[chimerax-users] Measuring volume inside virus capsid
Tom Goddard
goddard at sonic.net
Fri Nov 5 15:26:31 PDT 2021
Hi Heather,
I looked at the ChimeraX session and see you opened 60 copies of your alphafold model, then ran matchmaker 60 times to align those to the 1LP3 virus capsid, then ran molmap 60 times. That is a lot of tedious work and does not get quite what you want. So here are some commands to try go get the enclosed volume.
open 1lp3 format pdb
open ~/Downloads/ChimeraX/AlphaFold/prediction_23/best_model.pdb
matchmaker #2 to #1
sym #2 symmetry #1 copies true
molmap #3 12
volume #4 level 0.07
# 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 #4.1
view position #5 sameAs #4
hide #4,5.1 model
measure volume #5.2
-> 2.5 million cubic Angstroms
Here I aligned a single copy of the AlphaFold model (#2) to the 1lp3 capsid monomer (#1) with matchmaker, then applied the symmetry of 1lp3 to the AlphaFold model to produce all 60 copies (#3), then made a density map from those 60 copies (#4), then set a low enough density map threshold so that their are no holes connecting the inside and outside of the capid, then colored the outside surface different from the inside with the blobs mouse mode, then split that two color surface into two pieces (outside #5.1, inside #5.2), then realigned the split surface to the density map (it was a bug that it did not preserve the alignment), then measured the volume of the inside surface.
If you have questions about any of these commands the ChimeraX user manual has thorough documentation on all of them, so read about them.
I described a slightly simpler case of finding the interior volume of 1lp3 on the ChimeraX Recipes web page.
https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html <https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html>
Tom
> Begin forwarded message:
>
> From: "Noriega, Heather"
> Subject: measuring volume
> Date: November 5, 2021 at 2:25:42 PM PDT
> To: Tom Goddard
>
> Hello Tom,
>
> I hope this email finds you well. I am very grateful for your email a couple days ago with chimeraX and trying to compute the interior volume in a virus capsid shell. I am very new to all this molecular modeling software, but am trying very hard to learn and understand. I have been working on a few different capsids particularly through alpha fold predictions on ChimeraX. I have created this one below through one-by-one aligning the predictions to create T=1 (1LP3 as biological assembly reference). Now, I one-by-one again used the molmap application for each copy and changed to volume level 0.676 and colored dark blue. My issue is when I go to measure volume it says the surface selected is wrong. I am unsure how to fix it or if I can fix it. Also, I do not know if this has anything to do with it, but I am using a Windows computer, I have noticed most of your videos are done through apple. Would this make a huge difference? I await your response and again thank you very much for your help.
>
> Thank you,
>
> Heather Noriega
> On Nov 3, 2021, at 11:49 AM, Tom Goddard <goddard at sonic.net> wrote:
>
> 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 <mailto: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/ <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 <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 <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 <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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>>
>>
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