From peter@cherwell.com Mon Jun 9 12:47:51 1997 Received: from cherwell.com for peter@cherwell.com by www.ccl.net (8.8.3/950822.1) id MAA01043; Mon, 9 Jun 1997 12:16:38 -0400 (EDT) Received: from mersey.cherwell.com by cherwell.com (4.1/SMI-4.1) id AA08174; Mon, 9 Jun 97 17:16:56 BST Message-Id: <3.0.1.32.19970609171638.007da4a0@cherwell.com> X-Sender: peter@cherwell.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 09 Jun 1997 17:16:38 +0100 To: charwel@chrs1.chem.lsu.edu From: Peter Tebbutt Subject: animation Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Chris & CCLers, Animation is one of the features of ChemSymphony (URL below) which is a publishing tool for including structures in HTML documents. This essentially works by creating a series of frames which are rendered in series. It recognises most file formats (XYZ, XMOL, PDB and so on) and allows the net user to change orientation and manipulate the structure whilst the animation is going on. A free demo is available from the Cherwell web site. Peter Tebbutt ----------------------------------------------------------- Peter Tebbutt | e-mail: peter@cherwell.com Development Support | Tel: +44 (0)1865 784812 Cherwell Scientific Publishing| Fax: +44(0)1865 784801 Oxford OX4 4GA, UK | http://www.cherwell.com ----------------------------------------------------------- Check Out ChemSymphony - rated top 1% Java applet by JARS http://www.cherwell.com/chemsymphony ----------------------------------------------------------- From jsu@ugcs.caltech.edu Tue Jun 10 00:47:57 1997 Received: from envy.ugcs.caltech.edu for jsu@ugcs.caltech.edu by www.ccl.net (8.8.3/950822.1) id AAA04613; Tue, 10 Jun 1997 00:40:48 -0400 (EDT) Received: from pride.ugcs.caltech.edu (pride.ugcs.caltech.edu [131.215.134.133]) by envy.ugcs.caltech.edu with ESMTP (8.8.5/UGCS:4.44) id VAA11842 for ; Mon, 9 Jun 1997 21:40:47 -0700 (PDT) From: jsu@ugcs.caltech.edu (Julius Su) Received: by pride.ugcs.caltech.edu (8.8.5/UGCS:4.43) id VAA10606; Mon, 9 Jun 1997 21:40:43 -0700 (PDT) Message-Id: <199706100440.VAA10606@pride.ugcs.caltech.edu> Subject: Molecular modeling software for non-theorists? To: chemistry@www.ccl.net Date: Mon, 9 Jun 1997 21:40:42 -0700 (PDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hello, I work for a research group that uses laser spectroscopy to investigate the basic dynamics of chemical systems on a short time scale. Some members of our group have done fairly high level ab initio and molecular dynamics simulations in the past; however, the main focus of the group has definitely been experimental. Because of this, there has been no standard way to model chemical systems in our group. Individuals in the group have either written their own molecular dynamics routines or have had access to facilities where programs like Gaussian 92 could be run, but no convenient in-group facility to do simple molecular modeling has existed. We are currently seeking to change this. We would like to have some standard way of finding the geometries of small to medium molecules at a reasonable level of theory (semiemperical would be fine) and for doing molecular dynamics of photoexcited systems. This system would have to be accessible and easy enough to use that any experimentalist that wished to carry out an experiment would be able to quickly throw together a rough simulation of the system in question. Our group plans to purchase two fairly high end PCs to run the software that would be needed to do this. I have recently purchased a copy of Chem3D Pro with MOPAC for my personal use, and have found the interface for molecule building and geometry optimization to be intuitive and easy to use. We also have some simple code that was written within the group to do molecular dynamics on small clusters of rigid molecules. This code can be easily interfaced with Chem3D. Alternatively, we have found information on the Web about HyperChem, which appears to have the ability to do model building, geometry optimization, and a feature that would be especially useful to us, reactive molecular dynamics. It also appears to have facilities built in to visualize vibrational modes and molecular oribtals (althought the latter feature would not be nearly as important.) Since our group already has a copy of Gaussian 94, the added ab initio capabilities of the program are nice but not essential. The main concern at this point, however, is how easy HyperChem would be to use. Chem3D has impressed us with its intuitive interface and its tight integration with ChemDraw. We have not been able to find a demo of version of HyperChem with enabled building facilities to compare. Since 90% of the time will probably be spent doing simple model building and geometry optimization, this is particularly important to us. So, has anyone on this list had experience with HyperChem and Chem3D? How easy is it to build molecules in HyperChem? Does it have a reasonably useable interface? Can it generate publication quality graphics? Can experimentalists who don't want to spend too much time learning the nitty-gritty of semiemperical theory do simple calculations using it? Thank you very much for your help. Later, Julius Su jsu@cco.caltech.edu From rlahana@syntem.eerie.fr Thu Jun 12 02:48:24 1997 Received: from syntem.eerie.fr for rlahana@syntem.eerie.fr by www.ccl.net (8.8.3/950822.1) id CAA19384; Thu, 12 Jun 1997 02:44:02 -0400 (EDT) Received: from roger.eerie.fr by syntem.eerie.fr via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id IAA11190; Thu, 12 Jun 1997 08:43:10 +0200 Date: Thu, 12 Jun 1997 08:43:10 +0200 Message-Id: <199706120643.IAA11190@syntem.eerie.fr> X-Sender: roger@syntem.eerie.fr Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Ojitos , chemistry@www.ccl.net From: rlahana@syntem.eerie.fr (Roger Lahana) Subject: CCL:Qsar programs X-Mailer: >I'm intersted in any a program that can make a regresion analisis of a >group of descriptors for a molecule and a set of analogues. TSAR (Tools for Structure Activity Relationships) is to my knowledge the most comprehensive one. It also includes as an option a semi-empirical package, VAMP. All these programs are distributed by Oxford Molecular Group. Web site: http://www.oxmol.co.uk Email: sales@oxmol.co.uk or sales@oxmol.com **************************************************************** Dr Roger Lahana Synt:em Development Director Parc Scientifique G.Besse Molecular Modeling 30000 Nimes email: rlahana@syntem.eerie.fr France Tel: +33 (0)466 048 666 Fax: +33 (0)466 048 667 **************************************************************** Discover New Drugs, Discover Synt:em **************************************************************** From hillisch@imb-jena.de Thu Jun 12 03:48:23 1997 Received: from guiness.imb-jena.de for hillisch@imb-jena.de by www.ccl.net (8.8.3/950822.1) id DAA19617; Thu, 12 Jun 1997 03:41:57 -0400 (EDT) Received: (from hillisch@localhost) by guiness.imb-jena.de (950413.SGI.8.6.12/950213.SGI.AUTOCF/hsk) id JAA16575 for CHEMISTRY@www.ccl.net; Thu, 12 Jun 1997 09:43:30 +0200 From: "Alexander Hillisch" Message-Id: <9706120943.ZM16573@guiness.imb-jena.de> Date: Thu, 12 Jun 1997 09:43:30 -0600 In-Reply-To: Ojitos "CCL:Qsar programs" (Jun 11, 4:16pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Qsar programs Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jun 11, 4:16pm, Ojitos wrote: > Subject: CCL:Qsar programs > Hi. > > I'm intersted in any a program that can make a regresion analisis of a > group of descriptors for a molecule and a set of analogues. > > Does anyone know of a program for modeling drug receptor interaction with > semiempirical or ab initio methods? Hi Adrian, The program VAMP from Oxford Molecular, Inc., can be used to model drug receptor interactions semiempirically. The complete protein or receptor can be defined as a fixed environment while optimizing the ligand in the binding pocket. Instead of this quantum mechanical/molecular mechanical approach, VAMP can also handle parts of the receptor (e.g. the active site) plus the ligand fully semiempirical. Parts of the receptor can be fixed in coordinate space and the ligand and receptor optimized. The size of such a system is limited to approximately 500 to 600 atoms depeding on the computers you use. Best regards Alex -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Alexander Hillisch _/ _/ Institute of Molecular Biotechnology _/ _/ Department of Molecular Biology _/ _/ Beutenbergstrasse 11 Phone: +49-3641-65-6203 _/ _/ D-07745 Jena Fax: +49-3641-65-6210 _/ _/ GERMANY Email: hillisch@imb-jena.de _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ "And all this science I don't understand it's just my job five _/ _/ days a week..." _/ _/ Elton John - Rocket man _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From qftramos@usc.es Thu Jun 12 06:48:25 1997 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.8.3/950822.1) id FAA20053; Thu, 12 Jun 1997 05:57:47 -0400 (EDT) Received: by uscmail.usc.es (5.67b/1.34) id AA25623; Thu, 12 Jun 1997 11:57:04 +0200 Date: Thu, 12 Jun 1997 11:57:03 +0200 (MET DST) From: Antonio Fernandez Ramos To: chemistry@www.ccl.net Subject: CCL:Splitting in HCN dimer Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: Do you know if there are available experimental data of the splitting in the HCN dimer? Thanks, *********************************************** Antonio Fernandez Ramos E-mail:qftramos@usc.es Dept. de Quimica Fisica Facultade de Quimica Avda das Ciencias s/n 15706 Santiago de Compostela SPAIN *********************************************** From cdemeyer@nets.ruca.ua.ac.be Thu Jun 12 08:48:27 1997 Received: from nets.ruca.ua.ac.be for cdemeyer@nets.ruca.ua.ac.be by www.ccl.net (8.8.3/950822.1) id HAA20456; Thu, 12 Jun 1997 07:54:56 -0400 (EDT) Received: (from cdemeyer@localhost) by nets.ruca.ua.ac.be (8.7.1/8.7.1) id NAA03116 for chemistry@www.ccl.net; Thu, 12 Jun 1997 13:54:53 +0200 (METDST) From: Christiaan De Meyer Message-Id: <199706121154.NAA03116@nets.ruca.ua.ac.be> Subject: polarisability To: chemistry@www.ccl.net Date: Thu, 12 Jun 1997 13:54:53 METDST X-Mailer: Elm [revision: 212.2] Which software progamm(s) are capable to compute ATOMIC POLARISABILITIES in molecules? mail answer to:cdemeyer@ruca.ua.ac.be From orzenil@guarany.cpd.unb.br Thu Jun 12 09:48:27 1997 Received: from guarany.cpd.unb.br for orzenil@guarany.cpd.unb.br by www.ccl.net (8.8.3/950822.1) id JAA20980; Thu, 12 Jun 1997 09:38:10 -0400 (EDT) Received: by guarany.cpd.unb.br (AIX 3.2/UCB 5.64/4.03) id AA45896; Thu, 12 Jun 1997 10:36:09 -0300 Date: Thu, 12 Jun 1997 10:36:08 -0300 (GRNLNDST) From: "Orzenil Bonfim da Silva Junior]" To: chemistry@www.ccl.net Subject: QM / MM Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all , Few days ago I posted a question about use of combined QM/MM methods with special attention to ligand-receptor interactions.I'm very gratefull to all who answered . I'll summarize soon . Thanks . Orzenil B. S. Junior Departament of Chemistry Universidade de Brasilia Brasil From karin.fmq.uh.edu.cu!norge@ceniai.inf.cu Thu Jun 12 10:00:17 1997 Received: from ceniai.net.cu for karin.fmq.uh.edu.cu!norge@ceniai.inf.cu by www.ccl.net (8.8.3/950822.1) id JAA20798; Thu, 12 Jun 1997 09:02:53 -0400 (EDT) Received: from ceniai.inf.cu by ceniai.net.cu with smtp (Smail3.1.29.1 #1) id m0wc9a6-0000P0C; Thu, 12 Jun 97 09:06 EDT Received: from karin.fmq.uh.edu.cu by ceniai.inf.cu with UUCP (Smail3.1.29.1) id m0wc5oB-0002k4C; Thu, 12 Jun 97 09:04 Received: from karin.fmq.uh.edu.cu by ffuh with smtp (Smail3.1.29.1 #23 fisuh.fmr.uh.cu ) id m0wc9Cu-000Ke1C; Thu, 12 Jun 97 08:42 CDT Received: (from norge@localhost) by karin.fmq.uh.edu.cu (8.6.12/8.6.9) id IAA03573; Thu, 12 Jun 1997 08:54:23 -0400 Date: Thu, 12 Jun 1997 08:54:23 -0400 (CDT) From: Norge Cruz Hernández To: chemistry@www.ccl.net Subject: 2nd. School of Computational Chemistry in Havana Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE UNIVERSIDAD DE LA HABANA SOCIEDAD CUBANA DE F=CDSICA SOCIEDAD CUBANA DE QU=CDMICA Havana, Cuba, January 5 to 16, 1998=20 **** 2nd Iberoamerican School on Computational Chemistry and Molecular=20 Design **** 7th Cuban School of Theoretical Chemistry La Habana, Cuba, 5 al 16 de enero de 1998=20 **** II Escuela Iberoamericana de Qu=EDmica Computacional y Dise=F1o Molecu= lar **** VII Escuela Cubana de Qu=EDmica Te=F3rica Comit=E9 Cient=EDfico=A0- Scientific Committee: Esther Agacino (La Habana), Raul =C1lvarez-Idaboy (La Habana), Gerardo Delgado-Barrio (Madrid), Lourdes A. D=EDaz (La Habana), Jos=E9 M. Garc=EDa = de la Vega (Madrid), Jos=E9 Molina (Granada), Luis A. Montero (La Habana), Mario Piris (La Habana), Luis R. Sierra (La Habana), Yves Smeyers (Mexico, DF)Informaci=F3n General - General Information *************************************************************************** El Laboratorio de Qu=EDmica Computacional y Te=F3rica organiza la II Escuel= a Iberoamericana de Qu=EDmica Computacional y Dise=F1o Molecular y VII Escuel= a Cubana de Qu=EDmica Te=F3rica, que tendr=E1 lugar en la Universidad de La= =20 Habana, Cuba, entre el 5 y el 16 de enero de 1998. En la Escuela se impartir=E1n cursos b=E1sicos (5 al 9 de enero) y varios cursos especializados (12 al 16 de enero) por importantes figuras de esta ciencia a nivel mundial. --------------------------------------------------------------------------- The Laboratory of Computational and Theoretical Chemistry presents the 2nd Iberoamerican School on Computational Chemistry and Molecular Design and 7th Cuban School of Theoretical Chemistry, in the period January 5 to 16, 1998. Basic courses are scheduled in the first week (January 5 to 9) and several advanced courses in the second week (January 12 to 16), by several top level lecturers in their respective fields. *************************************************************************** Programa Preliminar - Preliminary Program =3D> Generalidades - General topics =C1lvarez - Idaboy, Raul (La Habana). MODELACI=D3N MOLECULAR EN COMPUTADORA= S PERSONALES Bader, Richard (Hamilton). THE THEORY OF ATOMS IN MOLECULES Clark, Tim. APPLICATIONS OF SEMIEMPIRICAL MOLECULAR ORBITAL THEORY Daza, Edgar (Santafe de Bogota). EL CONCEPTO DE ESTRUCTURA QU=CDMICA: EVOLUCI=D3N Y PERSPECTIVAS Eliel, Ernest (Chapel Hill), tentativo. AN=C1LISIS CONFORMACIONAL Evleth, Earl (Paris). POST HARTREE - FOCK METHODS Garc=EDa de la Vega, Jos=E9 M. (Madrid). CALIDAD Y OPTIMIZACI=D3N DE BASES = EN QU=CDMICA CU=C1NTICA Gerratt, Joseph (Bristol). MODERN VALENCE BOND THEORY Ghio, Caterina (Pisa). INTERMOLECULAR FORCES=A0: HYDROGEN BONDS AND BSSE Hoffmann, Roald (Ithaca). QUALITATIVE MODELS OF BONDING IN THE AGE OF COMPUTATIONAL CHEMISTRY Noga, Josef (Bratislava). ALTERNATIVE COUPLED CLUSTER ANS=C4TZE Piris, Mario (La Habana). EL FORMALISMO DE LA SEGUNDA CUANTIZACI=D3N Ortiz, Vicente (Manhattan, KS). LA TEOR=CDA DE PROPAGADORES DEL ELECTR=D3N = Y SUS APLICACIONES EN LA QU=CDMICA CU=C1NTICA Seijo, Luis (Madrid). POTENCIALES EFECTIVOS DE CORE Rinc=F3n, Luis (M=E9rida). REACTIVIDAD QU=CDMICA Y LA TEOR=CDA DEL ENLACE D= E VALENCIA Smeyers, Yves (Mexico, D.F.) . INTRODUCCION A LA TEORIA DE HARTREE-FOCK GENERALIZADO =3D> T=F3picos Avanzados y Aplicaciones - Advanced Themes and Applications =09 Albretch, Andreas (Ithaca). NON LINEAR SPECTROSCOPY. AN INTRODUCTION AND RECENT DEVELOPMENTS Barandiar=E1n, Zoila (Madrid). TRATAMIENTO CU=C1NTICO DEL EMBEDDING EN CRISTALES CON DEFECTOS LOCALES Berthier, Gaston (Paris). INTRODUCTION TO INTERSTELLAR CHEMISTRIES AND THEIR CALCULATION METHODS Eriksson, Leif (Stockholm). CALCULATION OF MAGNETIC AND RELATED PROPERTIES Fraga, Seraf=EDn (Edmonton). LA ECUACI=D3N DE SCHR=D6DINGER - RICCATI Gonz=E1lez - Jonte, Raul (Pinar del R=EDo). MODELIZACI=D3N DE REACCIONES=20 QU=CDMICAS Y BIOQU=CDMICAS POR M=C9TODOS SEMIEMP=CDRICOS Lazzeretti, Paolo (Modena). PROPIEDADES MAGN=C9TICAS MOLECULARES Otto, Peter (Erlangen). QUANTUM CHEMICAL CONCEPTS FOR THEORETICAL MATERIAL SCIENCES=A0: HOW TO TAILOR POLYMERS Palma, Alejandro (Puebla). ESTRUCTURA MOLECULAR Y MOLECULAS INTERESTELARES Poveda, Flor M. (Santafe de Bogota). MODELADO DE REACCIONES CATALITICAS Sierra, Luis Ren=E9 (La Habana). MODELOS Y T=C9CNICAS DE C=C1LCULO EN CAT= =C1LISIS HETEROG=C9NEA Soscun, Humberto (Maracaibo). M=C9TODOS DE LA MEC=C1NICA CU=C1NTICA MOLECUL= AR PARA EL DISE=D1O DE MATERIALES =D3PTICOS NO LINEALES Villa, Mar=EDa y Smeyers, Yves (Mexico, DF). MODELACION TEORICA DE LA ESPECTROSCOPIA DEL INFRAROJO LEJANO EN MOLECULAS Y=E1=F1ez, Manuel (Madrid). C=C1LCULOS AB INITIO DE ALTO NIVEL PARA EL EST= UDIO DE REACTIVIDAD QU=CDMICA Y CLUSTERS =3D> Funcionales de la Densidad - Density Functionals Boustani, Ihsan (Wuppertal). DENSITY FUNCTIONAL THEORY IN CHEMISTRY CONCEPTS AND APPLICATIONS. EXAMPLE: FORMATION OF BORON CLUSTERS Boyd, Russell (Halifax). ELECTRON DENSITY DISTRIBUTIONS AND PROPERTIES Contreras, Renato (Santiago de Chile). REACTIVIDAD QU=CDMICA INTR=CDNSECA Y= EN FASES CONDENSADAS EN EL CONTEXTO DE LA TEOR=CDA DE FUNCIONALES DE LA=20 DENSIDAD Fuentealba, Patricio (Santiago de Chile). =CDNDICES DE REACTIVIDAD EN DFT Scuseria, Gustavo (Houston). M=C9TODOS DE FUNCIONALES DE LA DENSIDAD. DESARROLLOS RECIENTES EN M=C9TODOS DE ESCALAMIENTO LINEAL EN QU=CDMICA=20 CU=C1NTICA Toro - Labbe, Alejandro (Santiago de Chile). USO DE CONCEPTOS DE LA TEOR=CD= A DE FUNCIONALES DE LA DENSIDAD EN LA DESCRIPCI=D3N Y RACIONALIZACI=D3N DE REACCIONES QU=CDMICAS =3D> Modelaci=F3n de los Efectos del Ambiente Molecular - Modeling Effects = of=20 the Molecular Environment Canuto, Sylvio (Sao Paulo). Monte Carlo Simulation of Solvent Effects Cossi, Maurizio (Pisa). APPLICATIONS OF THE PCM SOLVENT METHODS J=F8rgensen, William L. (New Haven). COMPUTER MODELING OF ORGANIC CHEMISTRY IN SOLUTION Montero, Luis (La Habana). MODELACI=D3N DE LOS EFECTOS DEL AMBIENTE=20 MOLECULAR MEDIANTE LA EXPLORACION DE HIPERSUPERFICIES DE M=DALTIPLES M=CDNIMOS DE SUPERMOL=C9CULAS Morokuma, Keiji (Atlanta). 1) POTENTIAL ENERGY SURFACES AND CROSSING/AVOIDED CROSSING=A0; 2) MO + MM HYBRID METHODS Olivares del Valle, F.J. (Badajoz). SOLVATACI=D3N. MODELOS TE=D3RICOS E INFORM=C1TICOS Tomasi, Jacopo (Pisa). CONTINUUM SOLVATION METHODS: BASIC ASPECTS, EXTENSIONS AND SOME APPLICATIONS =3D> Din=E1mica de Colisiones Moleculares - Dynamics of Molecular Collision= s Delgado - Barrios, Gerardo (Madrid). DIN=C1MICA DE COMPLEJOS DE VAN DER=20 WAALS Houston, Paul (Ithaca). THE COMPARISON OF EXPERIMENTAL RESULTS ON THE PHOTODISSOCIATION OF HCO WITH THE RESULTS OF QUANTUM AND CLASSICAL TRAJECTORY CALCULATIONS ON AN AB INITIO POTENTIAL ENERGY SURFACE. R=EDos, Miguel A. (Santiago de Compostela)INTRODUCCI=D3N A LA DIN=C1MICA QU= =CDMICA Rubayo, Jes=FAs (La Habana). DISOCIACI=D3N MOLECULAR ** Otros conferencistas confirmados=A0- Also confirmed: Agacino, Esther (La Habana) Cruz, Zoila (Pinar del R=EDo) Hern=E1ndez - Laguna, Alfonso (Granada) Micha, David (Gainesville), tentativo. Molina, Jos=E9 (Granada). Mu=F1oz, Francisco (Palma de Mallorca) tentativo. Ruiz, Mar=EDa Bel=E9n (Erlangen). Samuel Trickey (Gainesville), tentativo. Vela, Alberto (Mexico, D.F.). Villaveces, Jos=E9 L. (Santafe de Bogota). Zhidomirov, Georgi (Novosibirsk), tentativo. *************************************************************************** Organizaci=F3n - Organization --------------------------------------------------------------------------- Los cursos se impartir=E1n en Espa=F1ol o Ingl=E9s, en dependencia del idio= ma=20 del t=EDtulo. Por el momento no se dispone de posibilidad alguna de beca a los participantes por parte de los organizadores de la Escuela. No obstante,=20 se mantendr=E1 informados a los inscritos con respecto a las posibilidades que puedan abrirse al respecto en el futuro. As=ED mismo, el Laboratorio se ofrece para facilitar la gesti=F3n ante terceros de cualquier proposici=F3n= =20 por parte de los interesados. Es posible que en ciertos casos se reduzca o elimine el costo de la matr=EDcula. La matr=EDcula para residentes fuera de Cuba se abonar=E1 al arribar a la oficina de inscripci=F3n en pesos cubanos convertibles equivalentes a=20 d=F3lares US o en esa moneda, indistintamente. En este caso, su valor es de $ 350.00 para la matr=EDcula completa (las dos semanas) y de $ 200.00 para la matr=EDcula parcial (una sola de las dos semanas). Para residentes en Cuba= =20 se abonar=E1 de la misma forma en pesos cubanos y ascender=E1 a $ 40.00 para l= a matr=EDcula completa y $ 25.00 para la matr=EDcula parcial. El alojamiento y manutenci=F3n se puede organizar a partir de la oferta en cualquier agencia de viajes, a la que deben solicit=E1rsele hoteles cercano= s al centro de la ciudad de La Habana, donde se encuentra la Universidad.=20 Los hoteles m=E1s conocidos en esa zona son el Hotel Habana Libre, Hotel Nacional, Hotel Colina, Hotel Capri, Hotel St. John's, Hotel Victoria y Hotel Vedado, aunque a distancias medias existen muchas otras=20 posibilidades de alojamiento. La Universidad de La Habana puede ofrecer servicios de=20 este tipo, para los que se puede dirigir a=A0: Direcci=F3n de Eventos Universidad de La Habana La Habana 10400, Cuba. E-mail=A0: eventos@comuh.uh.cu. ---------------------------------------------------------------------------= --- Lectures are in English or Spanish as indicated in the title. At the moment we do not expect any fellowship support for students. However, the organizers will keep interested persons informed if such support becomes available later. The organizers are prepared to assist students to obtain support from other sources. In certain very exceptional cases the registration fee may be waived upon request. The registration fee for students not resident in Cuba is to be be paid upon arrival at the School in pesos cubanos convertibles (CU$ 1.00 =3D US$ 1.00) or US dollars, as preferred. The fee amounts $ 350.00 for full time students (two weeks) and $ 200.00 for half time (only one week). Accommodation and board should be arranged through a travel agency. Hotels near the university are suggested. Recommended hotels in this area are Hotel Habana Libre, Hotel Nacional, Hotel Colina, Hotel Capri, Hotel St. Johns, Hotel Victoria and Hotel Vedado, although there are many other possibilities at somewhat larger distances from the campus. The University of Havana can also arrange accomodation and board. If interested please contact: Direcci=F3n de Eventos Universidad de La Habana La Habana 10400, Cuba. E-mail=A0: eventos@comuh.uh.cu. ***************************************************************************= *** Dirigirse a: - Address inquiries and applications to=A0: Prof. Luis A. Montero II QUICEDIMO Lab. de Qu=EDmica Computacional y Te=F3rica, Facultad de Qu=EDmica, Univers= idad de La Habana, La Habana 10400, Cuba telf. (537) 78 1263, (537) 70 3922, (537) 79 4734 fax: (537) 33 3502, (537) 33 4247 e-mail: escuela@karin.fmq.uh.edu.cu=A0 Luis A. Montero Universidad de La Habana Laboratorio de Quimica Computacional y Teorica Facultad de Quimica La Habana, 10400, Cuba e-mail: lmc@karin.fmq.uh.edu.cu, qct@infomed.sld.cu Fax: (537) 33 3502, (537) 33 4247 Telf: (537) 78 1263, (537) 70 3922, (537) 79 4734, (537) 79 6153 From charwel@chrs1.chem.lsu.edu Thu Jun 12 10:48:36 1997 Received: from chrs1.chem.lsu.edu for charwel@chrs1.chem.lsu.edu by www.ccl.net (8.8.3/950822.1) id KAA21473; Thu, 12 Jun 1997 10:29:21 -0400 (EDT) Received: by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA18084; Thu, 12 Jun 1997 09:32:46 -0500 Date: Thu, 12 Jun 1997 09:32:46 -0500 (CDT) From: Chris Harwell To: CHEMISTRY@www.ccl.net Subject: CCL animation summary (text) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII here is a text version of the animation responses. thank you very much for contributing! sorry if anyone had a problem w/ MIME (this ver. of pine does that automatically w/ all attatchments). Frits Daalmans sugested that we tar and gzip all mail on the list to save bandwidth - but i think that may be going a little too far :> Chris Harwell charwel@chrs1.chem.lsu.edu "Everything positive originates in a positive attitude from someone" :> Simple Animation Links for Atoms & Molecules These are in responce to a CCL query for a program to animate pictures of molecules and change color (to represent charge) during the process. ---------------------------------------------------------------------------- * Spartan http://www.wavefun.com This seems to be do-able in unix Spartan (supports AIX4.1) which is commercial. The molecular builders allow you to construct the molecules one by one, and then you group them together as a list. The list dialog has animation feature to scan through the list frame by frame. Color information can be altered by users. * Rasmol http://www.umass.edu/microbio/rasmol/ Rasmol 2.6 has a minor fix (SET WRITE ON) that allows reading a series of atom coord files and writing corresponding .ppm files within a script; the .ppm files can be made into an MPEG animation using mpeg_encode. There does seem to be a limit on either the number of text lines in a script, or the number of coordinate files read, etc. within Rasmol. I've appended a partial example . * VMD http://www.ks.uiuc.edu/Research/vmd there is a program called VMD which is free, is supposed to do more than you want and as far as I know runs on a pc as long as you have OpenGL on it. But for what you want, is perfect. [editorial note: only if the PC is running a version of the lynux kernel with Mesa (www.redhat.com) to emulate OpenGL] You can represent the molecules any way you want, you can render the image, you can animate it by loading multiple pdb files or a trajectory, you can ask the program to change any color you want for any atom you want during the animation and you can also take a snapshot of each frame. All these you can have set up in one script using Tcl or do you by hand. For a sample of the animations you can do with it check the web at the same location. * VMD http://www.ks.uiuc.edu/Research/vmd/ can write to various 3D file formats, like POV-Ray{2,3}, Raster3D and VRML, as well as do trajectory animations and run in batch mode. VMD is free and runs best on SGIs, but slower version (because of the emulated OpenGL) are available for HPs and Linux. The biggest problem is that no one with a strong rendering background has worked on the code so there aren't really the hooks to tweak things that one might expect (eg, for making all the carbons be ebony or the surface be made of semi-transparent glass. We are open to suggestions, and you can get the VMD source to add your own tweaks. For a short tutorial I wrote a few months ago for making movies (with Raster3D), see http://www.ks.uiuc.edu/Research/vmd/workshop/movie.html (The general workshop notes, which help give an idea what VMD can do are at http://www.ks.uiuc.edu/Research/vmd/workshop/ .) * gOpenMol http://laaksonen.csc.fi/gopenmol/gopenmol.htmls * Re_View http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm It sounds like Re_View(2) is exactly what you want. It provides complete control of atom colours, etc; enables multistructure XYZ files to be read in; displays animations and even drives POV-ray without the user having to know anything about the ray-tracing processes so that mpeg and AAplay movies are automatically generated. Best of all it runs under Window3.1/95/NT. PS: Re_View contains many more features including 'active' graphs of data, etc. * ICMlite (see http://molsoft.com ) can do 1,2,3. It is now free for academics. You can do something like this: for i=1,100 read pdb "frm"+i # i.e. frm1.brk, frm2.brk etc. display xstick color a_//* Charge(a_//*) color background i # this is crazy, though delet a_ endfor * http://www.povray.org For those of you interested in rendering high-quality movies, I can recommend PovRay, a highly sophisticated public domain renderer (there is a usenet newsgroup on it out there). I know there are several conversion filters, e.g. pdb->pov for itaround. In a Unix environment, one would most likely use pipes, or a batch soldering individual frames into a movie. The new version, povray3, has many improvements, including orthographic projection and several internal changes to increase rendering efficiency. If you tried PovRay over a year ago and thought that it was too slow for animation, I'd suggest trying it again. You can also use the features of PovRay to make animations based on a single coordinate set, e.g. rotations, pans and zooms, lighting changes, etc. A caveat about pdb2pov-- it creates one or two large compound objects using the constructive solid geometry (CSG) feature of PovRay; this defeats most of the new changes for efficiency, which in general apply divide-and-conquer approaches based on the number of objects and their distribution in space. Removing the CSG statements (e.g. merge or union) results in 50-fold decreases in rendering time for scenes with a few thousand atoms. I modified the copy of pdb2pov at our local site to avoid the use of CSG in the output .pov files. I've forwarded this information to the author of pdb2pov, who is working on a new version (as time allows). Like any programming language, it takes a little time to learn how to make the best use of PovRay. However, the documentation is available in HTML format and is very good for a public domain program. The results are also well worth the effort; PovRay has many pre-defined textures (e.g. glass, stone, wood, ...) and other features that can be used to produce journal-cover quality molecular images. * ChemSymphony http://www.cherwell.com/chemsymphony Animation is one of the features of ChemSymphony (URL below) which is a publishing tool for including structures in HTML documents. This essentially works by creating a series of frames which are rendered in series. It recognises most file formats (XYZ, XMOL, PDB and so on) and allows the net user to change orientation and manipulate the structure whilst the animation is going on. A free demo is available from the Cherwell web site. Check Out ChemSymphony - rated top 1% Java applet by JARS ---------------------------------------------------------------------------- Comments? mail me!