ChimeraX