From h.rzepa@ic.ac.uk Fri Sep 17 08:53:06 1993 Message-Id: <9309170756.AA28171@cscmgb.cc.ic.ac.uk> Date: Fri, 17 Sep 1993 08:53:06 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: posters on workstations? Delos Detar writes; . > Wouldn't it be nice if the posters could be run INTERACTIVELY > on the workstations! (Is this a "novel" idea or has it been > done already?). You may be interested that I gave a similar poster at a Molecular Graphics Society meeting about 2-3 years ago at Oxford, using a CACHe workstation and the stereo glasses. Hence people could not only rotate the (x-ray) structures, but view them in stereo. I have now moved up to using the Persuasion slideshow, incorporating Quicktime movies of eg transition states vibrating, and perhaps IRCs etc etc. This was done at the University of St Andrews this year in July, although it did require a BARCO projector, facilities few venues yet have!! We have applied a similar concept to published PAPERS. Our last 4-5 submitted papers (one has appeared; Chem Commun, 1993, p 1337) have associated animated diagrams that are accessed using our gopher+ server argon-fddi.ch.ic.ac.uk (155.198.224.33). Thus people can view our diagrams from at least some directions (and even hear my dulcet tones explaining the points of interest in some of them!!) and then download coordinates and other supplemental material. This aspect has also beeen actively promoted by the journal Protein Science, which distributes a diskette containing a protein viewer. That is presumably not a cheap option for the journal however. Does anyone know of plans for chemistry journal to do this? I know that Todd Wipke has broadcast something similar to this forum about 5 months ago, ie an ftp archive containing animations of coordinates submitted with papers. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.4, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From chp1aa@surrey.ac.uk Fri Sep 17 08:14:52 1993 From: Mr Andrew D Allen Message-Id: <9309171133.AA08440@central.surrey.ac.uk> Subject: Posters - electronic To: chemistry@ccl.net Date: Fri, 17 Sep 93 12:33:43 BST Detar, Delos F. has posed a very interesting point, I am currently facing problems of which stereo pair pictures to paste onto a poster. If computer facillities could be made available for poster sessions the visualisation would be 1000% better. I have spent several days printing out postscript stereo pair pictures, trying to get the perfect veiw of the molecules / proteins that I am working with. The fact remains that if you can see the molecule rotating, then you get a much better idea of spacial relationships. The idea could work very simply by having a selection of the more popular software appplications, running on appropriate platforms. This kind of visualisation would have to be the way forward for all future presentations. Not just posters presentations, but what about lectures as well. At Surrey we have a PC connected to an overhead projector, why not have an SG or ESV etc... connected via a PAL encoder to a video output on an overhead projector. I sure there may even be systems available which could take the RGB signal direct, and project it on an OHP. The possibilities for future presentations are only a matter of getting a few heads together and putting the right hardware together. Andy. From h.rzepa@ic.ac.uk Fri Sep 17 16:32:03 1993 Message-Id: <9309171535.AA03253@cscmgb.cc.ic.ac.uk> Date: Fri, 17 Sep 1993 16:32:03 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: posters on workstations? This was sent, but several colleagues tell me only the first few lines arrived? Anyway, here is another go at sending it . > Wouldn't it be nice if the posters could be run INTERACTIVELY > on the workstations! (Is this a "novel" idea or has it been > done already?). You may be interested that I gave a similar poster at a Molecular Graphics Society meeting about 2-3 years ago at Oxford, using a CACHe workstation and the stereo glasses. Hence people could not only rotate the (x-ray) structures, but view them in stereo. I have now moved up to using the Persuasion slideshow, incorporating Quicktime movies of eg transition states vibrating, and perhaps IRCs etc etc. This was done at the University of St Andrews this year in July, although it did require a BARCO projector, facilities few venues yet have!! We have applied a similar concept to published PAPERS. Our last 4-5 submitted papers (one has appeared; Chem Commun, 1993, p 1337) have associated animated diagrams that are accessed using our gopher+ server argon-fddi.ch.ic.ac.uk (155.198.224.33). Thus people can view our diagrams from at least some directions (and even hear my dulcet tones explaining the points of interest in some of them!!) and then download coordinates and other supplemental material. This aspect has also beeen actively promoted by the journal Protein Science, which distributes a diskette containing a protein viewer. That is presumably not a cheap option for the journal however. Does anyone know of plans for chemistry journal to do this? I know that Todd Wipke has broadcast something similar to this forum about 5 months ago, ie an ftp archive containing animations of coordinates submitted with papers. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.4, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From lnp@linus.rtpnc.epa.gov Fri Sep 17 09:01:24 1993 Date: Fri, 17 Sep 93 13:01:24 -0400 From: Lan Lewis-Bevan Message-Id: <9309171701.AA12861@linus.rtpnc.epa.gov> To: CHEMISTRY@ccl.net Subject: AM1 calculation for reactions Dear friends: I am trying to use AMPAC/AM1 to optimize the energy of an assembly of a neutral molecule and a cationic molecule to see if there is a possibility for certain reaction to happen. Is there any information about using AM1 or other programs for chemical reactions of this type? Thanks. Lan Lewis-Bevan From mercie@med.cornell.edu Fri Sep 17 09:07:41 1993 Date: Fri, 17 Sep 1993 13:07:41 -0400 (EDT) From: Gustavo Mercier Subject: XPLOR To: chemistry@ccl.net Message-Id: HI! I need some help! Does anybody have info regarding the vendor for XPLOR? Any description of its capabilities? thanks gus mercier mercie@cumc.cornell.edu From r0603001@ccms.ntu.edu.tw Fri Sep 17 22:34:03 1993 Date: Sat, 18 Sep 93 04:34:03 CST From: r0603001@ccms.ntu.edu.tw (Chia M. Chang) Message-Id: <9309172034.AA29327@ccms.ntu.edu.tw> To: chemistry@ccl.net Subject: Se Extended Huckel Parameters Hi! Netters, I need more info...... I wonder if anybody could send the parameters of selenium (Se) for extended Huckel (and charge iterative EH) calculation to us? Thank you for your cooperation. Chia M. Chang r0603001@ccms.ntu.edu.tw From r0603001@ccms.ntu.edu.tw Fri Sep 17 22:44:21 1993 Date: Sat, 18 Sep 93 04:44:21 CST From: r0603001@ccms.ntu.edu.tw (Chia M. Chang) Message-Id: <9309172044.AA29388@ccms.ntu.edu.tw> To: chemistry@ccl.net Subject: Se Extended Huckel Parameters Hi! Netters, I need more info...... I wonder if anybody could send the parameters of selenium (Se) for extended Huckel (and charge iterative EH) calculation to us? Thank you for your cooperation. Chia r0603001@ccms.ntu.edu.tw From gjt@t12.LANL.GOV Fri Sep 17 08:32:41 1993 Date: Fri, 17 Sep 93 14:32:41 MDT From: gjt@t12.LANL.GOV (Gregory J. Tawa (T-12)) Message-Id: <9309172032.AA07426@t12> To: chemistry@ccl.net Subject: Geometries and Partial Charges Dear scientists, I need to find the geometries, i.e., the 3d coordinates of the following molecules: amino-anthroquinone and hydroxi-anthroquinone Does anyone know of references regarding the geometries of these molecules? Secondly, I need to know the partial charge at each atom center for both of the above molecules, again references would be helpful. Thanx! ------------------------------------------------------------------------------- Gregory J. Tawa | | K723 | Theoretical Chemistry and Physics Group (T-12)| Phone : 505-667-0324 Los Alamos National Laboratory | E-mail : gjt@nitrogen.lanl.gov Los Alamos, N.M. 87545 | ------------------------------------------------------------------------------- From carlos@pap.chem.uic.edu Fri Sep 17 11:51:37 1993 Date: Fri, 17 Sep 93 16:51:37 CDT From: Carlos Simmerling Message-Id: <9309172151.AA10658@pap.chem.uic.edu> To: CHEMISTRY@ccl.net Subject: Overlap algorithm Hi everyone, Does anyone have a reference for a quaternion-based algorithm for overlapping two structures to minimize rms? I have one reference to J. Mol. Sim. but I am having trouble locating the journal. I would appreciate any help. Carlos Simmerling carlos@pap.chem.uic.edu