Subject: CCL:Generating the 3D lattice from crystallographic data

From: Chaitanya Krishna A <icymist82/at/yahoo.com>
Date: Mon, 20 Jun 2005 12:52:45 -0700 (PDT)

Hi all,

I am a novice to crystallography. My description of the problem may not
be that good. Please bear.

I have the crystallographic data (cell parameters, coordinates of the
asymmetric unit and the point group) about an inorganic solid (brucite)
Mg(OH)2.

I would like to generate the 3D lattice (say 3x3x3 unit cells) from
this information and also get the xyz coordinates of all the atoms so
that I can use them in my simulation. I hope I am clear on the problem.
I have come across Diamond which can do this. I would like to know of
the alternatives. It would be better if they run on Linux and is free.

Also I have Mercury installed on my system. Is it possible to use the
information that I have and use it with Mercury to generate the
lattice. If yes, how can I do it?

Thanks for your time.

Regards,
Chaitanya.

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From: René Kanters <rkanters = richmond.edu>
Date: Mon, 20 Jun 2005 17:32:54 -0400

Hi,

A long time ago (about 13 years) I wrote two small C programs that can  
help you with this. They are available at the CCL software repository:

http://www.ccl.net/cca/software/SOURCES/C/fractional_coordinates/ 
index.shtml

matfract allows you to generate the rest of the unit cell based on the  
symmetry of your space group. Note that you will have to define the  
matrix elements yourself.
fract2xyz allows you to convert a fractional coordinate file to an xyz  
file.

Hope this helps.

Reni

On Jun 20, 2005, at 3:52 PM, Chaitanya Krishna A wrote:

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From: jaccos..at..ccdc.cam.ac.uk
Date: Mon, 20 Jun 2005 22:57:38 +0100 (BST)

> lattice. If yes, how can I do it?

Yes, that is possible with Mercury.

Switch on packing (the check box in the left-hand bottom cormner of the
main window), then under "Calculate" from the menu bar select
"Packing/Slicing...". In the dialogue that pops up, set the ranges for a,
b and c all from 0.0 to 3.0.

Then, from the menu bar, select "File" and "Save As...". Save your file as
a PDB file (*.pdb) or as a Mol2 (*.mol2) if you want orthogonal
coordinates (which I guess is what you want) or save as a Cif file (*.cif)
if you want fractional coordinates.

If you only require x, y, z, then that is possible by clicking on "More
Info" then "Atom List...", and then to customise what is displayed in the
columns by clicking "Costumise..." and adding Xorth, Yorth and Zorth while
removing everything else. If you then save the spread sheet by clicking
"Save...", the file will contain the orthogonal coordinates in tab
separated form.

Best wishes,
-- 
Dr Jacco van de Streek
Research Scientist
Cambridge Crystallographic Data Centre
Cambridge, United Kingdom