From Jeffrey.Gosper {*at*} brunel.ac.uk Tue Sep 17 05:55:35 1996 Received: from ceres.brunel.ac.uk for Jeffrey.Gosper[ AT ]brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id EAA13665; Tue, 17 Sep 1996 04:46:40 -0400 (EDT) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by ceres.brunel.ac.uk with SMTP (PP); Tue, 17 Sep 1996 09:46:30 +0100 Date: Tue, 17 Sep 1996 09:46:29 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper%!at!%brunel.ac.uk Subject: Re: CCL:fractional coordinates > full data To: chemistry \\at// www.ccl.net cc: Jeffrey.Gosper:~at~:brunel.ac.uk Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII 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 -8 at 8- 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 \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/