[Proteopedia] Structural alignment?

[Eran Hodis]

Hi Dan,

I don't recall. I would consult the Jmol documentation, and if you are still stuck, ask the Jmol user mailing list.

Eran

-----Original Message-----
>From Dan Bolser <dan.bolser at gmail.com>
Sent Wed 2/17/2010 11:00 AM
To Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
Subject Re: [Proteopedia] Structural alignment?

On 16 February 2010 19:03, Eran Hodis <eran.hodis at weizmann.ac.il> wrote:
> 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).

Unfortunately I get redirected to the main page when I try to view
that page (no java here at work). What I'd expect to see is the big
"Java is required ..." warning banner, but be allowed to view the
content of the page none the less.


Thanks for the tip about structure alignment. Do you know how easy it
is to pass the appropriate rotation / translation matrix to Jmol?


Cheers,
Dan.

> 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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