id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3589 Saving instance in session Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description I have a class, `ResidueStepper`, whose role is to handle smoothly ""stepping"" the view through a model one residue at a time. Currently on creation I add it as a property of the `AtomicStructure` it's attached to. It would be nice to be able to save and restore it with the session so the user can easily pick up where they left off. I've made it a subclass of `State` and implemented `take_snapshot()` and `restore_snapshot()`... but now I realise I don't know how to actually register it to take part in session save/restore (it seems all my other cases have been subclasses of classes for which this is already handled automatically). What do I need to do here? Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open test.cxs Deleting atomic symmetry model... Deleting (LIVE) MDFF potential Deleting (LIVE) 2mFo-DFc_sharp_29 Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting Crystallographic maps (3io0-sf.mtz) restore_snapshot for ""RotamerRestraintMgr"" returned None Log from Mon Aug 3 18:15:24 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open /home/tic20/test.cxs format session restore_snapshot for ""RotamerRestraintMgr"" returned None Log from Mon Aug 3 18:11:42 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open test.cxs Deleting atomic symmetry model... Deleting (LIVE) 2mFo-DFc Deleting (LIVE) MDFF potential Deleting (LIVE) 2mFo-DFc_sharp_29 Deleting (LIVE) mFo-DFc Deleting Crystallographic maps (3io0-sf.mtz) restore_snapshot for ""RotamerRestraintMgr"" returned None Log from Mon Aug 3 18:11:04 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./.cache/ChimeraX/1.0/installers/ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper~=0.13.0 in ./.local/share/ChimeraX/1.0/site-packages (from ChimeraX-ISOLDE==1.0rc1) (0.13.0) Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX- Core~=1.0rc202005052344 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0) Installing collected packages: ChimeraX-ISOLDE Attempting uninstall: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0rc1 Uninstalling ChimeraX-ISOLDE-1.0rc1: Successfully uninstalled ChimeraX-ISOLDE-1.0rc1 Successfully installed ChimeraX-ISOLDE-1.0rc1 Lock 139937780277904 acquired on /home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock Lock 139937780277904 released on /home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock WARNING: You are using pip version 20.1; however, version 20.2 is available. You should consider upgrading via the '/usr/bin/chimerax -m pip install --upgrade pip' command. > isolde demo crystal_intro > set selectionWidth 4 before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description 1.2/A | predicted microcompartment protein WARNING: multiple experimental reflection datasets found: (dataset) FOBS, SIGFOBS, (dataset) IOBS, SIGIOBS, (dataset) DANO, SIGDANO, (dataset) F(+), SIGF(+), F(-), SIGF(-), (dataset) I(+), SIGI(+), I(-), SIGI(-) Automatically choosing ""(dataset) IOBS, SIGIOBS"". Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Loaded crystallographic demo: PDB ID 3io0 Done loading forcefield > save test.cxs opened ChimeraX session > isolde stepto > isolde stepto > isolde stepto > isolde stepto > save test.cxs opened ChimeraX session > isolde stepto > isolde stepto > isolde stepto > isolde stepto > save test.cxs opened ChimeraX session > isolde stepto > 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"") OpenGL version: 3.3.0 NVIDIA 450.51.05 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 6.0G 43G 207M 13G 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 Sessions not a bug all ChimeraX