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

[Marco Sette]

If you search for the sequences the PDB Data Bank (RCSB) provides both 
the pdb file and the sequence in fasta format.

Best regards,

Marco

Il 30/04/2021 17:59, Ralph Loring ha scritto:
> 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 <mailto:r.loring at northeastern.edu>
>
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-- 
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
e-mail: m77it at yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette


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