[Chimera-users] What do you do for comparative modeling if the pdb is so new it's not in UniProt?

[Elaine Meng]

Hi Ralph,
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.

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.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit>

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:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment>

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.

There is some discussion of how to get inputs for comparative modelling in Chimera here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 30, 2021, at 8:59 AM, Ralph Loring <rhloring at gmail.com> wrote:
> 
> Hi,
> 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.
> Thanks for your help,
> 
> Ralph Loring
> Associate Professor of Pharmacology
> Department of Pharmaceutical Sciences
> 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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