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

[Elaine Meng]

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