[chimerax-users] filling with water and counting water

[Noriega, Heather]

I completely understand and thank everyone who has answered on this thread.
My issue is I am not a computer major nor have I ever done molecular
modeling, therefore I do not know how to manipulate the software completely
and am learning. I assumed there was a command for my need just not listed
and I was advised to ask questions to the help email. I will work on trying
to figure it out and do my due diligence as a Phd student and again thank
you for all your help.

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, 2:21 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> I don't know if it would work on your specific case, but there is a "3V"
> server that makes maps that fill cavities and tunnels that you could try.
> Namely, I don't know if it works for fully enclosed cavities.
>
> <http://3vee.molmovdb.org/>
>
> If it gave a suitable output (a map blob that fits inside your capsid)
> then you can use "measure volume" after opening it in ChimeraX and showing
> its isosurface.
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>
>
> I'm sure there are other creative ways if you think about it... like
> trying to make a sphere that fits inside and calculating the volume of the
> sphere from the standard geometric formula.
>
> I was trying to think of a way involving a low-resolution surface (e.g.
> from using "molmap" on the capsid atoms) and "volume onesmask"  but
> couldn't come up with anything.  The problem with just using a molecular
> surface or low-res surface from molmap is that it is hollow, and the volume
> calculation will just include the shell with the atoms, not the big empty
> part inside.
>
> As you can see, none of these are like a one-step thing that is already
> figured out for you. Part of being a PhD student is trying to solve
> problems that haven't been worked out for your specific situation!
>
> Elaine
>
> > On Nov 3, 2021, at 10:38 AM, Noriega, Heather via ChimeraX-users <
> 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
> > 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,
> >
> > _______________________________________________
> > ChimeraX-users mailing list
> > ChimeraX-users at cgl.ucsf.edu
> > Manage subscription:
> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211103/4f53391b/attachment.html>