id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3309 some color commands should only target atomic models Tristan Croll Tom Goddard "{{{ 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: 1.0rc202005242323 (2020-05-24 23:23:37 UTC) Description Color by attribute commands probably shouldn't apply to markers. I just did ""color bychain; color byhet"" and all my colour-coded markers turned white. Log: UCSF ChimeraX version: 1.0rc202005242323 (2020-05-24) © 2016-2020 Regents of the University of California. All rights reserved. > open working_renumbered_and_renamed.cxs restore_snapshot for ""RotamerRestraintMgr"" returned None Log from Mon May 25 23:00:27 2020UCSF ChimeraX version: 1.0rc202005242323 (2020-05-24) © 2016-2020 Regents of the University of California. All rights reserved. > open working.cxs restore_snapshot for ""RotamerRestraintMgr"" returned None Log from Mon May 25 22:28:45 2020 > save working.cxs > save working.cxs > sequence chain /aa Alignment identifier is 1.2.aa > sequence chain /BA Alignment identifier is 1.2.BA > sequence chain /AA Alignment identifier is 1.2.AA > sequence chain /AA Alignment identifier is 1.2.AA > view lse Expected an objects specifier or a view name or a keyword > view sel > sequence chain /BA Alignment identifier is 1.2.BA > sequence chain /BB Alignment identifier is 1.2.BB > sequence chain /ba Alignment identifier is 1.2.ba > view sel > isolde stepto /BA Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > isolde stepto /ba Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bb Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bc Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bd Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > view sel > select up 7 atoms, 6 bonds, 1 model selected > delete sel > isolde stepto /bd Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > isolde stepto /be Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > isolde stepto /bf Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > isolde stepto /bg Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bh Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > view sel > select up 7 atoms, 6 bonds, 1 model selected > delete sel > isolde stepto /bh Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bg Multiple residues selected! Going to the first... > isolde stepto /bg Multiple residues selected! Going to the first... > isolde stepto /bh Multiple residues selected! Going to the first... > isolde stepto /bi Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bj Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bk Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > isolde stepto /bl Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > isolde stepto /bm Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bn Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > select clear > isolde stepto /bo Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > view sel > select up 7 atoms, 6 bonds, 1 model selected > delete sel > isolde stepto /bo Multiple residues selected! Going to the first... > isolde stepto /bo Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > isolde stepto /bp Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > isolde stepto /bq Selection contains no residues! > select clear > save working.cxs opened ChimeraX session > setattr /AF c chain_id QF Assigning chain_id attribute to 1 item > setattr /AF r chain_id QF Assigning chain_id attribute to 2 items > setattr /BF c chain_id RF Assigning chain_id attribute to 1 item > setattr /BF r chain_id RF Assigning chain_id attribute to 1 item > setattr /QF c chain_id BF Assigning chain_id attribute to 1 item > setattr /QF r chain_id BF Assigning chain_id attribute to 2 items > setattr /RF r chain_id AF Assigning chain_id attribute to 46 items Cannot set attribute 'chain_id' to 'AF' > setattr /RF c chain_id AF Assigning chain_id attribute to 1 item > setattr /RF r chain_id AF Assigning chain_id attribute to 1 item > select /AD,AE,AF 2589 atoms, 2655 bonds, 13 pseudobonds, 3 models selected > select /AD,AE,AF,AG 3455 atoms, 3541 bonds, 17 pseudobonds, 3 models selected > select clear > setattr /AG c chain_id QG Assigning chain_id attribute to 1 item > setattr /AG r chain_id QG Assigning chain_id attribute to 2 items > setattr /BG c chain_id RG Assigning chain_id attribute to 1 item > setattr /BG r chain_id RG Assigning chain_id attribute to 1 item > setattr /QG c chain_id BG Assigning chain_id attribute to 1 item > setattr /QG r chain_id BG Assigning chain_id attribute to 2 items > setattr /RG c chain_id /AG Assigning chain_id attribute to 1 item > setattr /RG r chain_id /AG Assigning chain_id attribute to 1 item > select /AD,AE,AF,AG 2589 atoms, 2655 bonds, 13 pseudobonds, 3 models selected > select clear > select /AG Nothing selected > select /AD 863 atoms, 885 bonds, 4 pseudobonds, 2 models selected > select /AD,AE,AF 2589 atoms, 2655 bonds, 13 pseudobonds, 3 models selected > select /AG Nothing selected > select clear > 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"") > isolde start > set selectionWidth 4 Done loading forcefield > select /AA-AW 19950 atoms, 20455 bonds, 93 pseudobonds, 3 models selected > select /AA-AX 20813 atoms, 21340 bonds, 97 pseudobonds, 3 models selected > select clear > isolde stepto /AA Multiple residues selected! Going to the first... > select /AA-AX 20813 atoms, 21340 bonds, 97 pseudobonds, 3 models selected > select clear > isolde stepto /BA Multiple residues selected! Going to the first... > select /B*,b* 34747 atoms, 35556 bonds, 161 pseudobonds, 4 models selected > select /B 369 atoms, 375 bonds, 1 pseudobond, 2 models selected > view sel Traceback (most recent call last): File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2570, in _xtal_mask_to_selection self._xtal_mask_to_atoms(sel, focus) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2579, in _xtal_mask_to_atoms atoms, 0, context, cutoff, focus=focus) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/symmetry.py"", line 972, in isolate_and_cover_selection extra_padding=extra_padding) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/map_mgr.py"", line 358, in cover_atoms zm.set_symmetry_map(atoms, transforms, transform_indices) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 111, in set_symmetry_map self.structure = self._unique_structure(atoms) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') TypeError: All atoms for zone mask must be from a single model! TypeError: All atoms for zone mask must be from a single model! File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') See log for complete Python traceback. > select /B 369 atoms, 375 bonds, 1 pseudobond, 2 models selected > isolde stepto /BX Multiple residues selected! Going to the first... > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero No template found for residue AA57 (BCL) Doing nothing > isolde stepto /BX Multiple residues selected! Going to the first... > save working_renumbered_and_renamed.cxs opened ChimeraX session > select :UA Nothing selected > select /UA 320 atoms, 319 bonds, 1 model selected > 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 > clipper spotlight radius 17.00 > ui tool show ""Build Structure"" > build start peptide #1.2 AAAAAAAAAAAAAAA -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 > rotLib Dunbrack chainId UB > select /UB 76 atoms, 75 bonds, 1 model selected > style sel stick Changed 76 atom styles > show sel cartoons > color sel bychain > color sel byhetero > 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"") > isolde ignore ~sel ISOLDE: currently ignoring 4889 residues in model 1.2 ISOLDE: currently ignoring 3824 residues in model 2 ISOLDE: currently ignoring 40 residues in model 3 No template found for residue UB1 (ALA) Adding hydrogens Summary of feedback from adding hydrogens to extended_rough.cif #1.2 --- notes | No usable SEQRES records for extended_rough.cif (#1.2) chain AA; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AB; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AC; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AD; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AE; guessing termini instead 82 messages similar to the above omitted Chain-initial residues that are actual N termini: extended_rough.cif #1.2/C ALA 15, extended_rough.cif #1.2/H1 MET 1, extended_rough.cif #1.2/H2 SER 1, extended_rough.cif #1.2/L ALA 1, extended_rough.cif #1.2/M MET 1, extended_rough.cif #1.2/aa HIS 2, extended_rough.cif #1.2/ab MET 1, extended_rough.cif #1.2/ac MET 1, extended_rough.cif #1.2/ad MET 1, extended_rough.cif #1.2/ae MET 1, extended_rough.cif #1.2/af MET 1, extended_rough.cif #1.2/ag MET 1, extended_rough.cif #1.2/ah MET 1, extended_rough.cif #1.2/ai MET 1, extended_rough.cif #1.2/aj MET 1, extended_rough.cif #1.2/ak MET 1, extended_rough.cif #1.2/al MET 1, extended_rough.cif #1.2/am MET 1, extended_rough.cif #1.2/an MET 1, extended_rough.cif #1.2/ao MET 1, extended_rough.cif #1.2/ap MET 1, extended_rough.cif #1.2/UB ALA 1 Chain-initial residues that are not actual N termini: extended_rough.cif #1.2/AA HIS 2, extended_rough.cif #1.2/AB HIS 2, extended_rough.cif #1.2/AC HIS 2, extended_rough.cif #1.2/AD HIS 2, extended_rough.cif #1.2/AE HIS 2, extended_rough.cif #1.2/BF GLY 6, extended_rough.cif #1.2/BG GLY 6, extended_rough.cif #1.2/AH HIS 2, extended_rough.cif #1.2/AI HIS 2, extended_rough.cif #1.2/AJ HIS 2, extended_rough.cif #1.2/AK HIS 2, extended_rough.cif #1.2/AL HIS 2, extended_rough.cif #1.2/AM HIS 2, extended_rough.cif #1.2/AN HIS 2, extended_rough.cif #1.2/AO HIS 2, extended_rough.cif #1.2/AP HIS 2, extended_rough.cif #1.2/AQ HIS 2, extended_rough.cif #1.2/AR HIS 2, extended_rough.cif #1.2/AS HIS 2, extended_rough.cif #1.2/AT HIS 2, extended_rough.cif #1.2/AU HIS 2, extended_rough.cif #1.2/AV HIS 2, extended_rough.cif #1.2/AW HIS 2, extended_rough.cif #1.2/AX HIS 2, extended_rough.cif #1.2/BA GLY 6, extended_rough.cif #1.2/BB GLY 5, extended_rough.cif #1.2/BC GLY 6, extended_rough.cif #1.2/BD GLY 5, extended_rough.cif #1.2/BE GLY 5, extended_rough.cif #1.2/AF HIS 2, extended_rough.cif #1.2/AG HIS 2, extended_rough.cif #1.2/BH GLY 6, extended_rough.cif #1.2/BI GLY 5, extended_rough.cif #1.2/BJ GLY 6, extended_rough.cif #1.2/BK GLY 6, extended_rough.cif #1.2/BL GLY 6, extended_rough.cif #1.2/BM GLY 6, extended_rough.cif #1.2/BN GLY 6, extended_rough.cif #1.2/BO GLY 6, extended_rough.cif #1.2/BP GLY 6, extended_rough.cif #1.2/BQ GLY 6, extended_rough.cif #1.2/BR GLY 6, extended_rough.cif #1.2/BS GLY 6, extended_rough.cif #1.2/BT GLY 6, extended_rough.cif #1.2/BU GLY 6, extended_rough.cif #1.2/BV GLY 5, extended_rough.cif #1.2/BW GLY 5, extended_rough.cif #1.2/BX GLY 6, extended_rough.cif #1.2/H2 ASP 9, extended_rough.cif #1.2/ba GLY 6, extended_rough.cif #1.2/bb GLY 6, extended_rough.cif #1.2/bc GLY 6, extended_rough.cif #1.2/bd GLY 6, extended_rough.cif #1.2/be GLY 6, extended_rough.cif #1.2/bf GLY 6, extended_rough.cif #1.2/bg GLY 6, extended_rough.cif #1.2/bh GLY 6, extended_rough.cif #1.2/bi GLY 6, extended_rough.cif #1.2/bj GLY 6, extended_rough.cif #1.2/bk GLY 6, extended_rough.cif #1.2/bl GLY 6, extended_rough.cif #1.2/bm GLY 6, extended_rough.cif #1.2/bn GLY 5, extended_rough.cif #1.2/bo GLY 6, extended_rough.cif #1.2/bp GLY 6, extended_rough.cif #1.2/UA ALA 2 Chain-final residues that are actual C termini: extended_rough.cif #1.2/BF PHE 44, extended_rough.cif #1.2/BG PHE 44, extended_rough.cif #1.2/BA PHE 44, extended_rough.cif #1.2/BB PHE 44, extended_rough.cif #1.2/BC PHE 44, extended_rough.cif #1.2/BD PHE 44, extended_rough.cif #1.2/BE PHE 44, extended_rough.cif #1.2/BH PHE 44, extended_rough.cif #1.2/BI PHE 44, extended_rough.cif #1.2/BJ PHE 44, extended_rough.cif #1.2/BK PHE 44, extended_rough.cif #1.2/BL PHE 44, extended_rough.cif #1.2/BM PHE 44, extended_rough.cif #1.2/BN PHE 44, extended_rough.cif #1.2/BO PHE 44, extended_rough.cif #1.2/BP PHE 44, extended_rough.cif #1.2/BQ PHE 44, extended_rough.cif #1.2/BR PHE 44, extended_rough.cif #1.2/BS PHE 44, extended_rough.cif #1.2/BT PHE 44, extended_rough.cif #1.2/BU PHE 44, extended_rough.cif #1.2/BV PHE 44, extended_rough.cif #1.2/BW PHE 44, extended_rough.cif #1.2/BX PHE 44, extended_rough.cif #1.2/C ARG 302, extended_rough.cif #1.2/L LYS 273, extended_rough.cif #1.2/ba PHE 44, extended_rough.cif #1.2/bb PHE 44, extended_rough.cif #1.2/bc PHE 44, extended_rough.cif #1.2/bd PHE 44, extended_rough.cif #1.2/be PHE 44, extended_rough.cif #1.2/bf PHE 44, extended_rough.cif #1.2/bg PHE 44, extended_rough.cif #1.2/bh PHE 44, extended_rough.cif #1.2/bi PHE 44, extended_rough.cif #1.2/bj PHE 44, extended_rough.cif #1.2/bk PHE 44, extended_rough.cif #1.2/bl PHE 44, extended_rough.cif #1.2/bm PHE 44, extended_rough.cif #1.2/bn PHE 44, extended_rough.cif #1.2/bo PHE 44, extended_rough.cif #1.2/bp PHE 44, extended_rough.cif #1.2/UB ALA 15 Chain-final residues that are not actual C termini: extended_rough.cif #1.2/AA TYR 46, extended_rough.cif #1.2/AB TYR 46, extended_rough.cif #1.2/AC TYR 46, extended_rough.cif #1.2/AD TYR 46, extended_rough.cif #1.2/AE TYR 46, extended_rough.cif #1.2/AH TYR 46, extended_rough.cif #1.2/AI TYR 46, extended_rough.cif #1.2/AJ TYR 46, extended_rough.cif #1.2/AK TYR 46, extended_rough.cif #1.2/AL TYR 46, extended_rough.cif #1.2/AM TYR 46, extended_rough.cif #1.2/AN TYR 46, extended_rough.cif #1.2/AO TYR 46, extended_rough.cif #1.2/AP TYR 46, extended_rough.cif #1.2/AQ TYR 46, extended_rough.cif #1.2/AR TYR 46, extended_rough.cif #1.2/AS TYR 46, extended_rough.cif #1.2/AT TYR 46, extended_rough.cif #1.2/AU TYR 46, extended_rough.cif #1.2/AV TYR 46, extended_rough.cif #1.2/AW TYR 46, extended_rough.cif #1.2/AX TYR 46, extended_rough.cif #1.2/AF TYR 46, extended_rough.cif #1.2/AG TYR 46, extended_rough.cif #1.2/H1 LYS 53, extended_rough.cif #1.2/H2 ALA 8, extended_rough.cif #1.2/H2 PRO 7, extended_rough.cif #1.2/M TYR 324, extended_rough.cif #1.2/aa ALA 60, extended_rough.cif #1.2/ab ALA 60, extended_rough.cif #1.2/ac ALA 60, extended_rough.cif #1.2/ad ALA 60, extended_rough.cif #1.2/ae ALA 60, extended_rough.cif #1.2/af ALA 60, extended_rough.cif #1.2/ag ALA 60, extended_rough.cif #1.2/ah ALA 60, extended_rough.cif #1.2/ai ALA 60, extended_rough.cif #1.2/aj ALA 60, extended_rough.cif #1.2/ak ALA 60, extended_rough.cif #1.2/al ALA 60, extended_rough.cif #1.2/am ALA 60, extended_rough.cif #1.2/an ALA 60, extended_rough.cif #1.2/ao ALA 60, extended_rough.cif #1.2/ap ALA 60, extended_rough.cif #1.2/UA ALA 33 4893 hydrogen bonds extended_rough.cif #1.2/AA TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AB TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AC TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AD TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AE TYR 46 is not terminus, removing H atom from 'C' 38 messages similar to the above omitted 96 hydrogens added > select clear > select up 10 atoms, 9 bonds, 1 model selected > select up 130 atoms, 129 bonds, 1 model selected > select /UB 153 atoms, 152 bonds, 1 model selected > select /UA 320 atoms, 319 bonds, 1 model selected > select /UB 153 atoms, 152 bonds, 1 model selected > clipper spotlight radius 18.00 > clipper spotlight radius 19.00 > clipper spotlight radius 20.00 > clipper spotlight radius 21.00 > clipper spotlight radius 22.00 > clipper spotlight radius 23.00 > clipper spotlight radius 24.00 > clipper spotlight radius 25.00 > ui mousemode right ""mark point"" > marker #3 position 141.5,132.2,158.9 color #ef2929 radius 1 > select /UB 153 atoms, 152 bonds, 1 model selected > isolde ~ignore No template found for residue bg7 (MET) Doing nothing > delete sel > select /UA 320 atoms, 319 bonds, 1 model selected > select /UB 153 atoms, 152 bonds, 1 model selected > select clear Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > select up 12 atoms, 11 bonds, 1 model selected > select up 172 atoms, 171 bonds, 1 model selected > select down 12 atoms, 11 bonds, 1 model selected > select up 172 atoms, 171 bonds, 1 model selected > select clear > ui mousemode right swapaa > swapaa mousemode #1.2/UB:4 ALA > delete sel > select up 6 atoms, 5 bonds, 1 model selected > select up 126 atoms, 125 bonds, 1 model selected No template found for residue UB4 (ALA) Doing nothing > delete sel > select up 5 atoms, 4 bonds, 1 model selected > select up 125 atoms, 124 bonds, 1 model selected > delete sel > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select /UB 175 atoms, 174 bonds, 1 model selected > select clear > save working.cxs > build start peptide #1.2 AAAAAAAAAAAAAAA -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 > rotLib Dunbrack chainId UC > select /UC 76 atoms, 75 bonds, 1 model selected > color sel bychain > color sel byhetero > style sel stick Changed 76 atom styles > show sel cartoons > addh Summary of feedback from adding hydrogens to multiple structures --- warning | Not adding hydrogens to extended_rough.cif #1.2/UB ALA 4 CA because it is missing heavy-atom bond partners notes | No usable SEQRES records for extended_rough.cif (#1.2) chain AA; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AB; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AC; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AD; guessing termini instead No usable SEQRES records for extended_rough.cif (#1.2) chain AE; guessing termini instead 83 messages similar to the above omitted Chain-initial residues that are actual N termini: extended_rough.cif #1.2/C ALA 15, extended_rough.cif #1.2/H1 MET 1, extended_rough.cif #1.2/H2 SER 1, extended_rough.cif #1.2/L ALA 1, extended_rough.cif #1.2/M MET 1, extended_rough.cif #1.2/aa HIS 2, extended_rough.cif #1.2/ab MET 1, extended_rough.cif #1.2/ac MET 1, extended_rough.cif #1.2/ad MET 1, extended_rough.cif #1.2/ae MET 1, extended_rough.cif #1.2/af MET 1, extended_rough.cif #1.2/ag MET 1, extended_rough.cif #1.2/ah MET 1, extended_rough.cif #1.2/ai MET 1, extended_rough.cif #1.2/aj MET 1, extended_rough.cif #1.2/ak MET 1, extended_rough.cif #1.2/al MET 1, extended_rough.cif #1.2/am MET 1, extended_rough.cif #1.2/an MET 1, extended_rough.cif #1.2/ao MET 1, extended_rough.cif #1.2/ap MET 1, extended_rough.cif #1.2/UC ALA 1 Chain-initial residues that are not actual N termini: extended_rough.cif #1.2/AA HIS 2, extended_rough.cif #1.2/AB HIS 2, extended_rough.cif #1.2/AC HIS 2, extended_rough.cif #1.2/AD HIS 2, extended_rough.cif #1.2/AE HIS 2, extended_rough.cif #1.2/BF GLY 6, extended_rough.cif #1.2/BG GLY 6, extended_rough.cif #1.2/AH HIS 2, extended_rough.cif #1.2/AI HIS 2, extended_rough.cif #1.2/AJ HIS 2, extended_rough.cif #1.2/AK HIS 2, extended_rough.cif #1.2/AL HIS 2, extended_rough.cif #1.2/AM HIS 2, extended_rough.cif #1.2/AN HIS 2, extended_rough.cif #1.2/AO HIS 2, extended_rough.cif #1.2/AP HIS 2, extended_rough.cif #1.2/AQ HIS 2, extended_rough.cif #1.2/AR HIS 2, extended_rough.cif #1.2/AS HIS 2, extended_rough.cif #1.2/AT HIS 2, extended_rough.cif #1.2/AU HIS 2, extended_rough.cif #1.2/AV HIS 2, extended_rough.cif #1.2/AW HIS 2, extended_rough.cif #1.2/AX HIS 2, extended_rough.cif #1.2/BA GLY 6, extended_rough.cif #1.2/BB GLY 5, extended_rough.cif #1.2/BC GLY 6, extended_rough.cif #1.2/BD GLY 5, extended_rough.cif #1.2/BE GLY 5, extended_rough.cif #1.2/AF HIS 2, extended_rough.cif #1.2/AG HIS 2, extended_rough.cif #1.2/BH GLY 6, extended_rough.cif #1.2/BI GLY 5, extended_rough.cif #1.2/BJ GLY 6, extended_rough.cif #1.2/BK GLY 6, extended_rough.cif #1.2/BL GLY 6, extended_rough.cif #1.2/BM GLY 6, extended_rough.cif #1.2/BN GLY 6, extended_rough.cif #1.2/BO GLY 6, extended_rough.cif #1.2/BP GLY 6, extended_rough.cif #1.2/BQ GLY 6, extended_rough.cif #1.2/BR GLY 6, extended_rough.cif #1.2/BS GLY 6, extended_rough.cif #1.2/BT GLY 6, extended_rough.cif #1.2/BU GLY 6, extended_rough.cif #1.2/BV GLY 5, extended_rough.cif #1.2/BW GLY 5, extended_rough.cif #1.2/BX GLY 6, extended_rough.cif #1.2/H2 ASP 9, extended_rough.cif #1.2/ba GLY 6, extended_rough.cif #1.2/bb GLY 6, extended_rough.cif #1.2/bc GLY 6, extended_rough.cif #1.2/bd GLY 6, extended_rough.cif #1.2/be GLY 6, extended_rough.cif #1.2/bf GLY 6, extended_rough.cif #1.2/bg GLY 6, extended_rough.cif #1.2/bh GLY 6, extended_rough.cif #1.2/bi GLY 6, extended_rough.cif #1.2/bj GLY 6, extended_rough.cif #1.2/bk GLY 6, extended_rough.cif #1.2/bl GLY 6, extended_rough.cif #1.2/bm GLY 6, extended_rough.cif #1.2/bn GLY 5, extended_rough.cif #1.2/bo GLY 6, extended_rough.cif #1.2/bp GLY 6, extended_rough.cif #1.2/UA ALA 2, extended_rough.cif #1.2/UB ALA 18 Chain-final residues that are actual C termini: extended_rough.cif #1.2/BF PHE 44, extended_rough.cif #1.2/BG PHE 44, extended_rough.cif #1.2/BA PHE 44, extended_rough.cif #1.2/BB PHE 44, extended_rough.cif #1.2/BC PHE 44, extended_rough.cif #1.2/BD PHE 44, extended_rough.cif #1.2/BE PHE 44, extended_rough.cif #1.2/BH PHE 44, extended_rough.cif #1.2/BI PHE 44, extended_rough.cif #1.2/BJ PHE 44, extended_rough.cif #1.2/BK PHE 44, extended_rough.cif #1.2/BL PHE 44, extended_rough.cif #1.2/BM PHE 44, extended_rough.cif #1.2/BN PHE 44, extended_rough.cif #1.2/BO PHE 44, extended_rough.cif #1.2/BP PHE 44, extended_rough.cif #1.2/BQ PHE 44, extended_rough.cif #1.2/BR PHE 44, extended_rough.cif #1.2/BS PHE 44, extended_rough.cif #1.2/BT PHE 44, extended_rough.cif #1.2/BU PHE 44, extended_rough.cif #1.2/BV PHE 44, extended_rough.cif #1.2/BW PHE 44, extended_rough.cif #1.2/BX PHE 44, extended_rough.cif #1.2/C ARG 302, extended_rough.cif #1.2/L LYS 273, extended_rough.cif #1.2/ba PHE 44, extended_rough.cif #1.2/bb PHE 44, extended_rough.cif #1.2/bc PHE 44, extended_rough.cif #1.2/bd PHE 44, extended_rough.cif #1.2/be PHE 44, extended_rough.cif #1.2/bf PHE 44, extended_rough.cif #1.2/bg PHE 44, extended_rough.cif #1.2/bh PHE 44, extended_rough.cif #1.2/bi PHE 44, extended_rough.cif #1.2/bj PHE 44, extended_rough.cif #1.2/bk PHE 44, extended_rough.cif #1.2/bl PHE 44, extended_rough.cif #1.2/bm PHE 44, extended_rough.cif #1.2/bn PHE 44, extended_rough.cif #1.2/bo PHE 44, extended_rough.cif #1.2/bp PHE 44, extended_rough.cif #1.2/UC ALA 15 Chain-final residues that are not actual C termini: extended_rough.cif #1.2/AA TYR 46, extended_rough.cif #1.2/AB TYR 46, extended_rough.cif #1.2/AC TYR 46, extended_rough.cif #1.2/AD TYR 46, extended_rough.cif #1.2/AE TYR 46, extended_rough.cif #1.2/AH TYR 46, extended_rough.cif #1.2/AI TYR 46, extended_rough.cif #1.2/AJ TYR 46, extended_rough.cif #1.2/AK TYR 46, extended_rough.cif #1.2/AL TYR 46, extended_rough.cif #1.2/AM TYR 46, extended_rough.cif #1.2/AN TYR 46, extended_rough.cif #1.2/AO TYR 46, extended_rough.cif #1.2/AP TYR 46, extended_rough.cif #1.2/AQ TYR 46, extended_rough.cif #1.2/AR TYR 46, extended_rough.cif #1.2/AS TYR 46, extended_rough.cif #1.2/AT TYR 46, extended_rough.cif #1.2/AU TYR 46, extended_rough.cif #1.2/AV TYR 46, extended_rough.cif #1.2/AW TYR 46, extended_rough.cif #1.2/AX TYR 46, extended_rough.cif #1.2/AF TYR 46, extended_rough.cif #1.2/AG TYR 46, extended_rough.cif #1.2/H1 LYS 53, extended_rough.cif #1.2/H2 ALA 8, extended_rough.cif #1.2/H2 PRO 7, extended_rough.cif #1.2/M TYR 324, extended_rough.cif #1.2/aa ALA 60, extended_rough.cif #1.2/ab ALA 60, extended_rough.cif #1.2/ac ALA 60, extended_rough.cif #1.2/ad ALA 60, extended_rough.cif #1.2/ae ALA 60, extended_rough.cif #1.2/af ALA 60, extended_rough.cif #1.2/ag ALA 60, extended_rough.cif #1.2/ah ALA 60, extended_rough.cif #1.2/ai ALA 60, extended_rough.cif #1.2/aj ALA 60, extended_rough.cif #1.2/ak ALA 60, extended_rough.cif #1.2/al ALA 60, extended_rough.cif #1.2/am ALA 60, extended_rough.cif #1.2/an ALA 60, extended_rough.cif #1.2/ao ALA 60, extended_rough.cif #1.2/ap ALA 60, extended_rough.cif #1.2/UA ALA 33, extended_rough.cif #1.2/UB ALA 17 4911 hydrogen bonds extended_rough.cif #1.2/AA TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AB TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AC TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AD TYR 46 is not terminus, removing H atom from 'C' extended_rough.cif #1.2/AE TYR 46 is not terminus, removing H atom from 'C' 39 messages similar to the above omitted Termini for 5y5s (#2) chain C determined from SEQRES records Termini for 5y5s (#2) chain L determined from SEQRES records Termini for 5y5s (#2) chain M determined from SEQRES records Termini for 5y5s (#2) chain H determined from SEQRES records Termini for 5y5s (#2) chain A determined from SEQRES records 31 messages similar to the above omitted Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: 5y5s #2/C CYS 23, 5y5s #2/L ALA 2, 5y5s #2/M PRO 2, 5y5s #2/H ILE 5, 5y5s #2/A ALA 6, 5y5s #2/B SER 5, 5y5s #2/D ASN 5, 5y5s #2/E LEU 9, 5y5s #2/F ASN 5, 5y5s #2/G SER 5, 5y5s #2/I THR 3, 5y5s #2/J SER 5, 5y5s #2/K THR 3, 5y5s #2/N SER 5, 5y5s #2/O MET 4, 5y5s #2/P SER 5, 5y5s #2/Q THR 3, 5y5s #2/R LEU 6, 5y5s #2/S THR 3, 5y5s #2/T LYS 4, 5y5s #2/U THR 3, 5y5s #2/V SER 5, 5y5s #2/W ASN 5, 5y5s #2/X LEU 6, 5y5s #2/Y THR 3, 5y5s #2/Z THR 7, 5y5s #2/1 MET 4, 5y5s #2/2 LEU 6, 5y5s #2/3 MET 4, 5y5s #2/4 SER 5, 5y5s #2/5 ALA 6, 5y5s #2/6 SER 5, 5y5s #2/7 THR 3, 5y5s #2/8 LEU 6, 5y5s #2/9 THR 3, 5y5s #2/0 LYS 4 Chain-final residues that are actual C termini: 5y5s #2/L TRP 281, 5y5s #2/H LEU 259, 5y5s #2/B LEU 46, 5y5s #2/E LEU 46, 5y5s #2/G LEU 46, 5y5s #2/J LEU 46, 5y5s #2/N LEU 46, 5y5s #2/P LEU 46, 5y5s #2/R LEU 46, 5y5s #2/T LEU 46, 5y5s #2/V LEU 46, 5y5s #2/X LEU 46, 5y5s #2/Z LEU 46, 5y5s #2/2 LEU 46, 5y5s #2/4 LEU 46, 5y5s #2/6 LEU 46, 5y5s #2/8 LEU 46, 5y5s #2/0 LEU 46 Chain-final residues that are not actual C termini: 5y5s #2/C THR 333, 5y5s #2/M THR 319, 5y5s #2/A GLY 59, 5y5s #2/D GLY 59, 5y5s #2/F GLY 59, 5y5s #2/I GLY 59, 5y5s #2/K GLY 59, 5y5s #2/O GLY 59, 5y5s #2/Q GLY 59, 5y5s #2/S LEU 58, 5y5s #2/U LYS 60, 5y5s #2/W LYS 60, 5y5s #2/Y GLY 59, 5y5s #2/1 GLY 59, 5y5s #2/3 GLY 59, 5y5s #2/5 GLY 59, 5y5s #2/7 GLY 59, 5y5s #2/9 GLY 59 Missing OXT added to C-terminal residue 5y5s #2/H LEU 259 5782 hydrogen bonds Adding 'H' to 5y5s #2/C CYS 23 Adding 'H' to 5y5s #2/L ALA 2 Adding 'H' to 5y5s #2/H ILE 5 Adding 'H' to 5y5s #2/A ALA 6 Adding 'H' to 5y5s #2/B SER 5 30 messages similar to the above omitted 5y5s #2/C THR 333 is not terminus, removing H atom from 'C' 5y5s #2/M THR 319 is not terminus, removing H atom from 'C' 5y5s #2/A GLY 59 is not terminus, removing H atom from 'C' 5y5s #2/D GLY 59 is not terminus, removing H atom from 'C' 5y5s #2/F GLY 59 is not terminus, removing H atom from 'C' 13 messages similar to the above omitted 30197 hydrogens added > isolde ignore ~sel ISOLDE: currently ignoring 3824 residues in model 2 ISOLDE: currently ignoring 4922 residues in model 1.2 ISOLDE: currently ignoring 41 residues in model 3 > select up 10 atoms, 9 bonds, 1 model selected > select up 130 atoms, 129 bonds, 1 model selected Traceback (most recent call last): File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2697, in _start_sim_or_toggle_pause self.start_sim() File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2717, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 586, in __init__ self._prepare_mdff_managers() File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 862, in _prepare_mdff_managers focus = False) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/symmetry.py"", line 972, in isolate_and_cover_selection extra_padding=extra_padding) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/map_mgr.py"", line 358, in cover_atoms zm.set_symmetry_map(atoms, transforms, transform_indices) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 111, in set_symmetry_map self.structure = self._unique_structure(atoms) File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') TypeError: All atoms for zone mask must be from a single model! TypeError: All atoms for zone mask must be from a single model! File ""/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') See log for complete Python traceback. > isolde ~ignore > color bychain > color byhetero > select /UC 153 atoms, 152 bonds, 1 model selected > isolde ignore ~sel ISOLDE: currently ignoring 3824 residues in model 2 ISOLDE: currently ignoring 4907 residues in model 1.2 ISOLDE: currently ignoring 41 residues in model 3 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 Memory: total used free shared buff/cache available Mem: 62G 5.2G 48G 142M 8.6G 56G 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: 5.12.8 }}} " defect closed normal Depiction wontfix Elaine Meng Eric Pettersen all ChimeraX