[chimerax-users] filling with water and counting water

[Noriega, Heather]

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
520-203-1883

On Wed, Nov 3, 2021, 12:09 PM Elaine Meng <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> 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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