id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2478 CCD templates should us different XYZ fields Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 0.91 (2019-09-18) Description When a template is fetched from the CCD using mmcif.find_template_residue, the coordinates are currently taken from _chem_comp_atom.model_Cartn_{x,y,z}. Looks to me like these should instead be taken from _chem_comp_atom.pdbx_model_Cartn_{x,y,z}_ideal, since it turns out the former can have some coordinates undefined (3PE, for instance). This caused rather a lot of head-scratching this afternoon! Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-09-18) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0b3.dev5-cp37-cp37m-linux_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /home/tic20/.cache/ChimeraX/0.91/installers/ChimeraX_ISOLDE-1.0b3.dev5-cp37-cp37m-linux_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX- ISOLDE==1.0b3.dev5) (0.91) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.9 in /home/tic20/.local/share/ChimeraX/0.91/site-packages (from ChimeraX- ISOLDE==1.0b3.dev5) (0.9.9) Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX- ISOLDE==1.0b3.dev5) (1.0) Installing collected packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0b3.dev5 Uninstalling ChimeraX-ISOLDE-1.0b3.dev5: Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev5 Successfully installed ChimeraX-ISOLDE-1.0b3.dev5 Lock 140711558216400 acquired on /home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock Lock 140711558216400 released on /home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock > open Mouse-d-coot-9_real_space_refined.pdb Chain information for Mouse-d-coot-9_real_space_refined.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available > select /H:3PE 266 atoms, 264 bonds, 1 model selected > hide ~sel > toolshed show Shell /opt/UCSF/ChimeraX-daily/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"") > select clear > cofr centerOfView > cofr centerOfView showPivot true > select up Nothing selected > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero OpenGL version: 3.3.0 NVIDIA 415.27 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Input/Output fixed all ChimeraX