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

[Elaine Meng]

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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