Re: Howto lengthen a collagen strand (which tool to use)

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 09 2007 - 09:47:28 CDT

Hi Marcus,
the best way to do this is going to be to make new pdb files (initially
identical to the one you start with) for the copy, and then use VMD's
matrix operations to translate/rotate them (see the matrix routines
section in the VMD user's guide for how to do this). You can then use
psfgen to get them all into a usable coordinate/topology pair.
Best,
Peter

Marcus Rölz wrote:
> Hello out there ;)
>
> I'd like to lengthen a collagen-strand (Triple-Helix).
> To do this i'd like to create new atoms, copy existing atoms, and do translations and rotations on atom selections via matrix operations.
>
> I'm not sure which program to use for this purpose. Is VMD + psfgen capable of doing this? I'd like to select some atoms copy them and relocate them.
>
> Can pdb-files be imported in sciLab? Or is there any other tool around?
>
>
> Thx,
>
> Marcus Rölz
>
>
>

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