export figure from Jmol

Jalview Discussion
#1

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?

Thanks again

John

···

--
John Berrisford

Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge
CB2 0XY
WEB: www.mrc-mbu.cam.ac.uk
TEL: +44 (01223) 252918

#2

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
The University of Dundee is a Scottish Registered Charity, No. SC015096.

#3

Dear Paul

Thanks for the suggestion. Chimera is new to me and, after a quick play, does indeed do everything I need.
Thanks again

John

Paul Pillot wrote:

··· 
-- 
John Berrisford

Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge
CB2 0XY
WEB: [www.mrc-mbu.cam.ac.uk](http://www.mrc-mbu.cam.ac.uk)
TEL: +44 (01223) 252918