id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5537	Add tool to measure pocket volumes	meng@…	Tom Goddard	"Begin forwarded message:

From: Elaine Meng 
Subject: Re: [chimerax-users] filling with water and counting water
Date: November 3, 2021 at 1:11:30 PM PDT
To: Tom Goddard 

One ""hole"" (no pun intended, or maybe it is intended) in Chimera/ChimeraX functionality has been the lack of ways to measure pocket volumes, especially for open-ended pockets and tunnels.  There is CASTp, but it isn't really for large assemblies or complexes, and their website is really Pymol-centric -- the provided download is just for Pymol visualization. 

http://sts.bioe.uic.edu/castp/index.html?4jii

It isn't that easy to get something reasonable out of 3V, and MOLEonline, which does have a Chimera download, is intended for visualization rather than quantification.

I recall some other program(s) allowing you to fill a pocket up to a user-controlled planar cap position and then being able to report the volume enclosed.  I no longer remember which programs did that or whether they are still in existence, however.

Elaine
"	enhancement	assigned	moderate		Structure Analysis								all	ChimeraX