VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 05 2012 - 01:50:28 CDT

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.