id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3583 Better feedback for loading CIF templates Tristan Croll Greg Couch "{{{ 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 Now that ISOLDE's veering towards allowing active addition of residues, I'm working on adding a button to allow users to load CIF templates for their own custom residues. A couple of stumbling blocks I've run across: - `mmcif.load_mmCIF_templates()` is silent - so if I deliberately feed it a CIF file that doesn't contain templates (e.g. a model, or structure factors) there is no feedback to say I've done the wrong thing. Probably shouldn't throw an error - but would be really helpful if it could return a list of the templates it just loaded (and possibly add an argument to decide whether or not to replace any existing templates with the same name). - the attached file is an example of the output from phenix.elbow, which is used to generate refinement restraints for new ligands by anyone using phenix.refine (that is, just about everyone in the community). Unfortunately (but unsurprisingly...) it's not strictly dictionary-compliant - it uses non-standard labels for the atomic coordinates: {{{ _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z }}} The result is a bit pathological: mmcif.load_template_residues() creates a template called D3R, but with no atoms in it. A couple of options I can think of that would help here: - try to get Nigel Moriarty to fix this on the Phenix side - make `load_template_residues()` lenient enough to handle these - provide a method to convert an existing residue loaded in ChimeraX from some other format into a `TmplResidue` (and/or write it out to a template CIF file so it can be loaded back in) Log: UCSF 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 /home/tic20/.cache/ChimeraX/1.0/installers/ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Clipper~=0.13.0 in /home/tic20/.local/share/ChimeraX/1.0/site-packages (from ChimeraX- ISOLDE==1.0rc1) (0.13.0) 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-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 139783708619792 acquired on /home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock Lock 139783708619792 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 start > set selectionWidth 4 Done loading forcefield Loaded CIF templates for [r2ycgsf] from /run/media/tic20/storage/Downloads/2ycg-sf.cif Loaded CIF templates for [r5lh0sf] from /run/media/tic20/storage/Downloads/5lh0-sf.cif Loaded CIF templates for [r5lh7sf] from /run/media/tic20/storage/Downloads/5lh7-sf.cif Loaded CIF templates for [6I2M] from /run/media/tic20/storage/Downloads/6i2m.cif Loaded CIF templates for [r6i2mAsf] from /run/media/tic20/storage/Downloads/6i2m-sf.cif Loaded CIF templates for [r6idosf] from /run/media/tic20/storage/Downloads/6ido-sf.cif Loaded CIF templates for [6O24] from /run/media/tic20/storage/Downloads/6o24_final.cif Loaded CIF templates for [comp_list, comp_BAM] from /run/media/tic20/storage/Downloads/bam.cif Loaded CIF templates for [comp_list, comp_BAM] from /run/media/tic20/storage/Downloads/BAM.cif Loaded CIF templates for [CDL] from /run/media/tic20/storage/Downloads/CDL.cif Loaded CIF templates for [D3R] from /run/media/tic20/storage/Downloads/D3R.cif You will now be able to add these residues to your model with ""isolde add ligand {ID}"". To be able to simulate them, you will need to provide matching ffXML MD parameterisations. > 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"") > open 1k82 format mmcif fromDatabase pdb 1k82 title: Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA [more info...] Chain information for 1k82 #1 --- Chain | Description A B C D | formamidopyrimidine-DNA glycosylase E F G H | 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3' I J K L | 5'-D(*CP*CP*ap*GP*GP*ap*(ped)P*GP*ap*ap*GP*CP*C)-3' Non-standard residues in 1k82 #1 --- PED — pentane-3,4-diol-5-phosphate (open form of 1'-2'-dideoxyribofuranose-5'-phosphate) ZN — zinc ion 1k82 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly 1k82 title: Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA [more info...] Chain information for 1k82 --- Chain | Description 1.2/A 1.2/B 1.2/C 1.2/D | formamidopyrimidine-DNA glycosylase 1.2/E 1.2/F 1.2/G 1.2/H | 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3' 1.2/I 1.2/J 1.2/K 1.2/L | 5'-D(*CP*CP*ap*GP*GP*ap*(ped)P*GP*ap*ap*GP*CP*C)-3' Non-standard residues in 1k82 #1.2 --- PED — pentane-3,4-diol-5-phosphate (open form of 1'-2'-dideoxyribofuranose-5'-phosphate) ZN — zinc ion 1k82 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > close #1 Deleting atomic symmetry model... 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 4.5G 49G 165M 8.7G 57G 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 File attachment: elbow.D3R_cif.001.cif }}} [attachment:""elbow.D3R_cif.001.cif""] " enhancement assigned normal Input/Output all ChimeraX