Add tool to measure pocket volumes

[meng@…]

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

[Tom Goddard]

From: Tom Goddard
Subject: Re: [chimerax-users] filling with water and counting water
Date: November 3, 2021 at 1:18:18 PM PDT
To: Elaine Meng

The tricky part is figuring out the algorithm or user interface that plugs the holes to define the fully enclosed pocket space. Maybe we could do something simple and highly useful if we had a simple idea for plugging the holes. I guess it is almost sure to need some user interaction since the definition of the pocket is so vague.

Tom

[Tom Goddard]

From: Elaine Meng
Subject: Re: [chimerax-users] filling with water and counting water
Date: November 3, 2021 at 1:35:33 PM PDT
To: Tom Goddard

I imaging something much like the per-model clipping interface, which allows the user to rotate and translate a plane.

It is hard to see in ChimeraX, though. I liked what we had in Chimera where it looked like a translucent CD.

Elaine