id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3539 Problems with large de novo mmCIF structure 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 Something seems slightly weird about this mmCIF file (which, for the record, will be to my knowledge the first big new experimental complex built essentially entirely in ChimeraX/ISOLDE, starting from homology models for individual chains). Up-front: it's unpublished and confidential, so could you remove it off the bug tracker once you have a local copy? Anyway, I noticed after opening it that one ligand (CDL, /a:1025) was shown in sphere representation like the protein, rather than sticks like all the many other ligands. Also, looking at the mmCIF file in a text editor I see a number of different ligands (as in, different residue names) have the same _struct_asym.entity_id. This *may* be because I ""mutated"" quite a few of the lipids (i.e. renamed the residue and rebuilt from the template for the new one, keeping atoms common between the old and new). 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 > open Tristan_working_edited_Sc_20July20.cif Summary of feedback from opening Tristan_working_edited_Sc_20July20.cif --- warnings | Unknown polymer entity '1' near line 376 Unknown polymer entity '2' near line 2754 Unknown polymer entity '3' near line 5432 Unknown polymer entity '4' near line 8583 Unknown polymer entity '5' near line 15222 25 messages similar to the above omitted Atom H1 is not in the residue template for MET /A:1 Atom H1 is not in the residue template for LEU /B:14 Atom H3 is not in the residue template for ALA /C:4 Atom H3 is not in the residue template for ASP /D:2 Atom HH11 is not in the residue template for 2MR /D:65 Atom H1 is not in the residue template for MET /E:1 Atom H3 is not in the residue template for GLN /E:9 Atom H3 is not in the residue template for ALA /G:2 Atom H1 is not in the residue template for ALA /H:2 Atom H4 is not in the residue template for P5S /H:1003 Atom H1 is not in the residue template for ALA /I:2 Atom H1 is not in the residue template for MET /J:1 Atom H1 is not in the residue template for MET /K:1 Atom H4 is not in the residue template for P5S /L:2003 Atom H1 is not in the residue template for MET /M:1 Atom H3 is not in the residue template for ALA /P:3 Atom H1 is not in the residue template for MET /Q:1 Atom H1 is not in the residue template for THR /Z:2 Atom H4 is not in the residue template for P5S /a:1017 Atom H1 is not in the residue template for ALA /b:212 Atom H1 is not in the residue template for ALA /e:212 Atom H1 is not in the residue template for GLN /h:30 Atom H1 is not in the residue template for ALA /i:2 Atom H3 is not in the residue template for THR /j:8 Atom H1 is not in the residue template for GLN /l:30 Atom H1 is not in the residue template for ALA /m:2 Atom H1 is not in the residue template for THR /n:8 Atom H3 is not in the residue template for PHE /o:2 Atom H1 is not in the residue template for PHE /p:2 Atom H1 is not in the residue template for MET /q:1 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for Tristan_working_edited_Sc_20July20.cif #1 --- Chain | Description A | ? B | ? C | ? D | ? E | ? F | ? G | ? H | ? I | ? J | ? K | ? L | ? M | ? N | ? P | ? Q | ? R | ? Z | ? a | ? b e | ? c | ? d | ? f | ? g k | ? h l | ? i m | ? j n | ? o | ? p | ? q | ? > open 375Box_Default_BFactor_postprocess_job1571_1_048_pix.mrc Opened 375Box_Default_BFactor_postprocess_job1571_1_048_pix.mrc, grid size 375,375,375, pixel 1.05, shown at level 0.0235, step 2, values float32 > volume #2 level 0.03367 > cartoon > hide protein > volume #2 step 1 > select /a:1025@O1 1 atom, 1 model selected > select up 256 atoms, 255 bonds, 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 /BT:51 Nothing selected > select /C:51 19 atoms, 18 bonds, 1 model selected > select /a:1025@C75 1 atom, 1 model selected > select /BK Nothing selected > select /AA Nothing selected 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 12G 37G 249M 13G 49G 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: Tristan_working_edited_Sc_20July20.cif }}} [attachment:""Tristan_working_edited_Sc_20July20.cif""] " defect closed normal Input/Output limitation Eric Pettersen all ChimeraX