Summary: Crystal structure and XYZ coordinates

From: Sergei Tretiak <serg (+ at +) markov.chem.rochester.edu>
Subject: Summary: Crystal structure and XYZ coordinates
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)" <r40757 (+ at +)
 email.sps.mot.com>
 The MSI crystal bulider does the best for that purpose.
 http://www.msi.com/
 Cheers,
 Anatoli
 __________________________________________________________
 From: Jeffery Brian Klauda <klauda (+ at +) ChE.UDel.Edu>
 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 <hofmann (+ at +) aca-berlin.de>
 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" <tcg (+ at +)
 chem.unipune.ernet.in>
    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 <vmilman (+ at +) msi-eu.com>
 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 <dgallagher (+ at +) cachesoftware.com>
 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 <Didier.Mathieu (+ at +) cea.fr>
 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