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Jalview Discussion
1

Have you tried the Chimera software ? It performs sequence alignments, maps it to the 3D structure and allows you probably as many further analysis as you might dream off ?

  • Paul
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Le 11 mars 2010 à 15:19, John Berrisford a écrit :

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

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2

Have you tried the Chimera software ? It performs sequence alignments, maps it to the 3D structure and allows you probably as many further analysis as you might dream off ?

paul is right here - Chimera has a built in MSA viewer/editor, and a very flexible system for transferring information onto a structure. Indeed, Consurf can generate Chimera output!

Jim.

ps. thanks for telling me about my carbon-unit error, Paul!

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