[Jalview-discuss] export figure from Jmol

[Jim Procter]

Hi John.
> Thanks for the suggestion, a useful feature, but this doesn't do exactly
> what I want.
> I try a different way.  I have performed a sequence alignment in Jalview
> and then mapped the sequence onto a structure - this is a great feature
> in Jalview and the reason I use the program.
> However, the subsequent analysis which I want to do on the structure is
> a bit too complicated for the jmol structure viewer, so I would like to
> output a list of conserved residues out of Jalview (at various
> thresholds). A simple text file would do, so I can use another program
> such as pymol to continue my analysis. Is this possible?
>    
Re-reading your original email, it looks like you'd prefer to have the 
conservation values written in to the PDB file. I can see how this could 
be generally useful, and there isn't a function to do this at the 
moment, but it wouldn't be hard to implement.... however - I won't be 
able to do this for a few weeks, at least.

For the moment, might I suggest you try the ConSurf server ?
Wizard is : http://consurftest.tau.ac.il/
Full form is : http://consurftest.tau.ac.il/index_full_form_PROT.php

This takes a structure and a multiple sequence alignment, and will 
generate conservation values for each position in the structure. Its 
algorithm is much cleverer than the one used by Jalview, and in addition 
to a number of tables, the server also generates a PDB file where the 
conservation is encoded in the BFactor column.

Does that help ? If not, let me know and we can discuss it further (on 
or off list).
Jim.

-- 
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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
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