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

[Ralph Loring]

Hi Elaine,
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 (www.rcsb.org), 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?
Ralph

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

On Fri, Apr 30, 2021 at 12:25 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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,
> >
> >
> > 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
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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