VMD-L Mailing List
From: Sebastián Gutiérrez (segumal_at_gmail.com)
Date: Thu Jul 05 2012 - 11:33:43 CDT
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Thanks Axel, I'll try that.
On Thu, Jul 5, 2012 at 2:50 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Thu, Jul 5, 2012 at 12:16 AM, Sebastián Gutiérrez <segumal_at_gmail.com>
> wrote:
> > Dear VMD Users,
> >
> > i've been wanting to build a chitosan polymer from a crystal, but it only
> > contains a single glucosamine residue.
> > One should be able to build a disaccharide from this monomer, but i
> haven't
> > been able to figure out how.
> > I know it has something to do with the transformation matrix associated
> with
> > a specific space group (in this case, it is P212121), and even though i
> have
> > been reading some info on the topic, i still don't understand how to do
> it.
>
> the short version is:
> - get your hands on a copy of: Ralph W.G. Wyckoff , Crystal Structures
> - look up the list of transformations
> - take the coordinates given and apply the transformations (=symmetry
> operations)
> - remove all duplicate coordinates
> - remove all redundant coordinates that are on the corners or faces of
> the crystal cell
>
> a step by step description for simple systems like diamond or graphite is
> here
> (mind you, Q-E software uses scaled coordinates, but that is easily fixed).
> http://www.vlab.msi.umn.edu/events/download/tutorial_wyckoff.pdf
>
> HTH,
> axel.
>
> > Any help is much appreciated :-)
> >
> >
> > Best regards,
> >
> > Sebastián E. Gutiérrez Maldonado
> > B.Sc. in Biochemistry
> > Research assistant
> > Computational Biology Lab (DLab)
> > Center for Mathematical Modeling (CMM)
> > Facultad de Ciencias Físicas y Matemáticas
> > Universidad de Chile
> > http://dlab.cl
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
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