[chimerax-users] Making multiple icosahedral pentamers (assembly 3)

[Noriega, Heather]

Yes! Thank you.

Thank you,

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

On Mon, Nov 1, 2021, 2:51 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Heather,
> If you open 1lp3 from a PDB-format file (not the default format, mmCIF)
> then you can use its BIOMT information to make the whole capsid from your
> alphafold model.  There is no choice to make only a subset of the capsid
> (only certain pentamers or hexamers) but you can delete or hide all the
> subunits of the whole capsid that you don't want to see.  Start ChimeraX,
> then
>
> (1) Open 1LP3 but from PDB format, e.g. command: open 1lp3 format pdb
>
> (2) Open your alphafold model (now it will be #2)
>
> (3) Superimpose alphafold model onto 1LP3, e.g. command: mm #2 to #1
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
>
> (4) Apply BIOMT symmetry from the 1LP3 PDB model (#1) to the alphafold
> model (#2), command:
>
> sym #2 symmetry #1 copies true
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry>
>
> Then you will have a model #3 that is the whole capsid made from your
> alphafold model.  The individual subunits in that capsid will be submodels
> #3.1, #3.2, ... #3.60.  One way to show/hide is by using the checkboxes
> under the eye icon in the Models panel.
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.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 Oct 30, 2021, at 2:25 PM, Noriega, Heather via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> > I am trying to make different monomer amounts of the icosahedral for my
> alphafold prediction. Now, I am able to use 1LP3 as my reference to create
> a icoshedral pentamer, but that is only 5. I would like to be able to do
> 10-mer, 15-mer, 20-mer, etc. I however can not seem to connect the
> pentamers to create the portions of virus capsid. Can you direct me?
> > Thank you,
> > Heather Noriega
> > PhD-Pharmaceutical Science student
> > College of Pharmacy
> > Howard University
> > heather.noriega at bison.howard.edu
> > 520-203-1883
>
>
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