[chimerax-users] The ChimeraX-Modeller interface

Thu Feb 17 17:26:10 PST 2022

Hi Ralph,
I wouldn't suggest running AlphaFold on a system this large.  My first reply had the commands to assemble your model from the pre-existing free AlphaFold database (i.e. not running any AlphaFold calculation).  I do understand that may not be quite as desired since you can't control what was used as a template, but it might be a better starting point for further structure editing since it takes care of some of the residue numbering and chain ID correspondences, at least.

For reasons stated before and repeated here (stemming from multiple chains and lack of chain ID correspondence between the starting models, as well as tedium in trying to figure out what residue number ranges need to be deleted), it may be difficult to assemble a model using the workflow you had in mind.

By the way, if you use any icons or menu items, the corresponding command shows up in the Log.  So that is one way to learn commands. All of the tutorials contain many examples of commands as well.
<https://www.rbvi.ucsf.edu/chimerax/tutorials.html>

ChimeraX does not yet have a join models tool like in Chimera that simultaneously combines two models into one and bonds them while moving one model to a reasonable location.  So in ChimeraX you have to position the models appropriately first (taken care of by the matchmaker commands I sent you earlier), then (if needed) delete all the extra residues (easier said than done), then combine into a single model, then add bond(s).  Unfortunately the chain IDs will not match up automatically after the combine command, so for a usable a result it would probably entail writing out the single combined model as PDB, doing a lot of manual text-editing of the PDB file to fix up PDB IDs, and then reopening the file and bonding the atoms (well actually the text-editing could take care of that too).

You cannot bond atoms that are in different models (#1 and #2 in your example), and I should put something about that in the "bond" documentation, although you will get an error message that says so if you try to do it.  That is why you would have to use "combine" to create a single combined model first.  You don't have to use command-line specification to bond the atoms with a command.  If you hide ribbons and show backbone atoms you can select 2 backbone atoms (Shift-click, Shift-Ctrl-click on them in the graphics window) and then use command "bond sel reasonable false" (by default you can't see backbone atoms when the ribbon is shown).  If you did want to specify in command line, as alluded to above, hovering the mouse over some atom will show its chain ID, residue number, and atom name.  Usually backbone atoms are named N, CA, C, O but it may be different on the terminal residues.  #1:25 at ca means model 1, residue 25, atom CA.  There are several examples like that in the "atom specification" page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy>

"bond"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
"combine"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>

It may be quite difficult/tedious to figure out what residue ranges overlap (or comes from some unrelated fusion protein), and thus what should be deleted.  Keep in mind also that the numbering may not even be the same between the two structures, e.g. residue 10 in the uniprot seq might be 8 in one structure and 9 in the other.  How I looked up the residue numbers of the fusion protein part of one structure before my first reply was by looking at the RCSB PDB page for that structure and mousing over the sequence view.  You could also keep hovering the mouse over the structures (while hiding the others) to see balloon help to figure out where some residue number falls on the chain and writing down the ranges of residue numbers that are present in each.  Personally I'd do it by looking at the RCSB PDB page  and/or viewing the contents of the PDB files using a text editor, but that may be worse if you're not familiar with PDB files.  Another way is to associate each structure with the uniprot sequence and then determining what's present/absent in each structure in the sequence window.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 17, 2022, at 3:48 PM, Ralph Loring <rhloring at gmail.com> wrote:
> 
> 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
> 
> <Superimposed AF- & native Mu-conotoxins.jpg><Bond AF-mu CTX to mu-CTX.cxs><Superimposed 7KOO without BGT and 7RPM Meng's method.jpg><Superimposed 7EKI and 7RPM.jpg><Superimposed 7KOO without BGT and 7RPM.jpg>