Subject: Re: CCL:fractional coordinates > full data

From: Jeffrey J Gosper <[email-masked]>
Date: Tue, 17 Sep 1996 09:46:29 BST

Dear computational chemistry and other interested parties,

Here are the replies I received concerning my recent query about 
fractional coordiantes to full XYZ data. 

Original posting:

Dear all,

I was wondering what non-commerical software is around that will take primative 
fractional unit cell coordinates and space group information and generate 
orthogonal atomic coordinates for all atoms in a unit cell.

Cheers

Replies with comments.

*********************
Jeffrey,

Despite the fact that you develop a code which is NOT available for the Mac,
I will still give some free advice!!!  Julian Gale's program GULP which
is a very powerful code for simulating crystals can take the fractional
coordinates and space group of a crystal and generate a full set of cartesian
coordinates.  Julian's email address is:

   [email-masked]

     Andrew Rohl

Comment/reply from JJG:

Thanks Andrew for the information about GULP. I will have to get hold of a copy.

Also most sincerely applogies for my PC bias. The fact is I program in Visual 
Basic (in order to readily produce Windows programs) and to the best of my 
knowledge there is no equivalent on the MAC. Can't the MAC emulate (or run) 
Windows3/95/NT?
***********************

there is always the old standby - ortep (OakRidge Thermal Ellipsoid
Program) now available in an executable form that runs straight away on
most PC's.  The full printed output option will provide this.  It can be
downloaded for free from their web site
http://www.ornl.gov/ortep/ortep.html
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr. William T. Winter                  Phone: (315)470-6876
315 Baker Lab                          FAX:   (315)470-6856
SUNY-ESF                               Internet: [email-masked]
Syracuse, NY 13210-2786                URL     http://www-chem.esf.edu
*************************

Check out the combinations of programs called

  matfract.c
  fract2xyz.c

available at (you can also get to them from the link on my list of
publications of my home page, see
below):

gopher://www.ccl.net:73/00/software/SOURCES/C/fractional_coordinates
/matfract.c

gopher://www.ccl.net:73/00/software/SOURCES/C/fractional_coordinate
s/fract2xyz.c

It will not take the spacegroup information, but allows you to generate the
rest of the molecules using matrix operations in fraction coordinate space
(matfract), and convert the output of that into cartesian coordinates using
fract2xyz.

Rene P.F. Kanters, Ph. D.
Chemistry Project Specialist
Chemistry Department
University of Richmond, VA 23173

phone:  (804) 287-6873
www:    http://www.science.urich.edu/~kanters/
***************************

Dear Dr. Gosper,

recently I had the same problem as you and wrote a 
corresponding FORTRAN program, using some existing
subroutines I had already. You can have the code
if you like (on your own risk, of course). I found the
program to work well. It constructs the unit cell
>from fractional coordinates and the space group
information. The latter must be given in a simplified
format. To perform

  \hat y, \hat x, z + 1/2

you must input three lines:

  2    1   3              (permutation)
 -1.  -1.  0.             (reflection)
  0.   0.  0.5            (translation)

This must be done for every symmetry operation. In addition
you tell the program to construct more than one unit cell,
e.g. to construct a MD simulation box.

If this is what you need, send me a mail.

             Best wishes, Gerald Kneller

-- 
Dr. Gerald Kneller
Science Division, Group TOFHR
Institut Laue-Langevin
B.P. 156
F-38042 GRENOBLE CEDEX 9

Tel.: (33) 76207516
Fax.: (33) 76483906

Comment/reply by JJG: Sounds interesting and very similar to what I had in mind 
so 
please forward a copy. I hope to get a student working on a Windows version of 
this 
very soon.

I think we'll add a database of symmtery operations which will be automatically 
picked up when the space group is entered.

************************

Dear Jeffrey,

I have recently wondered the same.  A summary of any replies, 
either via the list or directly to me would be much appreciated.

Regards,
Cedric.
************************
Dear Dr. Gosper,
INTERCHEM does what you want (and much more).  It is not strictly speaking
non-commercial, but to academic institutions it sells for £400 (or free 
if you are prepared to plead extreme poverty!).  The dowmside is that it
works only on SGI platforms.  For information see the web-site:-

           http://interchem.chem.strath.ac.uk/inter/interprobe.html

Yours sincerely,

Peter Bladon
************************
Hello.

Check out the crystallography archive on the web, and see about
XPMA/Zortep from Laslo Zolnai, or possibly STRUPLO, (which has evolved?
into STRUVIR).  There are some other programs or subroutines possibly of
interest there, but those two are the ones I've used in the past.  If you
find something not on the list that looks useful, please let me know, as
coordinate (and kpoint) generation is always an issue in our group.
(Professor Burdett, Solid-state theory).

                                                -fred

                                          Frederick P. Arnold, Jr.  
  The University of Chicago:              Dept. of Chem., U. of Chicago 
     Where the End of the World Began.    5735 S. Ellis Ave             
                                          Chicago, IL 60637             

**********************

 don't know about non-commercial.  I use Alchemy III from Tripos Assoc. 
which is not an expensive programme, to do just this - in fact, it's about
the only useful thing Alchemy does, but that's another story...

(address withheld by Jeff Gosper as I don't want to start a flame war.
**********************
Jeffrey,
I enclose 'tid-bits' of what I think you need to carry out your task. The
program is written in Fortran and is 'as is'.
Carlos

       PROGRAM CRYSTSYM
C generates crystallographic symmetry coordinates naturally from frac.coords.
C
###rest of program cut###

[email-masked] (Carlos Faerman)

comment by JJG: Interesting I'll spend so time looking at this, thanks.
**********************

Quanta will for Cambridge FDAT files.
And many programs can handle PDB files,
which are orthogonal Angstrom coords,
but need conversion back to fractional
in order to allow symmetry operations.

Regards,

Leif Norskov
Novo Nordisk A/S
Copenhagen
Denmark
[email-masked]

comment by JGG: Is Quanta free? I don't think so.
****************************

Dear Jeffrey,

Check out the freeware program called Babel, available at

http://mercury.aichem.arizona.edu/babel.html

It is available for a variety of platforms, and will convert coordinate 
data from almost any standard or proprietary format to almost any other.

Yours,
Dale Braden
Dept. of Chemistry
Univ. of Oregon
[email-masked]

comment by JJG: I don't think BABEL can really do this. It may be able to 
translate
the primative positions to XYZ but not produce the full cell (or multipl cells).

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 Dr. Jeff Gosper                                         
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