[chimerax-users] How do you submit a sequence text file to BLAST/Modeller in ChimeraX?

[Ralph Loring]

Hi Elaine,
No, no, no! I know how to run Blast in ChimeraX if I have a PDB and use a
sequence based on a selected chain.  What I want to do, and was able to do
in Chimera, is to start with just a sequence and no PDB and use Modeller to
generate a PDB.  I'd start out with Blast and there's a tab in Chimera
BLAST labeled "Plain Text".  I'd put my sequence into that, Blast against
the PDB database, pick the best templates, show them in MAV and then go to
Modeller to generate PDBs based on homology with the templates. How do I
put a plain text sequence into the Blast tool in ChimeraX?  There is no tab
for that.  And once I choose the best templates, how do I link those with
Modeller?  Are there any tutorials on this?  I learned how to use
Chimera/BLAST/Modeller using YouTube:

https://www.youtube.com/watch?v=6wSqI-iP_4w
Ralph

On Wed, Nov 23, 2022 at 11:39 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ralph,
> ChimeraX has the Modeller tools, which are totally separate from
> AlphaFold.  ChimeraX menu: Tools... Structure Prediction... Modeller
> Comparative, and Model Loops.  You can click Help on each tool dialog to
> see their documentation, or view copies at our website:
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>
>
> If you don't see these tools in your menu, you need to get a newer version
> of ChimeraX.
>
> The documentation linked above describes how you could get an associated
> sequence or sequence alignment.  Since you mentioned Blast I guess you want
> Modeller Comparative.  In that page, it lists several ways you could get
> the alignment, including by opening a sequence alignment file or running
> the "blastprotein" command.  I should update it to say you could also use
> the Blast Protein tool, menu: Tools... Sequence... Blast Protein, which is
> equivalent to using the command.  After you run Blast there is a table
> listing the hits, and buttons across the bottom including "Show Sequence
> Alignment"  which will open a sequence alignment of all of the hits you
> have chosen in the table.  See Blast Protein help:
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html#results>
>
> So you would get the sequence alignment, make sure your template is
> associated with it, and show the Modeller Comparative tool, as described in
> the Modeller Comparative help.  There is also a "modeller" command but it
> is easier to use the GUI tool, assuming you are not trying to script
> everything.
>
> The documentation mentioned above is complete so you wouldn't necessarily
> benefit from a tutorial.  I do have a loop-modeling tutorial
> <https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html>
> but that is different from the comparative modeling that I'm guessing you
> want to do.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 23, 2022, at 5:07 AM, Ralph Loring via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi,
> > When I was using Chimera and wanted to use Modeller, I would go to
> sequence/Blast, paste in my sequence text file, Blast and then pick
> homologous structures and then connect to Modeller.  Both Blast and
> Modeller appear to be present in ChimeraX, but I can't see how to enter my
> text file.  Is everything supposed to go to AlphaFold now?  Are there any
> tutorials on how to use Modeller in ChimeraX?  Thanks!
> > P.S. Hope you have a Happy Thanksgiving!  I'm not planning on doing
> anything with this until after the holidays, so don't rush in answering.
> > Ralph Lorini
> >
> > Ralph H. Loring
> > Associate Professor of Pharmacology
> > Department of Pharmaceutical Sciences
> > 166 TF
> > Northeastern University
> > 360 Huntington Avenue
> > Boston, MA 02115 USA
> > 617-373-3216 office
> > 617-373-8886 fax
> > r.loring at northeastern.edu
> > _______________________________________________
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>
>
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