id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3327 mmCIF output problem for inserted residues 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: 1.0rc202005270557 (2020-05-27 05:57:28 UTC) Description Residues inserted into the middle of a protein chain are appended to the *end* of the chain when writing to mmCIF, causing the model to be messed up on reloading. If I take 3io0, delete residue 299, then add it back using the method at https://github.com/tristanic/isolde/blob/0d72c4cbd0a12cfce7671d618d62b115eb96220f/isolde/src/atomic/building/build_utils.py#L110 ... using residue 298 as the ""prev_res"" argument and then adding the bond, then: {{{ m = session.models.list()[0] from chimerax.atomic import selected_residues m.residues.numbers # Lists the residue numbers in the correct order # With all atoms selected selected_residues(session).numbers # puts the new residue at the end }}} I've attached a session containing the model before and after saving to mmCIF and reopening (ignore the terrible geometry - didn't bother to energy minimise) - on re-opening the bonding to the preceding and following residues is correct, but there's a spurious bond from the C-terminus back to the N atom of the new residue, and a missing-structure pseudobond from the preceding to following residue (it wasn't there in the model before saving). Log: UCSF ChimeraX version: 1.0rc202005270557 (2020-05-27) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3io0 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 > show > hide cartoons > select /A:299@CA 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 1 model selected > delete /A:299 > select /A:300@N 1 atom, 1 model selected > 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"") > select /A:298@C 1 atom, 1 model selected > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select /A:299@C 1 atom, 1 model selected > preset custom ""make bond"" > open /home/tic20/chimerax_presets/make_bond.py executed make_bond.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > select #1 1667 atoms, 1689 bonds, 1 model selected > pwd Current working directory is: /home/tic20 > save build_test.cif #1 > select clear > hide #1 models > open build_test.cif Chain information for build_test.cif #2 --- Chain | Description A | EtuB protein build_test.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly > show > style #!2 stick Changed 1667 atom styles > hide #!2 cartoons > hide #!2 models > show #1 models > show #!2 models > save building_bug.cxs 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 5.3G 40G 433M 16G 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 File attachment: building_bug.cxs }}} [attachment:""building_bug.cxs""] " defect closed normal Input/Output fixed Greg Couch all ChimeraX