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 <[email protected]> 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
> [email protected] | off 305-243-2429 | lab 305-243-9799 | fax
> 305-243-3955 | www.farooqlab.net*
>
>
>
>
>
> On Thu, Aug 22, 2013 at 12:52 PM, <[email protected]> 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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>
>
>
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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
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