Subject: Re: CCL:Crystal Packing

From: [email-masked] (Rick Giaimo )
Date: Wed, 13 Mar 1996 10:51:14 -0800

Dave --

	Cerius2 (from MSI) can do everything that you describe here,
including selection across unit cell boundaries with distance criteria.

	Adding atoms to a crystal can be done with XYZ, ABC, or UVd 
coordinates.  Symmetric and periodic copies are constructed according to
the spacegroup and unit cell paramaters specified for the crystal.  Multiple
cells can be visualized.  Selection can find all of the atoms within the
radius specified, across cell boundaries, if necessary.

	-- Rick.

>   Reply to Hiroshi Ogura:
>   I am amazed at how many people have written this group in the past
> few years about generating crystal structures.  Each time someone
> responds with a hint about using a commercial package like Sybil or
> HyperChem.
>  
>   I don't have access to either of these programs, so have been
> working on this problems over the past few weeks.  My solution was
> to take the old Oak Ridge packages like ORFEE and ORTEP and modify
> them to generate any number of unit cells.  The appeal of using these
> packages is that one doesn't have to reinvent any codeing for mole-
> cular transformations.
>   So far I have a simple FORTRAN program that takes the xyz coordinates
> from a crystal paper and generates the unit cell.  For the old timers
> you know that the notation for the first molecule is 55501.  If there
> are 4 molecules in the unit cell, these are just specified as 55502,
> 55503 and 55504.  One can then move these up an axis (say b) by
> just specifying 565xx, etc.  Real simple.
>   My program does this and then outputs a file to BABEL.  I then
> use BABEL to generate an ALCHEMY file.  I use ALCHEMY to view the
> molecule.  It works.  But I can't streamline it because I don't
> have the BABEL source code.  If I did, I  could compile the whole.
> routine.  So there are several steps involved, but it seems to work.
>   I am sure that the people with commercial packages think this is
> all a waste of time.  I realize that commercial packages can generate
> a unit cell from the xyz coordiates, but can they really generate
> several unit cells?  This is really what's important if your looking
> for nearest neighbors.  I looked at several packages that could not
> determine, for example, all the atoms 4-5 Angstroms from a particular
> part of any molecule.  Since ORFEE is so good at doing this, I decided
> to modify the program rather that buy something that may or may not
> really work.
>   If this is of interest to anyone, write me and I will send you the
> FORTRAN code.
>   Regards, Dave Close.
> 
> 
Richard Giaimo
Molecular Simulations
[email-masked]