id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4177	Script for setting ligand chain IDs	Tristan Croll	Tom Goddard	"{{{
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
Little script for comment/suggestion (and donation to ChimeraX if you find it useful). The aim is to reassign chain-IDs and residue numbers to all ligands in a reasonably systematic fashion (because these usually get quite haphazard during model building). What it does:
- for covalent ligands that aren't sugars (or consist of a single sugar residue) the chain ID is assigned to be the same as the linked chain.
- larger branched sugars get their own chain ID ({parent chain ID}glyc{index}) where the glycan attached earliest in the chain gets index 0, etc. Residue numbering starts from the stem sugar, and goes out along the bonds through the lowest-numbered oxygens first. I personally think this distinction between single and multiple-sugar sites is ridiculous, but this is what the wwPDB in their infinite wisdom have decided upon.
- for all noncovalent ligands, assigns chain IDs according to which polymeric chain is closest to the most atoms in the ligand. Renumbers (non-waters first, then waters) starting from the next multiple of 1000 beyond the end of the polymeric chain (or the following 1000 if the gap between the last residue and the starting number is equal to or less than 100).
- any unbound ligands that are too far from the macromolecule to be captured in the first distance test (`find_close_points()` with a 5A cutoff) get a second chance - checked again against everything that's been assigned, this time with an 8A cutoff. If there are still unassigned residues, they get a chain ID of 'UNK' and a warning goes to the log.

It *appears* to work correctly in my tests (on the same system as in #4176 - 4974 protein residues, 814 ligands, two O-linked glycans, it takes about 1.3 seconds). Any comments or suggestions welcome!

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        8.4G        1.9G        326M         52G         53G
	Swap:          4.9G        6.5M        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
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File attachment: ligand_utils.py

}}}

[attachment:""ligand_utils.py""]
"	enhancement	assigned	normal		Structure Editing				Eric Pettersen				all	ChimeraX