[chimerax-users] Blob measurement question?

[Noriega, Heather]

Ok, thank you. I will look into it and discuss with my advisor. I
appreciate it.

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
College of Pharmacy
Howard University
heather.noriega at bison.howard.edu
520-203-1883

On Mon, Jan 10, 2022, 2:26 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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