<div dir="ltr"><div>Hi Elaine,</div><div>I'm trying to model single subunits, so this is what I need. However, something strange is going on with the BLAST protein function. If I BLAST the sequence NP_000737.1 in RSCB PDB (<a href="http://www.rcsb.org">www.rcsb.org</a>), it shows the following recently added PDBs (among others): 7EKT and 7KOO for human alpha7 receptors. However, if I blast the same sequence in chimera BLAST protein, the closest match is 6PV7 Human alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine [Homo sapiens]. For some reason, Chimera BLAST protein is not finding the appropriate structures. I would like to be able to use these structures in modeller. Is it something I'm doing, or is there a glitch in Chimera?<br></div><div>Ralph <br></div><div><br>
<div>Ralph H. Loring<br>Associate Professor of Pharmacology<br>Department of Pharmaceutical Sciences<br>166 TF</div>
<div>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></div>
</div><div></div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 30, 2021 at 12:25 PM 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>
I should say first that this may not be the right tool for your task, since it will only model a single chain (single subunit). However, if that is not a problem for you, I think I can answer your question.<br>
<br>
It doesn't matter if the template protein is in UniProt. If I understand correctly, you have already opened a sequence of your target (the chimeric protein), and now you are trying to add the sequence from your template(s) to make an alignment? In the Sequence window of that target sequence, choose "Edit... Add Sequence" and then use the "From Structure" tab. (I.e. you need to first open the structure of your template and then you can add its sequence to the existing ones in the alignment via that tab.) You can alternatively paste in sequences "From Text" but probably the other way is easier.<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html</a>><br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit</a>><br>
<br>
Another way is to just create the whole alignment in some other application (e.g. Jalview) and then save it in some sequence-alignment format that Chimera can read, then open it in Chimera. Sequence formats:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment</a>><br>
<br>
Presumably you already had to text-edit to make a fasta file or use some other application to create the sequence of your target in the first place.<br>
<br>
There is some discussion of how to get inputs for comparative modelling in Chimera here:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches</a>><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 Apr 30, 2021, at 8:59 AM, Ralph Loring <<a href="mailto:rhloring@gmail.com" target="_blank">rhloring@gmail.com</a>> wrote:<br>
> <br>
> Hi,<br>
> I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial.<br>
> Thanks for your help,<br>
> <br>
><br clear="all">
> Associate Professor of Pharmacology<br>
> Department of Pharmaceutical Sciences<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>
> _______________________________________________<br>
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</blockquote></div></div></div>