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

Elaine Meng meng at cgl.ucsf.edu
Mon May 24 08:25:24 PDT 2021

Hi Ralph,
The Blast web service uses a local (on our web server machine) copy of the blast-searchable PDB protein sequence database.  Although it is updated weekly, it may take a while for newly added structures to get into that database.

However, you do not have to use Blast to get your alignment.  First open your target sequence file (fasta or whatever) so that it is shown in the Chimera sequence viewer.   Then open whatever new structure(s) you want to use as template(s):  7ekt and 7koo, I guess from your e-mail. Then in the sequence window menu, use Edit... Add Sequence and in that dialog choose to add "From Structure" and specify the first template to add to the alignment, then Edit... Add Sequence again, From Structure, and specify the next template to add to the alignment, etc. for whatever number of templates you have, one or more.


If you'd added two template sequences to your target sequence, then now you should have an alignment of 3 sequences.  If you don't think they are aligned well enough, choose sequence window menu Edit... Realign and calculate a new alignment until you're happy with it.

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

> On May 24, 2021, at 5:51 AM, Ralph Loring <rhloring at gmail.com> wrote:
> 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 

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