id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4342	mmCIF format-compliance issues	Tristan Croll	Greg Couch	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Note from Oleg on the Phenix team, relating to the attached file. The first is not so important (although it might be worth logging a warning when writing an mmCIF file with chain IDs >4 characters?). The second is a compliance issue (still pretty minor in the grand scheme of things). The root cause is that I failed to re-order residues in the model after reassigning chain IDs (the original model deposited in the wwPDB had some sugar residues disconnected, causing the wwPDB's own scripts to assign them different chain IDs to the rest of their tree). I can do that, of course, but maybe this would be better handled in the writer?


First, wwPDB limits the chain id with 4 characters (https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files) in mmCIF:
PDB format allows only single-character chain IDs, while PDBx/mmCIF can accommodate chain IDs of up to four characters.
It is not clear from the document whether they mean label_asym_id or auth_asym_id. Both don't have limits in the formal mmCIF dictionary (e.g. https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.auth_asym_id.html). 


Another minor issue I found in your file (probably does not affect Phenix, but not format complaint). _atom_site.label_asym_id cannot be reused and have rather strict rules when it need to be changed to the next one. Basically, if chain is interrupted by another chain - need to change label_asym_id. See cctbx_project/iotbx/pdb/hierarchy.py def get_label_asym_id() for how we do it. It is based on a rather long and hand-waving e-mail exchange with John Berrisford that I can dig up if you are interested. In your file, e.g. label_asym_id corresponding to Aglyc3 is the same in two separate places.



Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 455.32.00
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         10G         38G        228M         13G         51G
	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: 5.12.9
Installed Packages:
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.0
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    ChimeraX-HKCage: 1.3
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
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    ChimeraX-STL: 1.0
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    ChimeraX-SwapAA: 2.0
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    ChimeraX-TapeMeasure: 1.0
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File attachment: 6xra_rebuilt_glycan_chains_reassigned.cif

}}}

[attachment:""6xra_rebuilt_glycan_chains_reassigned.cif""]
"	defect	closed	normal		Input/Output		fixed		Eric Pettersen				all	ChimeraX