[chimerax-users] filling with water and counting water

[Guillaume Gaullier]

Hello Heather,

Maybe measure distances between atoms chosen to get you as close as possible to the edges on the inside of the cavity, and then work out the volume geometrically? https://en.wikipedia.org/wiki/Regular_icosahedron#Area_and_volume (of course, adjust according to the type of icosahedron you are dealing with, if it’s not a "regular" one).
Seems like it would be a decent approximation.

Measuring distances between atoms in ChimeraX can be done two ways:

- interactively: https://www.cgl.ucsf.edu/chimerax/docs/user/tools/distances.html
- or with a command, if you know which atoms to select (this can be figured out interactively by hovering the mouse pointer on the atoms): https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html

I hope this helps,

Guillaume


On 3 Nov 2021, at 18:38, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

What other ways can you measure the inter space of the icosahedral?

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
College of Pharmacy
Howard University
heather.noriega at bison.howard.edu<mailto:heather.noriega at bison.howard.edu>
520-203-1883

On Wed, Nov 3, 2021, 12:09 PM Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:
Hi Heather,
I guess my first question is "why would you want to do that?"   If the goal is to measure the cavity volume, there may be other ways.  I'm not aware of any ChimeraX capability to fill it with waters (you may have to write your own code if that's what you really want to do).

In general you can count the waters (or any other residue type) in some structure using a similar method to what I described recently on the chimera-users list, except that to show the Selection Inspector you click the green magnifying glass on the top bar icons of ChimeraX instead of the lower-right corner of the Chimera window.
<https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html>

I hope this helps,
ELaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 3, 2021, at 6:20 AM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>
> Good morning,
> I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside?
> Thank you,

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