[chimerax-users] filling with water and counting water

[Tom Goddard]

Hi Heather,

Here is a tricky way to compute the interior volume in a virus capsid shell in ChimeraX.

	open 1LP3
	sym #1 assembly 1 copies true
	molmap #2 12
	volume #3 level 0.676
	# Choose "blob" mouse mode under the "Right Mouse" toolbar tab and right click (option key on Mac) the volume surface to color it.
	surface splitbycolor #3.1
	hide #4.1 model
	measure volume #4.2
	-> 2.6 million cubic Angstroms.

The idea is to make a low resolution (12 Angstrom) density map from the atomic model, low resolution so there are not holes in the capsid, set the map threshold so there are no holes connecting the inside and outside, then color the outside layer with the "pick blob" mouse mode, then split the surface by color (producing inside and outside surfaces), then measure the volume enclosed by the inside surface.

	Tom

Here's a cut in half view showing the interior surface produced by the above example


> On Nov 3, 2021, at 11:21 AM, Elaine Meng via ChimeraX-users <chimerax-users 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,
>> 
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