[Proteopedia] Structural alignment?

[Eran Hodis]

Currently the way to display aligned structures in Proteopedia is to align them in an external program, save the aligned pdb files as one pdb file, and upload that file to Proteopedia. Admittedly, this is not ideal by any measure and a simple process for displaying aligned pdb files needs to be implemented.

For an example of aligned structures in a Proteopedia page, see http://www.proteopedia.org/wiki/index.php/3fsr (scroll to the bottom applet).

Eran

-----Original Message-----
>From Dan Bolser <dan.bolser at gmail.com>
Sent Mon 2/15/2010 6:02 PM
To Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
Subject [Proteopedia] Structural alignment?

Hi all,

If I have two structures for which I have a pre-computed alignment,
can I load both into Jmol and apply the appropriate rotation /
transformation matrix to show them in alignment?

This would be a really cool way to demonstrate protein structure
evolution or functional divergence, for example.

I searched PP for the term 'alignment', but I didn't find any examples
of molecular scenes showing superimposed structures. Am I just being
dumb, or has this feature yet to be implemented in PP / Jmol?


Cheers,
Dan.

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