[chimerax-users] mmcif assemblies for alphafold prediction

[Noriega, Heather]

Ok, I see. I will try that 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 Sat, Oct 30, 2021, 10:17 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Heather,
> You would not use "sym" for the alphafold model, only "matchmaker" ...
> what I described is that if you already have open a similar assembly of
> known structure, then open multiple copies of the alphafold model, then
> match each alphafold model copy onto one subunit of the other assembly.
>
> It sounds like you are saying that the 1LP3 assembly is your known
> example.  After you make the 1LP3 assembly with "sym", then open however
> many copies of the alphafold model would be in a similar assembly (i.e.
> open the same thing several times), then use "matchmaker" several times,
> once for each copy of the alphafold monomer, to superimpose it with the
> corresponding monomer of the 1LP3 assembly.
>
> 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 4:35 AM, Noriega, Heather via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Yes, so that is what I did. The "4 and 6" are the number of the
> assemblies I wanted to recreate which is the asymmetrical unit and crystal
> version of the unit. I did open up 1LP3 from the PDB bank super imposed to
> my alphfold prediction with matchmaker and then used the sym command for
> assembly #4 and #6. However, only the 1LP3 create the sym. The alphafold
> stays as a single superimposed monomer and I don't know why or how to fix
> it.
> >
> > Thank you,
> >
> > Heather Noriega
> > PhD-Pharmaceutical Science student
> > College of Pharmacy
> > Howard University
> > heather.noriega at bison.howard.edu
> > 520-203-1883
> >
> > On Fri, Oct 29, 2021, 10:10 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Heather,
> > I don't know what you mean by "similar to 4 and 6."  The mmCIF
> information is for describing and applying symmetries, not making an
> asymmetric assembly.
> >
> > Assuming that your ultimate goal is to generate such an assembly of your
> AlphaFold-predicted monomeric chain structures:  If you have an assembly
> structure of some other similar proteins in that arrangement, you can open
> copies of your alphafold predictions and superimpose these copies onto the
> corresponding subunits of the known assembly (e.g. with "align" or
> "matchmaker" ... probably the latter, as it is easier if it works for your
> specific situation), then close that known assembly, leaving your
> approximately modeled assembly of AlphaFold models.
> >
> > Matchmaker tool and command
> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
> >
> > align command
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.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 29, 2021, at 6:53 PM, Noriega, Heather via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> > >
> > > Hello,
> > > I am trying to create an asymmetrical assembly similar to 4 and 6 with
> an alphafold prediction. There are no mmCIF assemblies connected with this
> prediction, is there a way to add the assemblies, if so how? Or is there
> another way to create this figure without the assembly?
> > > Thank you,
> > > Heather Noriega
> > > PhD-Pharmaceutical Science student
> > > Howard University
> > > heather.noriega at bison.howard.edu
> > > 520-203-1883
>
>
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