id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3435 2D molecule drawing Tristan Croll Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.10.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Would be nice to have built-in access to a library that can draw a 2D sketch of a molecule. My graph-matching ""find possible MD templates"" approach appears to be working reasonably nicely now - but the new problem is that the ""raw"" results are going to be quite confusing to the user. If I delete the sidechain amine from a lysine, for example, it finds the following potential templates: LYN, LYS, CLYS, NLYS, PTM_LYZ, PTM_MLY, PTM_MLZ, ZK ... which are all correct in that they're indeed variants of lysine - but without a more informative description it's going to be hard for the user to choose. I can see a few paths forward: - amend the OpenMM `ForceField` to allow longer descriptions of a residue to be stored directly with its template (I have a ticket in with them suggesting this) - get the description from the CCD template (will be possible when the MD template name contains the CCD template name, but quite difficult otherwise) - draw a 2D sketch highlighting mismatched atoms - do it in 3D, similarly to how I handle rotamer previews now (create an extra minimal molecule from the base residue, edit it to match the template, and find a display method to clearly highlight the mismatches) - some combination of the above. 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 ./.cache/ChimeraX/1.0/installers/ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl 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-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- 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-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-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 140545846217744 acquired on /home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock Lock 140545846217744 released on /home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock WARNING: You are using pip version 20.1; however, version 20.1.1 is available. You should consider upgrading via the '/usr/bin/chimerax -m pip install --upgrade pip' command. > open /home/tic20/chimerax_presets/test_find_templates.py format python 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 #1 --- Chain | Description A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > addh Summary of feedback from adding hydrogens to 3io0 #1 --- notes | Termini for 3io0 (#1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A PRO 76 Chain-final residues that are actual C termini: /A PHE 304 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A PHE 304 198 hydrogen bonds 1692 hydrogens added > isolde start > set selectionWidth 4 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 --- Chain | Description 1.2/A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly Num heavy atoms: 8 Name matches: Topology matches: LYN, LYS, CLYS, NLYS, PTM_LYZ, PTM_MLY, PTM_MLZ, ZK executed test_find_templates.py Done loading forcefield > 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"") Fetching CCD LYZ from http://ligand-expo.rcsb.org/reports/L/LYZ/LYZ.cif > help help:user OpenGL version: 3.3.0 NVIDIA 450.36.06 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 5.1G 48G 157M 9.2G 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 assigned normal Depiction Eric Pettersen Tom Goddard all ChimeraX