Re: CCL:fractional coordinates > full data

From: Jeffrey J Gosper <Jeffrey.Gosper &$at$& brunel.ac.uk>
Subject: Re: CCL:fractional coordinates > full data
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:
    gale &$at$& ri.ac.uk
      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: wtwinter &$at$& mailbox.syr.edu
 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###
 carlos &$at$& penelope.bio.cornell.edu (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
 lnl &$at$& novo.dk
 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
 genghis &$at$& darkwing.uoregon.edu
 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).
 /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\
  Dr. Jeff Gosper
  Dept. of Chemistry
  BRUNEL University
  Uxbridge Middx UB8 3PH, UK
  voice:  01895 274000 x2187
  facsim: 01895 256844
  internet/email/work:   Jeffrey.Gosper &$at$& brunel.ac.uk
  internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg
 Re_View's Home page (A molecular display/animation/analysis program):
    http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm
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