From chemistry-request@server.ccl.net Mon Nov 8 16:59:40 1999 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA12310 for ; Mon, 8 Nov 1999 16:59:39 -0500 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP); Mon, 8 Nov 1999 21:52:36 +0000 Message-ID: <003601bf2a34$60b1e340$072c2880@ucl.ac.uk> Reply-To: "Artem R. Oganov" From: "Artem R. Oganov" To: chemistry Subject: CCL: summary on MD-trajectories animations Date: Mon, 8 Nov 1999 21:58:23 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0033_01BF2A34.606EBFC0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0033_01BF2A34.606EBFC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL'ers, =20 My original enquiery was : I am looking for a program to animate MD trajectories, with polyhedral representation of crystal structures. I shall be grateful for any suggections, and summarise them. Also, does anyone know what is the = Web-site of Babel? Many thanks to Keith Refson, Robert Best and Ricardo Grau Crespo, whose = replies (slightly shortened) I summarise below: Keith Refson : Cerius 2 does this I think. But perhaps you are looking for something free. You probably need the MD modules as well as the crystal builder. AVS : there's Larry Finger's "crystal" AVS module which can be used for polyhedral representations. And you can use AVS to animate. However it has it's own unique structure format files. On a Win32 PC there's MSI's free WebLab viewer which I believe will do=20 this. I'm not aware of anything free for unix which does. Babel is pretty useless at converting between periodic crystal structure files and usually loses all symmetry and unit cell information. I have written some perl scripts for converting between PDB/Schakal and CASTEP formats if you are interested. They are in ftp://ftp.earth.ox.ac.uk/pub/keith/cteptouts.tar.gz Robert Best : =20 A good program for displaying trajectories and doing analysis is = gopenmol, available from http://laaksonen.csc.fi/gopenmol. Although the emphasis=20 is on analysis of amorphous systems, there is a facility for drawing = cubic cells, and you can draw any kind of cell using the built-in tcl = scripting. Of course there are crystallographic programs which make the cell = drawing easier, but I don't know of any that have the ability to display=20 trajectories as well. Ricardo Grau Crespo : Babel lives in a lot of places on the net, but the "official" distribution site is http://www.eyesopen.com/babel.html ********************************************************************** Artem R. Oganov, = =20 Doctorate Student in Crystallography and Mineral Physics,=20 Dept. of Geological Sciences, = =20 University College London, = =20 Gower Street, = =20 London WC1E 6BT, = =20 U.K. = =20 E-mail : a.oganov@ucl.ac.uk = Tel. : +44 (0)171-419-3449 Fax : +44 (0)171-387-1612 = =20 ********************************************************************** ------=_NextPart_000_0033_01BF2A34.606EBFC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 CCL'ers,
 
My original enquiery was :
I am = looking for a program=20 to animate MD trajectories, with polyhedral
representation of crystal = structures. I shall be grateful for any
suggections, and summarise=20 them. Also, does anyone know what is the Web-site
of = Babel?
Many=20 thanks to Keith Refson, Robert Best and Ricardo Grau Crespo, whose = replies=20 (slightly shortened) I summarise below:
 
Keith Refson :
Cerius 2 does this I think.  But = perhaps you=20 are looking for something
free.  You probably need the MD = modules as=20 well as the crystal builder.
AVS : there's Larry Finger's = "crystal" AVS=20 module which can be used for
polyhedral representations.  And = you can=20 use AVS to animate.  However
it has it's own unique structure = format=20 files.

On a Win32 PC there's MSI's free WebLab viewer which I = believe=20 will do
this.  I'm not aware of anything free for unix which=20 does.

Babel is pretty useless at converting between periodic=20 crystal
structure files and usually loses all symmetry and unit=20 cell
information.  I have written some perl scripts for = converting=20 between
PDB/Schakal and CASTEP formats if you are interested.
They = are in=20 ftp://ftp.ea= rth.ox.ac.uk/pub/keith/cteptouts.tar.gz

Robert Best : 
A good program for displaying = trajectories and=20 doing analysis is gopenmol,
available from http://laaksonen.csc.fi/gopenmo= l.=20 Although the emphasis
is on analysis of amorphous systems, there is = a=20 facility for drawing cubic
cells, and you can draw any kind of cell = using the=20 built-in tcl scripting.
Of course there are crystallographic programs = which=20 make the cell drawing
easier, but I don't know of any that have the = ability=20 to display
trajectories as well.
 
 
Ricardo Grau Crespo :
Babel lives in a lot of places on the = net,
but=20 the "official" distribution site is
http://www.eyesopen.com/babel= .html
 
 
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Artem=20 R.=20 Oganov,           =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;    =20
Doctorate Student in Crystallography and Mineral Physics,
Dept. = of=20 Geological=20 Sciences,          &nbs= p;            = ;            =          =20
University College=20 London,           =             &= nbsp;           &n= bsp;           &nb= sp;  =20
Gower=20 Street,           =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;          =20
London WC1E=20 6BT,           &nb= sp;           &nbs= p;            = ;            =            =20
U.K.           = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;=20
E-mail : a.oganov@ucl.ac.uk  &nbs= p;            = ;            =             &= nbsp;     =20
Tel. : +44 (0)171-419-3449        = Fax :=20 +44=20 (0)171-387-1612         &nbs= p;            = ;            =             &= nbsp;   
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