Date: Mon, 1 Jul 1996 07:41:04 EDT From: Donald Rosenthal Subject: Begin Discussion of Paper 6 CHEMCONF '96 New Initiatives in Chemical Education An On-Line Symposium, June 3 to July 19, 1996 Sponsored by the American Chemical Society's Division of Chemical Education Organized by: Donald Rosenthal, Department of Chemistry, Clarkson University, and Tom O'Haver, Department of Chemistry and Biochemistry, The University of Maryland at College Park. It is Monday, July 1, 1996. Until 8 AM EDST on Wednesday, July 3 - Paper 6 will be discussed "Recent Applications of Hyperactive Chemistry and the World-Wide-Web: Towards an Integrated Chemistry Information Environment" by Henry S. Rzepa, Omer Casher, Christopher Leach and Peter Murray-Rust Please use the Subject line to identify the paper (or papers), yourself and the topic(s), e.g. P6 - JS - D - Use of Integrated Chemistry Information in Organic Chemistry where D - Discussion, Q - Question, A - Answer ===================================================================== Discussion of Papers 6 to 9 will occur between July 1 and July 12 according to the following schedule: July 1 and 2 - Discussion of Paper 6 July 3 and 8 - Discussion of Paper 7 July 9 and 10 - Discussion of Paper 8 July 11 and 12 - Discussion of Paper 9 ===================================================================== Donald Rosenthal Symposium Co-Chair and Chair, Committee on Computers in Chemical Education Clarkson University Phone: 315-265-9242 E-mail: ROSEN1@CLVM.CLARKSON.EDU ===================================================================== ------------------------------ Date: Mon, 1 Jul 1996 10:47:41 -0400 From: Brian Tissue Subject: P6 - BT - D - Visualization of vibrations, etc. Henry, et al., My impression is that *.pdb and *.xyz files contain only atomic coordinates. Is that correct or can more information be incorporated into these formats? Will CML allow manipulation of parts of molecules? I'm thinking of the ability to anchor one part of a molecule and see the spatial volume a side group sweeps out when it can move freely, for example a linear alkyl chain on an aromatic ring. Similarly, can bond energies, etc. be incorporated to visualize vibrations and librations? I can imagine users wanting to do all kinds of interactive things such as push electrons around, and see the effect on one molecule when another species approaches it. Will these interactive functions be dependent on someone writing a plug-in to interpret the data? Brian *************************************************************** Prof. Brian M. Tissue phone: (540) 231-3786 Department of Chemistry FAX: (540) 231-3255 Virginia Tech e-mail: tissue@vt.edu Blacksburg, VA 24061-0212 http://www.chem.vt.edu/ ------------------------------ Date: Mon, 1 Jul 1996 16:57:01 +0100 From: "Rzepa, Henry" Subject: Re: P6 - HR - D - Visualization of vibrations, etc. >Henry, et al., >My impression is that *.pdb and *.xyz files contain only atomic coordinates. >Is that correct or can more information be incorporated into these formats? Vibrations are easily incorporated. For example, try http://www.ch.ic.ac.uk/hyperactive/backbone_atoms_cyclic_traj.xyz as an example of animating an MD run. We have not done much work in this area yet, but I think it has great potential. We certainly intend doing this in the very near future. >Will CML allow manipulation of parts of molecules? I'm thinking of the >ability to anchor one part of a molecule and see the spatial volume a side >group sweeps out when it can move freely, for example a linear alkyl chain >on an aromatic ring. Similarly, can bond energies, etc. be incorporated to >visualize vibrations and librations? CML has an addressing scheme that includes atoms, and if necessary functional groups. However, anchoring one part of a molecule is clearly in the area of "molecular modelling". We envisage an extensive class library of Java objects being created. Within that, I can easily see someone writing a Java applet to do what you suggest >I can imagine users wanting to do all kinds of interactive things such as >push electrons around, and see the effect on one molecule when another >species approaches it. Will these interactive functions be dependent on >someone writing a plug-in to interpret the data? Yes. I prefer to think in terms of Java classes, which are much more object oriented and extensible than "plug-ins". The latter do not really lend themselves to this sort of application. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ (Eudora Pro 3.0) ------------------------------ Date: Tue, 2 Jul 1996 08:09:26 -0400 From: George Long Subject: Re: P6 - GL - D - Visualization of vibrations, etc. >CML has an addressing scheme that includes atoms, and if necessary >functional groups. However, anchoring one part of a molecule is >clearly in the area of "molecular modelling". We envisage an extensive >class library of Java objects being created. Within that, I can easily see >someone writing a Java applet to do what you suggest > >>I can imagine users wanting to do all kinds of interactive things such as >>push electrons around, and see the effect on one molecule when another >>species approaches it. Will these interactive functions be dependent on >>someone writing a plug-in to interpret the data? > >Yes. I prefer to think in terms of Java classes, which are much more >object oriented and extensible than "plug-ins". The latter do not really >lend themselves to this sort of application. > This discussion has got me wondering, will the primary mechanism of communicating information about chemical structures be via an object oriented code? In many cases, chemistry departments have moved away from requiring computer languages, in favor of quote "computer literacy" classes. In fact, the last chemconf yielded a publication on what every chemistry student should know about computers. With the importance of Java, C++, and other languages in producing really interactive websites and in communicating information about chemical structures, Would chemistry students be well served to learn object oriented programming ?? should this be a requirement ?? Or is there an application on the horizon that will link the java applets to perhaps a drawing or MM program ? **************************************************************************** George R Long, Ph.D. Department of Chemistry Indiana University of Pennsylvania Indiana, PA 15705 grlong@grove.iup.edu 412-357-2575 Our lives are merely trees of possibilities - Marc Bolan **************************************************************************** ------------------------------ Date: Tue, 2 Jul 1996 16:02:52 +0100 From: "Rzepa, Henry" Subject: Re: P6 - HR - D - Visualization of vibrations, etc. >This discussion has got me wondering, will the primary mechanism of >communicating information about chemical structures be via an object >oriented code? In many cases, chemistry departments have moved away from >requiring computer languages, in favor of quote "computer literacy" classes. > In fact, the last chemconf yielded a publication on what every chemistry >student should know about computers. With the importance of Java, C++, and >other languages in producing really interactive websites and in >communicating information about chemical structures, Would chemistry >students be well served to learn object oriented programming ?? should this >be a requirement ?? Or is there an application on the horizon that will link >the java applets to perhaps a drawing or MM program ? I am certainly rethinking how we should respond in our teaching. With Java and other object oriented languages such as Limbo on the horizon, a case could be made for going to one of these as a teaching paradigm. I think it important to keep this application quite separate from "application" of these technologies. Let me tell from my direct experience two weeks ago. Sun hosted a Java "workshop". About 15 people assembled, admittedly many of them with C++ experience. In two days, four new applets were present, admitedly in primitive form. The use of class libraries means that one does not have to re-ivent the wheel, and one can achieve a high level of productivity. Of course, this is nothing new. I remember just a few years back looking at AVS or Explorer maps in the same light. However that was purely visualisation, whereas Java is much more broadly based. So the simple answer is that I think a strong case could be made for devising new courses in object oriented programming, but I doubt I would make them mandatory for all students Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ (Eudora Pro 3.0) ------------------------------