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

From: QMarcus_R=F6lz=22?= (m.roelz_at_gmx.de)
Date: Wed Oct 10 2007 - 08:08:17 CDT

Hi Peter,

thx for your input. I am considering to build a collagen strand residue by residue - so a copy of pdb files is not really handy for me. Any other ideas how to create or copy residues?

Marcus

> 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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