Not sure I know what you are talking about there... What might Jmol do?


On Thu, Aug 22, 2013 at 12:29 PM, Amjad Farooq <amjad@farooqlab.net> wrote:
Hi Geoff,

This is a great little widget . I just tried it and I think it is very useful to directly communicate with RCSB via Jmol.

But, is there a way to directly homology model a protein sequence using the RCSB to provide a best matching template such that the modeled structured can be directly accessed in Jmol?

How difficult would this be to implement? May be Bob can tell us more.

Thank you! Merci beaucoup!

AMJAD FAROOQ PhD DIC | Associate Professor
Dept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136
Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136
amjad@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net






On Thu, Aug 22, 2013 at 12:52 PM, <geoff.fucile@utoronto.ca> wrote:
Dear Jmol People,

I've implemented a novel method for evaluating conserved protein
features from databases such as CDD using JSmol. You can check it out
here:

http://bar.utoronto.ca/CDD3D

The user submits a query protein sequence of interest to search for
similar proteins from the RCSB or homology model databases. Selecting
a related structure will populate JSmol (or Jmol if you choose) and if
there are CDD features they will be mapped to the structure. To
evaluate conservation, there are interactive alignments as HTML text
that communicate directly with the structure model using Javascript.

You can try for example this sequence:
SVWRAINKQTGEVVAIKKMKKKYYSWDECINLREVKSLRRMNHPNIVKLKEVIRENDILYFVFEYMECNLYQLMKDRQKLFAEADIKNWCFQVFQGLSYMHQRGYFHRDLKPENLLVSKDIIKIADFGLAREVNSSPPFTEYVSTRWYRAPEVLLQSYVYTSKVDMWAMGAIMAELLSLRPIFPGASEADEIYKICSVIGTPTEETWLEGLNLANTINYQFPQLPGVPLSSLMPSASEDAINLIERLCSWDPSSRPTAAEVLQHPFFQSCFYVPPSLRPKPSVARTPPPVGPRGSFEHQSVKRYPVSLANAKPFNSYVSPKSNAAFGSGVQRKLDMVNQDGTRNTKPVRSSVRDSKYRPPGKKSPHNAAAASLNKNRVTRSSVSETADKLANMTIGATGSRRHSVSVVGQHQQLKPPPMKAGWVGETRDMFLRPTQ

I'd be very happy to receive feedback!

Perhaps you can help me with a problem - in JSmol the context menu is
obscured for some reason that I can't figure out... probably something
to do with the layout/CSS. Any help in this respect would be very much
appreciated!

Thank you all very much for your fantastic work on Jmol/JSmol.

~Geoff

--
Geoffrey Fucile, PhD
Université de Genève
Département de Biologie Moléculaire
Sciences III
30 quai Ernest-Ansermet
CH-1211 Genève 4


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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900