<div dir="ltr"><div>Hi Elaine,</div><div>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:
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><a href="https://www.youtube.com/watch?v=6wSqI-iP_4w" style="color:rgb(5,99,193);text-decoration:underline">https://www.youtube.com/watch?v=6wSqI-iP_4w</a><span></span></p>
</div><div>Ralph<br> </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 23, 2022 at 11:39 AM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Ralph,<br>
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:<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html</a>> <br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html</a>><br>
<br>
If you don't see these tools in your menu, you need to get a newer version of ChimeraX.<br>
<br>
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:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html#results" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html#results</a>><br>
<br>
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.<br>
<br>
The documentation mentioned above is complete so you wouldn't necessarily benefit from a tutorial. I do have a loop-modeling tutorial <br>
<<a href="https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html</a>><br>
but that is different from the comparative modeling that I'm guessing you want to do.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Nov 23, 2022, at 5:07 AM, Ralph Loring via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi,<br>
> 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!<br>
> 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.<br>
> Ralph Lorini<br>
> <br>
> Ralph H. Loring<br>
> Associate Professor of Pharmacology<br>
> Department of Pharmaceutical Sciences<br>
> 166 TF<br>
> Northeastern University<br>
> 360 Huntington Avenue <br>
> Boston, MA 02115 USA<br>
> 617-373-3216 office<br>
> 617-373-8886 fax<br>
> <a href="mailto:r.loring@northeastern.edu" target="_blank">r.loring@northeastern.edu</a><br>
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</blockquote></div>