[chimerax-users] The ChimeraX-Modeller interface

[Ralph Loring]

Hi Elaine Meng,

Thanks so much for your suggestions!  However, I’m not thrilled about the
Alphafold idea, as I’ve tried to use it for receptors and keep getting
booted out before the job finishes (I’d like to get Colab Pro, but I can’t
figure out how to sign up with a university credit card; it’s only $0.55
per month in taxes, but my account manager will go ballistic if I pay any
taxes and Google doesn’t answer my emails about how to pay with a tax
exempt card).  Anyway, I got Alphafold to work for a 22 amino acid
mu-conotoxin (Mu-Conotoxin P0C349.pdb) and the predicted structure (in
blue) wasn’t great (see attached).  The RMSD between the Alphafold
predicted pdb and the original (tan) was 4.1 angstroms, so not good.  If
there is some way to guarantee that Alphafold would use the 7RPM.pdb as a
model for the intracellular loop, it might work, but the human alpha7
prediction from Alphafold before 7RPM was released (AF-P36544) is not good
for the intracellular loop.  There is now another Alphafold version
(AF-A0A1W2PN81)
that is equally bad.

Your scripts were incredibly helpful, as I haven’t figured out the syntax
for using the command line.  Is there a tutorial on using commands in
ChimeraX? (I have the list of commands in the user guide [
https://www.cgl.ucsf.edu/chimerax/docs/user/index.html#commands], but only
rarely does that include examples of how the commands are used and I can't
figure out the syntax code).  What I’d like to do is to delete all the
overlapping amino acids in either 7EKI.pdb (which has eGFP in the
cytoplasmic loop instead of cytochrome) or 7KOO.pdb with one of the 7RPM
ensemble and then bond the ends together to get an approximation of what
the intact receptor would look like without overlaps.  But I can’t get the
bond command correct in a test case using the two versions of mu-contoxin
(see attached csx file).  I know I want to bond #1Cys22CA to #2Arg1, but I
don’t even know how to specify the N-terminal nitrogen. (I can make the
bond in Chimera using a combination of Select/Atom Specifier and then
Tools/Structure Editing/Build Structure/Join Models, but that approach
avoids using commands and I want to know how to do this in ChimeraX). I
know I’m going to have to futz with phi and psi after making the bond, but
I can’t even get that far (and there's two bonds to make).

By the way, Matchmaker does a good job of lining up the overlapping amino
acids with any combination of the receptor pdbs.  As you can see, they are
very comparable (the dotted lines point down rather than up in your
method). But I’d like to get a pdb with a single chain for each complete
subunit at some point.

Thanks for all your help! Any suggestions would be most appreciated.

Ralph Loring



On Mon, Feb 14, 2022 at 6:33 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> To clarify, the "alphafold match" command would get already-made
> single-chain models from the freely available AlphaFold Database.  It does
> not run a new AlphaFold calculation.  It just superimposes the single-chain
> predictions onto the multimer structure that was already open, which is not
> the same as using it to predict a multimer.  However, in practice the
> result is often quite reasonable, if there are already experimentally known
> structures with the same type of multimerization.
>
> I also meant to include more help links in the previous reply...
>
> matchmaker
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
>
> combine
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
>
> Model Loops
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>
>
> Best,
> Elaine
>
>
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