<div dir="ltr">
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Hi Elaine Meng,<span></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Thanks so much for your suggestions!<span> </span>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).<span>
</span>Anyway, I got Alphafold to work for a 22 amino acid mu-conotoxin (<span style="color:black">Mu-Conotoxin P0C349.pdb) and the predicted structure (in blue)
wasn’t great (see attached).<span> </span>The RMSD between
the Alphafold predicted pdb and the original (tan) was 4.1 angstroms, so not
good.<span> </span>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. <span> </span>There is now another Alphafold version (AF-</span>A0A1W2PN81)
that is equally bad.<span></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Your scripts were incredibly helpful, as I haven’t figured
out the syntax for using the command line.<span>
</span>Is there a tutorial on using commands in ChimeraX? (I have the list of
commands in the user guide [<a href="https://www.cgl.ucsf.edu/chimerax/docs/user/index.html#commands">https://www.cgl.ucsf.edu/chimerax/docs/user/index.html#commands</a>],
but only rarely does that include examples of how the commands are used and I can't figure out the syntax code).<span> </span>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.<span> </span>But I
can’t get the bond command correct in a test case using the two versions of
mu-contoxin (see attached csx file).<span> </span>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).<span></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">By the way, Matchmaker does a good job of lining up the
overlapping amino acids with any combination of the receptor pdbs. <span> </span>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.<span></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Thanks for all your help! Any suggestions would be most appreciated.<br></p><p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">Ralph Loring<br></p><p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="color:black"><span> </span></span></p>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Feb 14, 2022 at 6:33 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">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">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.<br>
<br>
I also meant to include more help links in the previous reply...<br>
<br>
matchmaker<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html</a>><br>
<br>
combine<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html</a>><br>
<br>
Model Loops<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>
Best,<br>
Elaine<br>
<br>
</blockquote></div>