Subject: Summary: Crystal structure and XYZ coordinates

From: Sergei Tretiak <[email-masked]>
Date: Fri, 6 Jan 2001 15:19:43 -0500 (EST)

Hi,

Thanks to all who helped with my questions about
Crystal structure and XYZ coordinates

This is the summary of the responses.

Thanks again.

Sincerely,

Sergei

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Original request:

> Dear Netters:
>
> Suppose I have cell parameters and would like to
> build a piece of crystal and save Cartesian coordinates
> of atoms that will be inside of sphere (ellipsoid, cube,
> etc.) with given radius.
>
> What software (free or commercial) could do that? (Easy to
> use, options, good visualization capability would be preferences).

Responses:
__________________________________________________________
From: "Anatoli Korkin (r40757)" <[email-masked]>

The MSI crystal bulider does the best for that purpose.

http://www.msi.com/

Cheers,

Anatoli

__________________________________________________________
From: Jeffery Brian Klauda <[email-masked]>

I would try Diamond version 2.  You can go to their website, which is
listed below.  The demo version can build structures and save them in
cartesian coordinates as well as save selected atoms in a sphere or cube.

http://www.crystalimpact.com/diamond/

Hope this helps,

Jeff Klauda

__________________________________________________________
From: Alexander Hofmann <[email-masked]>

I know MSI Cerius2, which is capable to cut spheres (no
intrinsic ellipsoids) and rectangular bodies with its GUI. You can save
your modified file into various formats. (commercial: www.msi.com)

Another idea is to use a program like xmol or jmol (the java version of
it) to edit a prebuilt supercell.
(free: http://www.msc.edu/msc/docs/xmol/ftp.html )only very old
architectures) and http://www.openscience.org/jmol/index.html)

Hope this helps

Alex
__________________________________________________________
From: "Students of Dr. S. R. Gadre" <[email-masked]>

   I think MSI's Weblab-viewer pro would be good enough for that.
you can look at www.msi.com for pricing and further details

Babu
__________________________________________________________
From: Victor Milman <[email-masked]>

You can use Materials Studio from MSI which allows you to select atoms
that are within a given distance from the selected atoms (or from a
specified point in space). You can also select atoms that have X, Y, or
Z that satisfy one of the criteria: Equal To, Greater Than, Less Than,
Greater Than or Equal To, Less Than or Equal To, Inclusive Range, or
Exclusive Range. The same will work for X, Y, Z relative to coordinates
of the selected atoms. I think you can combine these features to achieve
your goal of selecting atoms within a sphere or a cube (which is
presumably to apply cluster-based quantum chemistry methods to study
periodic solids - I am not a great fan of this approach). After you
selected what you wanted, you can copy these atoms into another model
space (MatStudio supports all then usual cut/copy/paste). alternatively
you can invert selection criteria, select only what you don't want and
delete those atoms.

You can find out more about Materials Studio at
http://www.msi.com/materials/studio/ and about other offerings from MSI
at http://www.msi.com/materials/index.html

Hope this helps
__________________________________________________________
David Gallagher <[email-masked]>

CAChe includes a crystal builder with all 230 space groups. You select the
space group from a pull-down menu and it highlights which parameters are
needed. You can paste in or type in the fractional coordinates and then
define the size and type of the crystal to be built along each of the 
three
axes. CAChe can also read Shel-X, Cambridge, etc. directly, and handles 
all
elements up to 103. CAChe has won several awards for ease-of-use. The
excellent visualization includes coordination polyhedra, thermal 
ellipsoids
and optional full-color stereoscopic. The crystal builder is in all
versions of CAChe including Personal CAChe on Windows and Mac at $495 for
academics. You can download a free evaluation copy from
www.cachesoftware.com or call 503 531 3600 for a CD and any questions.

Hope this helps, happy new year,
David Gallagher
__________________________________________________________
From: Didier MATHIEU <[email-masked]>

To convert the asymmetric cell into the orthorhombic cell, the crystal 
program
of the Tinker package is useful:
     http://dasher.wustl.edu/tinker
Not all space groups are implemented, but it is easy to has additional 
ones.

Then I can copy the unit cell obtained along the X,Y,Z axes to get a model
cluster.
It would be easy then to check for the atoms belonging to a shere, 
ellipsoid...

> use, options, good visualization capability would be preferences).

For visualization I use XMol but tinker provides an utility to generate 
.pdb
files that
can be read by most vizualization packages (e.g. VMD).

Regards

--
Didier Mathieu