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

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@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@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette


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