[chimerax-users] Blob measurement question?

[Elaine Meng]

Maybe you can try to find alternative ways of measuring the volume (other programs/web servers), then see if they corroborate the estimates from ChimeraX.

E.g. see suggestions in earlier posts,

Uppsala software factory: Flood + VOIDOO
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002868.html>

3V web server
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002871.html>

I also like Castp but have only used it on pockets in monomers. I don't know if it can be used for something like a virus capsid...
<http://sts.bioe.uic.edu/castp/calculation.html>

Elaine

> On Jan 10, 2022, at 11:07 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Heather,
> If there were a bug causing a calculation error, you would not get a value, and there would be an error message in the Log.  So even if you did run commands directly from the system prompt, I don't think that would give you any more information than you have already.
> 
> Stepping back, it sounds like you are expecting a much greater level of precision than this type of calculation can give.  Because ChimeraX cannot calculate the volume of a cavity surrounded by surface in which there are holes, it requires first making a density map and then adjusting the density map threshold to make a surface that does not have holes. It is not giving the exact precise volume value that would be given if you calculated a detailed molecular surface and then (in some way we don't have in ChimeraX) blocked off any small openings to the exterior.
> 
> Secondarily, I don't think you can predict a priori a bigger or smaller volume based solely on sequence length of the capsid protein.  Maybe it is a characteristic of this specific system (family of viruses) that I don't know, since I'm not an expert about it... but in general, it would depend on loop conformations, sidechain types and how they pack, etc.  For example, a longer sequence could just have an extra domain or loop that sits on the outside without affecting the interior volume.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jan 10, 2022, at 9:45 AM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago:
>> 
>> open 1lp3
>> open alphafold prediction
>> matchmaker #2 to #1
>> sym #2 symmetry #1 copies true
>> molmap #3 12
>> volume #4 level 0.07
>> choose "blob", right click to color it
>> surface splitbycolor #4.1
>> view position #5 sameAs #4
>> hide #4,5.1 model
>> measure volume #5.2
>> 
>> For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside:
>> 
>> AAV3B VP3 only: 2.348 X 10^6
>> AAV3B VP4 only: 2.488 x 10^6
>> 
>> However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me?
>> 
>> AAV8 VP3: 2.558 x 10^6
>> AAV8 VP4: 2.478 x 10^6
>> 
>> I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements. 
>> 
>> Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this.
>> 
>> Thank you, and I hope to hear from you soon.
>> 
>> Thank you,
>> 
>> Heather Noriega
>> PhD-Pharmaceutical Science student 
>> Howard University
>> heather.noriega at bison.howard.edu
>> 520-203-1883
>> <AAV3B VP3.pdb><AAV8_VP3.pdb><AAV8_VP4.pdb><AAV3BVP4_best_model.pdb><AAV3B_AAV8_MSA.afasta>
> 
> 
> 
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