id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3304 safeguard chain IDs 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: 1.0rc202005242323 (2020-05-24 23:23:37 UTC) Description First chance to try out the new chain renaming (swapping IDs for two pairs of chains), and I mess it up - accidentally renamed a chain to ""/AG"". Fixed my mistake with a little tinkering in the shell, but I'm guessing this wouldn't be recoverable via the command line only. Might want to add a catch to prevent the creation of illegal chain IDs? Log: UCSF 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 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 7.8G 41G 159M 13G 54G 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 }}} " enhancement closed normal Structure Editing wontfix all ChimeraX