[chimerax-users] filling with water and counting water

[vincent Chaptal]

Hi,

you can use the Uppsala software factory, Flood (to flood a volume with 
water), and then VOIDOO in volume mode (not sure here but you will see) 
to measure the volume of the water molecules.

Old stuff but works very well.
Best
Vincent

Le 03/11/2021 à 17:09, Elaine Meng via ChimeraX-users a écrit :
> 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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-- 

Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab


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