[Chimera-users] chimera to rebuild crystal

Miguel Ortiz Lombardia molatwork at yahoo.es
Wed Jan 17 00:32:31 PST 2007

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Hi Tom and chimera users,

I'm afraid I wasn't clear. What I would like to have is not all the asym
units within a specific radius, but all the symmetry-related molecules
(that may come from different asymmetric units and different unit cells)
that make contact to a specific selection within a certain distance.
Let's say my asymmetric unit contains two molecules A and B. If I am
interested in a loop in molecule A, I would like to see the
symmetry-related molecules (whether A or B, from any asymmetric unit in
the crystal) that are close to this loop _and_ only these ones, i.e. not
the whole asymmetric unit to which they belong. To get the positions of
these molecules you need to apply both the crystal symmetry operators
_and_ the lattice translations.

This is what the programs we use to build our models normally do, but I
understand that building a model in electronic density is something
different from chimera aims. That's why I suggested to put it in the
long-term wish-list ;-)



Thomas Goddard escribió:
> Hi Elaine,
>   I agree it would be nice to add to Unit Cell.  But that is a bigger
> project.
>   I do not know how many unit cells Brady wants.  It could be a
> million atoms.  The script I sent him only makes one PDB model and
> moves it around so the script will not run into memory limitations.
>   Miguel Ortiz-Lombardia sent email replying to the crystal coordinates
> email (but not to chimera-users, ugh) saying he wants all asym units
> within a specific radius.  A more common need I think is a all asym
> units that make contact with a specified distance.  So much to do and
> so little time.
> 	Tom
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: molatwork at yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.                          (Raoul Vaneigem)
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