[chimerax-users] The ChimeraX-Modeller interface

Fri Feb 18 14:31:28 PST 2022

Thanks Elaine!  It worked and formed 1 chain out of 2!  I had not combined
before trying to bond previously.  Oddly, I don't see in the bond command
description where that is mentioned.  Also, I surmise that the "reasonable"
modifier is not optional because when I omitted it, it didn't give an
error, but said 0 bonds were formed.
Ralph

On Fri, Feb 18, 2022 at 11:45 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ralph,
> Here is an example:
>
> bond #1/A:25 at C #1/A:38 at N reasonable false
>
> ... to add a bond in model 1 between residue 25 in chain A, atom name C,
> and residue 38 in chain A, atom name N.
>
> Again, you CANNOT make a bond between atoms that are in different models.
>  If you have the pieces in different models you have to combine them into a
> single model first and then form the bond within the new combined model.
> And of course, you have to substitute in your residue numbers, chain IDs,
> and atom names according to what is in your actual structure.
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
>
> In ChimeraX, you are allowed to give more than 2 atoms and form all
> pairwise bonds,  but you need the "reasonable false" part if you want them
> even if the distances are too long for a covalent bond.
>
> If you have trouble with the command-line atom spec part, you could just
> select the atoms from the screen like I explained in my previous reply and
> then use command:
>
> bond sel reasonable false
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/selection.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 Feb 18, 2022, at 4:01 AM, Ralph Loring <rhloring at gmail.com> wrote:
> >
> > Hi Tom,
> > No, I was running only one subunit (502 amino acids) at a time.  I'm
> trying other approaches with other software now to incorporate the ICD.
> When I bonded the different domains from multiple pdbs in Chimera, it
> really did turn into a Frankenstein. Also, I'd seen a youtube presentation
> suggesting that Modeller could handle more than one pdb, and I was hoping
> that would work as a way to combine the different domains.  That didn't
> work out either. But as far as learning syntax from the log, that only
> works for commands that you can run from pull-down menus.  All I know is
> that the syntax for the bond command in ChimeraX is different than the
> equivalent in Chimera.  If someone could just give me an example of a
> script that picks the atoms and makes a CN peptide bond, that would be very
> thankful.
> > Thanks for all your help,
> > Ralph
> >
> > On Fri, Feb 18, 2022 at 1:21 AM Tom Goddard <goddard at sonic.net> wrote:
> > Hi Ralph,
> >
> >   If you are trying to run alphafold to predict the acetylcholine
> receptor alpha7 pentamer, that is 2500 total amino acids (500 per alpha7
> monmer), then there is no way that is going to run on Google Colab which
> fails beyond about 1000 amino acids.  (Some alphafold size tests here:
> https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html)
> Colab Pro definitely will not help.  Also all Google Colab AlphaFold
> scripts including what ChimeraX uses run a limited alphafold with no
> structure templates.  See the main AlphaFold Google Colab page for more
> details
> >
> >
> https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb
> >
> > If you could install and run full AlphaFold on say an Nvidia RTX 3090
> with 24 GB of GPU memory it might succeed (not run out of memory), but it
> is near the size limit.  You would probably need a much more exotic Nvidia
> A40 (48 Gbytes) or A100 or similar.  And even if you run that, you are
> expecting too much if you think it is going to give you a fully accurate
> prediction -- AlphaFold produces lots of poor models for large structures.
> >
> >   One more reality check on the capabilities of AlphaFold.  It has no
> option to tell it exactly what PDB templates you want to use -- it chooses
> the "best 4", I have never seen the criteria documented for what "best 4"
> means, and further the log output from AlphaFold does not even tell you
> which 4 templates it uses.  You could probably point it to a PDB database
> with only 7RPM if you wanted to just use that as a template if you can
> setup your own AlphaFold installation.
> >
> >   In summary, definitely don't expect miracles or ease of use from
> AlphaFold.
> >
> >   Of course the hand construction of Frankenstein models described by
> Elaine is likewise no easy task.
> >
> >       Tom
> >
> >> On Feb 17, 2022, at 3:48 PM, Ralph Loring via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> 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>_______________________________________________
> >> ChimeraX-users mailing list
> >> ChimeraX-users at cgl.ucsf.edu
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> >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> >
>
>
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