id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3099 auto-wipe some commands? Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.93 (2020-04-03) Description Just a thought: certain commands (in particular, ""del selAtoms"") can be really dangerous if accidentally repeated (by hitting return with them still in the command bar). Might be a good idea if those wipe themselves from the command history so they have to be explicitly typed every time? Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6jyt_refine_3.pdb Summary of feedback from opening 6jyt_refine_3.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-04-21 Time 18:02:55 BST +0100 (1587488575.81 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/6jyt.mtz 56 messages similar to the above omitted Chain information for 6jyt_refine_3.pdb #1 --- Chain | Description A | No description available B | No description available > isolde start > set selectionWidth 4 Chain information for 6jyt_refine_3.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available Done loading forcefield WARNING: found multiple possible R-free arrays: (dataset) R-free-flags, (dataset) R-free-flags-1 Automatically choosing ""(dataset) R-free-flags"". If this is incorrect, please either provide a file with a single flag array, or load the file again using the free_flag_label argument. > set bgColor white > addh Summary of feedback from adding hydrogens to 6jyt_refine_3.pdb #1.2 --- warnings | Not adding hydrogens to /B THR 188 CB because it is missing heavy- atom bond partners Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens to it notes | No usable SEQRES records for 6jyt_refine_3.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 6jyt_refine_3.pdb (#1.2) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A ASN -1, /B ASN -1 Chain-initial residues that are not actual N termini: /A THR 351, /B SER 350 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ASN 596, /A PRO 335, /B ASN 596, /B VAL 340 1082 hydrogen bonds Adding 'H' to /A THR 351 Adding 'H' to /B SER 350 /A ASN 596 is not terminus, removing H atom from 'C' /A PRO 335 is not terminus, removing H atom from 'C' /B ASN 596 is not terminus, removing H atom from 'C' /B VAL 340 is not terminus, removing H atom from 'C' 9162 hydrogens added > hide HC > select :ZN 6 atoms, 1 model selected > delete sel > delete sel > delete sel > select #1 18354 atoms, 18516 bonds, 4 pseudobonds, 25 models selected > select clear > open2 > /run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb Summary of feedback from opening <_io.textiowrapper name=""/run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-04-22 Time 19:00:08 BST +0100 (1587578408.41 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/5wwp.mtz 72 messages similar to the above omitted Chain information for 5wwp_refine_2.pdb #2 --- Chain | Description A | No description available B | No description available > matchmaker #2/A to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6jyt_refine_3.pdb, chain A (#1.2) with 5wwp_refine_2.pdb, chain A (#2), sequence alignment score = 1865.5 RMSD between 375 pruned atom pairs is 0.913 angstroms; (across all 498 pairs: 1.884) > isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120 > isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120 > isolde restrain distances #1/B:439-600 templateAtoms #2/A RMSD between 156 pruned atom pairs is 1.638 angstroms; (across all 158 pairs: 1.750) > isolde restrain distances #1/A:439-600 templateAtoms #2/A RMSD between 156 pruned atom pairs is 1.541 angstroms; (across all 158 pairs: 1.787) > hide #1.2.6 models > hide #1.2.5 models > hide #!2 models > close #1.2.5-6 > movie record > show #!2 models > isolde restrain distances #1/A:439-600 templateAtoms #2/A RMSD between 156 pruned atom pairs is 1.541 angstroms; (across all 158 pairs: 1.787) > isolde restrain distances #1/B:439-600 templateAtoms #2/A RMSD between 156 pruned atom pairs is 1.638 angstroms; (across all 158 pairs: 1.750) > isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120 > isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120 > select #1/A,B:439-600 5012 atoms, 5058 bonds, 1 model selected > isolde adjust distances #1 displayThreshold 0.5 Loading residue template for SO4 from internal database > select clear > select clear > isolde release distances #1/A > isolde restrain distances #1/A:439-600 templateAtoms #2/A RMSD between 156 pruned atom pairs is 0.544 angstroms; (across all 158 pairs: 1.192) > isolde adjust distances #1 displayThreshold 0.5 Updating bulk solvent parameters... > select clear > movie stop > movie reset > close #1.2.5-6 > hide #!2 models > movie record > hide ~@CA > show #!2 models > show #1&~HC > isolde restrain distances #1/A:439-600 templateAtoms #2/A kappa 50 RMSD between 156 pruned atom pairs is 1.541 angstroms; (across all 158 pairs: 1.787) > isolde restrain distances #1/B:439-600 templateAtoms #2/A kappa 50 RMSD between 156 pruned atom pairs is 1.638 angstroms; (across all 158 pairs: 1.750) > isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120 > isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120 > hide ~@CA > hide #!2 models > select #1:439-600 5012 atoms, 5058 bonds, 1 model selected > select clear > show #1&~HC > isolde adjust distances #1 displayThreshold 0.5 > show #!2 models > movie stop > movie encode restrain_to_5wwp.mp4 Movie saved to restrain_to_5wwp.mp4 > select up 24 atoms, 23 bonds, 1 model selected > select up 210 atoms, 211 bonds, 1 model selected > isolde release torsions sel > isolde release distances sel Updating bulk solvent parameters... > select clear > show #1&~HC Updating bulk solvent parameters... > delete sel > select #1/B:436-600 2562 atoms, 2586 bonds, 1 model selected > hide #!2 models > select clear > isolde release distances sel > isolde release torsions sel > isolde release distances #1/B > isolde restrain distances #1/B:439-600 templateAtoms #2/A kappa 50 RMSD between 151 pruned atom pairs is 1.175 angstroms; (across all 156 pairs: 1.588) RMSD between 5 pruned atom pairs is 3.095 angstroms; (across all 5 pairs: 3.095) > isolde adjust distances #1 displayThreshold 0.5 > isolde release distances sel > isolde release torsions sel > isolde release distances sel > isolde release torsions sel > select clear > isolde release distances #1/B > isolde restrain distances #1/B:439-600 templateAtoms #2/A RMSD between 150 pruned atom pairs is 0.242 angstroms; (across all 156 pairs: 1.270) RMSD between 6 pruned atom pairs is 3.234 angstroms; (across all 6 pairs: 3.234) > isolde adjust distances #1 displayThreshold 0.5 > select up 20 atoms, 20 bonds, 1 model selected > isolde release distances sel > isolde release distances #1/B > isolde restrain distances #1/B:439-600 templateAtoms #2/A RMSD between 150 pruned atom pairs is 0.618 angstroms; (across all 156 pairs: 1.394) RMSD between 6 pruned atom pairs is 3.204 angstroms; (across all 6 pairs: 3.204) > isolde release distances sel > isolde release distances #1/B Updating bulk solvent parameters... > select #1 18292 atoms, 18454 bonds, 4 pseudobonds, 31 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. > select clear > select clear > isolde release distances #1/A > isolde restrain distances #1/A:439-600 templateAtoms #2/A RMSD between 155 pruned atom pairs is 0.722 angstroms; (across all 155 pairs: 0.722) > select clear > isolde release distances #1/A Updating bulk solvent parameters... > save working.pdb #1 > view /B:188 > close #1 Deleting atomic symmetry model... Deleting atomic symmetry model... Chain information for 5wwp_refine_2.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available Deleting (LIVE) mFo-DFc Deleting (LIVE) MDFF potential Deleting (LIVE) 2mFo-DFc Deleting (LIVE) 2mFo-DFc_sharp_22 Deleting Crystallographic maps (6jyt.mtz) > close #1 Deleting atomic symmetry model... > open2 > /run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/Refine_4/6jyt_refine_4.pdb Summary of feedback from opening <_io.textiowrapper name=""/run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/Refine_4/6jyt_refine_4.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-04-23 Time 09:40:22 BST +0100 (1587631222.72 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/6jyt.mtz 60 messages similar to the above omitted Chain information for 6jyt_refine_4.pdb #1 --- Chain | Description A | No description available B | No description available Chain information for 6jyt_refine_4.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available > dssp WARNING: found multiple possible R-free arrays: (dataset) R-free-flags, (dataset) R-free-flags-1 Automatically choosing ""(dataset) R-free-flags"". If this is incorrect, please either provide a file with a single flag array, or load the file again using the free_flag_label argument. > open2 > /run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb Summary of feedback from opening <_io.textiowrapper name=""/run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-04-22 Time 19:00:08 BST +0100 (1587578408.41 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/5wwp.mtz 72 messages similar to the above omitted Chain information for 5wwp_refine_2.pdb #2 --- Chain | Description A | No description available B | No description available > select #1 18292 atoms, 18454 bonds, 4 pseudobonds, 25 models selected > select clear > isolde restrain torsions #1/A:439-600 templateResidues #2/A > isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120 > isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120 > select #1 18292 atoms, 18454 bonds, 4 pseudobonds, 26 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. > select clear > isolde restrain distances #1/B:439-600 templateAtoms #2/A RMSD between 150 pruned atom pairs is 0.626 angstroms; (across all 156 pairs: 1.387) RMSD between 5 pruned atom pairs is 2.303 angstroms; (across all 6 pairs: 3.516) > isolde restrain distances #1/A:439-600 templateAtoms #2/A RMSD between 155 pruned atom pairs is 0.801 angstroms; (across all 155 pairs: 0.801) Updating bulk solvent parameters... > sequence chain /A Chains must have same sequence > sequence chain #1/A Alignment identifier is 1.2.A > view sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > toolshed 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"") Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add ligand SO4 > color sel bychain > color sel byhetero Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select clear > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... Updating bulk solvent parameters... Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel > select clear Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel > delete sel > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 model selected > delete sel Updating bulk solvent parameters... Updating bulk solvent parameters... > select clear Updating bulk solvent parameters... Updating bulk solvent parameters... > isolde add water > color sel bychain > color sel byhetero > isolde sim start sel Updating bulk solvent parameters... Updating bulk solvent parameters... > select clear OpenGL version: 3.3.0 NVIDIA 440.33.01 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 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 }}} " enhancement reopened normal Command Line Elaine Meng all ChimeraX