From JeanLuc.Verschelde@rug.ac.be Thu Dec 22 10:15:51 1994 Received: from mserv.rug.ac.be for JeanLuc.Verschelde@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id IAA00614; Thu, 22 Dec 1994 08:39:38 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA29343 (5.67b/IDA-1.5 for ); Thu, 22 Dec 1994 10:42:24 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA21092; Thu, 22 Dec 1994 10:42:56 +0100 Date: Thu, 22 Dec 1994 10:42:55 +0100 (MET) From: Jean-Luc Verschelde To: OHIO SUPER Subject: software Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 967 Hi all, For a friend of mine I am looking for a neural net that predicts the secondary structure content of a protein by looking at CD spectra.I know it exists but don't know where to find it. Also a docking program is needed. I would really appreciate any help. Greetings, Jean-Luc =================================================================================== Verschelde Jean-Luc University of Ghent Lab. for Mathematical Physics | Lab. for Biochemistry | Krijgslaan 286 S9 | K.L. Ledeganckstraat 35 9000 Ghent | 9000 Ghent Belgium. | Belgium. Tel.:09/264 47 94 Fax:09/264 49 89 Email:Jeanluc.Verschelde@rug.ac.be =================================================================================== From bartberg@qtp.ufl.edu Thu Dec 22 10:29:03 1994 Received: from crunch for bartberg@qtp.ufl.edu by www.ccl.net (8.6.9/930601.1506) id JAA01509; Thu, 22 Dec 1994 09:14:49 -0500 Received: by crunch (5.x/4.11) id AA14033; Thu, 22 Dec 1994 01:30:01 -0500 Date: Thu, 22 Dec 1994 01:30:01 -0500 From: "Micheal Bartberger" Message-Id: <9412220630.AA14033@crunch> To: chemistry@ccl.net Subject: Structure software summary Dear fellow netters: As promised, here is a summary of the responses I recieved to my question regarding MS-Windows-based molecular graphics programs, especially those that would generate publication-quality images. On the share/freeware side, there were a couple of references to RASMOL, which should be available from infomeister. Use of this program along with BABEL makes for a decent combination, IMO. On the commercial side, a few folks mentioned Hyperchem. Supposedly very nice (I haven't seen it for myself) but it's not inexpensive. Also, Cambridge Scientific has let me know they are in the final development stages of a version of Chem3D for Windows. Other programs / W^3 sites were also mentioned; I just haven't yet had time to follow up on all the leads. The responses (other than requests for a summary) are shown below. So, read on, and many thanks to those who responded. Regards, Michael bartberg@qtp.ufl.edu bartberg@chem.ufl.edu -------------------------------------------------------------------------- *********************************** * From: Steven Bachrach * *********************************** You might want to check out a database on my WWW/gopher site. You cna get to it via gopher to hackberry.chem.niu.edu or by WWW to URL http://hackberry.chem.niu.edu:70/0/webpage.html A number of offerings in this list will satisfy your needs. Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 ******************************** * From: imcvey@en.com * ******************************** Micheal, the handyest software for this task would I think be hyperchem by autocube, they're based in ontario, this has the cpacity to read several types of input, do all manner of geometry optimizations, and produce very nice images. I don't offhand know the price but it's not cheap. Oddly enough Alchemy produced by tripos while not being versatile on the calculations front produces very nice images, at least the version we have, but it takes forever for it to generate these images. On the shareware front the windows version of RASMOL does a prety nice job of displaying molecules but like Alchemy only reads one file type. But BABEL is a program that can translate between 30 or differnet formats so that makes it possible to use less polylingual sofware if they produce better images. BABEL and RASMOL are available by ftp from www.ccl.net Hope this helps. Iain imcvey@scorpio.kent.edu or imcvey@en.com ******************************** * From: Per-Ola Norrby * ******************************** Michael, What you want can be done by the Chem3D program. With this, you incidently also get access to a fair, albeit slow, MM2 implementation. I have only used it on Macs, but I believe it is now available for Windows, and also on Unix systems. If you have some www-tool, you can get info at the address: http://www.camsci.com Per-Ola Norrby * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk ************************** * From: Gerd Thys * ************************** Perhaps you can have a look at my WWW-homepage... I collected some links to and information on graphics programs for chemists (along with other chemical stuff). Point your lynx or mosaic or so to the URL in my .signature (at the end of this message). (In the menu, chose 'professional links'...) Have fun, Gerd ---------------------------------------------------------------------------- Gerd Thys Ph.D. Student Structural Chemistry Group University of Antwerp (UIA) Universiteitsplein 1 E-mail: thys@uia.ua.ac.be B-2610 wilrijk URL: http://www.uia.ac.be/u/thys/index.html BELGIUM ---------------------------------------------------------------------------- ******************************* * From: Dr. Jeffrey Gosper * ******************************* My program RE_VIEW can do this. It runs under windows. Contact me directly if you wish to persue this item Dr Jeff Gosper Jeffrey.Gosper@brunel.ac.uk ******************************** * From: Joel A. Wolff * ******************************** Michael, I thought you might be interested in the following information. It is a plug for an upcoming product from Cambridge Scientific Computing. We are in the final development stages of Chem3D Pro for Windows. This will be equivalent to our currently shipping Chem3D Plus for the Macintosh. The capabilities for creating 3D structures and creating publication quality structures seems to be exactly what you are looking for. Unfortunately, it is not quite available yet (shipping Q1 1995). The package itself is a lower end package than CAChe (only MM2 is supported). Educational pricing will be available. Let me know if you have any questions. Joel A. Wolff, Ph.D. Customer Service Manager Cambridge Scientific Computing 875 Massachusetts Avenue Cambridge, MA 02139 Phone: (617) 491-2200 Fax: (617) 491-7203 Compuserve: 76070,615 Internet: info@camsci.com ************************************** * From: Frederick P. Arnold, Jr. * ************************************** But having seen your address, doesn't QTP have something called QUIPU that displays molecular and electronic structures on a TEK terminal? It shouldn't be that hard to port. (I used the VMS version back in '89 when I worked for Allied-Signal). Failing that, if you're feeling flush, Hyperchem, especially with the Chemplus add-on, seems to be the nicest graphics I've seen so far, and it runs under windows. However, at $1000 academic price for the base kit, plus $500 for ChemPlus, it's not cheap. Mail to info@hyper.com for further information. If you find something better, or can lay hands on the QUIPU display codes, I would be appreciative if you would let me know, as I'm searching for roughly the same functionality, but a bit cheaper. -fred farnold@wotan.duch.udel.edu From AEMHC@CUNYVM.CUNY.EDU Thu Dec 22 10:30:16 1994 Received: from phem3 for AEMHC@CUNYVM.CUNY.EDU by www.ccl.net (8.6.9/930601.1506) id KAA03224; Thu, 22 Dec 1994 10:17:53 -0500 Received: from CUNYVM.CUNY.EDU (MAILER@CUNYVMV2) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HKX3KYPTLC94E0WX@phem3.acs.ohio-state.edu>; Wed, 21 Dec 1994 21:00:57 EDT Received: from CUNYVM.CUNY.EDU (NJE origin AEMHC@CUNYVM) by CUNYVM.CUNY.EDU (LMail V1.2a/1.8a) with RFC822 id 0122; Wed, 21 Dec 1994 20:59:58 -0500 Date: Wed, 21 Dec 1994 20:58:41 -0500 (EST) From: Artem Masunov Subject: Urea: Flat or Chiral in the Gas Phase? To: chemistry@ccl.net Message-id: <01HKX3KYQ38I94E0WX@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Hello All, Thank you very much for all your answers. The original message was: > Dear Netters, > Doing my PhD research in Theoretical Chemistry, I found (at PM3 and > MP2/G95** levels, but not at AM1 and HF), that urea, (H2N)2C=O, is > nonplanar with two conformations (Cs and C2 symmetry), instead of flat > C2v, like in crystal. Can anybody adwise me how to get references on > experimental (MW or ED) geometry of urea molecules in gase phase? > Vibrations and interconversion barriers are also wanted. > Somebody told me to ask Prof.B.P.Winnewisser. What is his E-mail address? > I'v heard, there is specific database on gase data like CCSDB > on crystals. > It showld locate somewhere in Germany. Does it have remote access? > Alternatively I am interested in new reference books (those old ones > I found in the library say nothing about urea). > I will be greately appreciated for all responces. > Send directly to me (I am not subscriber of CCL) and I'll summarize. Hear is the summary of responces: --------------------------------------------------------------------- >From Steve Williams I encourage you to post a summary. If you were interested in gas phase ion structures I could give you some hints about where to start looking, but these sources would not have anything useful on a neatral like urea. Good Luck... --------------------------------------------------------------------- >From Don McNaughton Brenda Winnewisser's email is Brenda.Winnewisser@phys.chemie.uni-giessen.de note He is she! There was some work done on the microwave spectrum of urea here at Monash University chemistry before my time. I think in the early 70's - you could probably track that thru chem abst. The databank of microwave data/structure is run from the university in Ulm, Germany by Dr. Juergen Vogt Sektion fur Spektren und Strukturdocumentation Universitat Ulm D-89069 Ulm. Juergen.Vogt@chemie.uni-ulm.de We get the hard copy version of the database but I think there is some sort of version on computer although I doubt it is accessible remotely. There is an issue of The Journal of Physical Chemistry Reference Data back in 1979 - I think no.15 that contains gas phase structures up to 1979 - urea should be in that. ------------------------------------------------------------------------- >From Stephen CJV Hello. I acquired the core excitation spectra (C 1s, O 1s and N 1s) of urea, phenyl urea and N,N' diphenyl urea a few years ago. I was interested in non-planarity of urea mostly in the case of the phenyl ureas, where the N-C(Ph) bond rotation will strongly affect carbonyl pi* and phenyl pi* mixing. I didn't explore this effect for urea at the time, as I didn't figure the effect on the spectrum would be very large. At any rate, I will be very interested in the results of your study. Urea is fairly involatile, phenyl ureas even more so, so electron diffraction will be fairly difficult. Not impossible - there is a group in the U.S. ... R.J. Mawhorter, M. Fink and J.G. Hartley, J. Chem. Phys., Vol 83, 1985, 4419. They have done alot since this paper and are still active... ------------------------------------------------------------------------- From: Dr. Dave Winkler I have forwarded your query to Prof. Ron Brown's group (where I did my PhD) who did the MW spectrum of urea. The CCDC can be reached on SOFTWARE@CHEMCRYS.CAM.AC.UK. ---------------------------------------------------------------------- >From Gregory L. Durst - DowElanco R&D You should take a look at the following papers as they deal with similar questions...(both in the same issue of J. Comp. Chem.) D. Smith, C. Ulmer, M. Gilbert, J. Comp. Chem., v13(5), (1992), 640. M. Kontoyianni and P. Bowen, J. Comp. Chem., v13(5), (1992), 657. ---------------------------------------------------------------------- >From Sergei Vyboishikov E-mail of Dr. Manfred Winnewisser is: ge28@liebig.hrz.uni-giessen.de Nonplanarity of urea was theoretically discowered AT FIRST by Frienking, Gobbi; J.Am.Che.Soc. 115 (1993) 2362. E-mail of Alberto Gobbi is: bgobbi@chbs.ciba.com ---------------------------------------------------------------------- From: Jennie.Weston@org.chemie.uni-giessen.de (Jennie Weston) B.P. Winnewisser is a she, not a he She is no prof, but a permanent dude in the research group of Prof. Manfred Winnewisser, Universitaet Giessen, Germany with email Brenda.Winnewisser@phys.chemie.uni-giessen.de ---------------------------------------------------------------------- Thank you again. Merry Christmas to everybody. Regards, Artem --------------------------Artem E. Masunov---------------------------- | Chemistry Department, Hunter College, City University of New York | | E-mail: AEMHC@cunyvm.cuny.edu, tel: 212/725-0317, fax:772-5332 | ---------------------------------------------------------------------- From snarey@pfizer.com Thu Dec 22 11:31:18 1994 Received: from pfizer.com for snarey@pfizer.com by www.ccl.net (8.6.9/930601.1506) id LAA04724; Thu, 22 Dec 1994 11:08:49 -0500 Received: from sdu003.sandwich.pfizer.com (sdu003.pfizer.com) by pfizer.com (4.1/3.1.090690-Pfizer Inc) id AA06075; Thu, 22 Dec 94 09:57:07 EST Received: from siris4 by sdu003.sandwich.pfizer.com (5.65/Ultrix3.0-C) id AA09728; Thu, 22 Dec 1994 14:59:52 GMT Received: by siris4 (931110.SGI/920502.SGI.AUTO) for @sdu003.pfizer.com:chemistry@ccl.net id AA04482; Thu, 22 Dec 94 14:59:52 GMT From: snarey@pfizer.com (Mike Snarey) Message-Id: <9412221459.AA04482@siris4> Subject: Combinatorial Libraries To: chemistry@ccl.net Date: Thu, 22 Dec 1994 14:59:52 +0000 (GMT) Reply-To: X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Content-Length: 1279 The Molecular Graphics and Modelling Society (MGMS) is pleased to announce that their 1995 Spring conference will be held at the University of Leeds, Leeds, England between the 10th and 12th of April.The subject of the conference will be Computational Aspects of Chemical Libraries The conference will contain sessions on the following topics: 1) Calculating chemical diversity for profiling libraries; 2) Data structures and databases for holding library information; 3) Computational analysis and data mining; 4) Searching of reaction databases and other computational aids to "wet" chemistry. The conference will have invited and contributed speakers. If you would like further information or would like to submit an abstract for consideration as a contributing seaker in one of the above sessions then please mail Dr Peter Johnson at the School of Chemistry, University of Leeds, Leeds, England (e-mail johnson@mi.leeds.ac.uk) to arrive not later by Jan 31st 1994. A poster session and trade exhibition are also being planned. The MGMS annual general meeting will be held during this conference. This conference is being organised on behalf of the MGMS by Drs Peter Johnson (Univ of Leeds), Mike Hann (Glaxo R&D), John Bradshaw (Glaxo R&D) and Kate Burt (Pfizer UK). From ANWAR@vms.huji.ac.il Thu Dec 22 09:30:23 1994 Received: from VMS.HUJI.AC.IL for ANWAR@vms.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id IAA00388; Thu, 22 Dec 1994 08:35:15 -0500 Received: by HUJIVMS (HUyMail-V7a); Thu, 22 Dec 94 15:34:51 +0200 Received: by HUJIVMS (HUyMail-V7a); Wed, 21 Dec 94 22:17:52 +0200 Date: Wed, 21 Dec 94 22:17 +0200 Message-id: <21120094221747@HUJIVMS> From: To: CHEMISTRY@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: stability of tetrahedral intermediates Status: R Dear netters, Could someone point me to reference for semiempirical or ab initio calculations on stability of tetrahedral intermediates (specially comparison between computational results with experimental ones). Thanks to all in advance anwar rayan anwar@vms.huji.ac.il From jkl@ccl.net Thu Dec 22 11:52:15 1994 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id LAA05173; Thu, 22 Dec 1994 11:30:09 -0500 Date: Thu, 22 Dec 1994 11:30:09 -0500 From: Jan Labanowski Message-Id: <199412221630.LAA05173@www.ccl.net> To: chemistry@ccl.net Subject: List intermission occured Cc: jkl@ccl.net Dear Netters, This is your administrator speaking... We had a power outage starting about 3pm Easter Time (Standard time -5 hrs) Wednesday and lasting until this morning (i.e., about 10am). It was only recently fixed (yes, it was a major thing...). If you have sent a message to the Comp.Chem.List (or its administrator) and you did not get the confirmation that it was received/processed, it is probably lost, so please resend. I use this occassion to wish you all good holidays (even if you already had them ...) and the happy New Year (even if it is not your New Year coming). Find some time to forget about chemical bonds and explore the family and friendship bonds for a while. *%\@/*%$%*\@/*%$%*\@/*%$%*\@/*%$%*\^/*%$%*\@/*%$%*\@/*%$%*\@/*%$%*\@/*%* * X ! X ! X ! X ! . ! X ! X ! X ! X * * O O O O .|. O O O O * * -*- * * Athbhliain Faoi Mhaise! 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Jan Labanowski jkl@ccl.net From C1790@SLVAXA.UMSL.EDU Thu Dec 22 13:30:14 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.9/930601.1506) id MAA06783; Thu, 22 Dec 1994 12:35:01 -0500 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HKXXWTLYC6A4L8W7@SLVAXA.UMSL.EDU>; Thu, 22 Dec 1994 11:37:33 CDT Date: Thu, 22 Dec 1994 11:37:33 -0500 (CDT) From: BILL WELSH Subject: Source materials for Neural Networks To: chemistry@ccl.net Message-id: <01HKXXWTLYC8A4L8W7@SLVAXA.UMSL.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Colleagues, Soon I will be teaching a course on Applications of Chemometrics and Neural Networks in Chemistry at the graduate and upper-level undergraduate level. I would appreciate receiving your input on good source materials for teaching it, such as (i) books, (ii) review article, (iii) software (free or commercial), and (iv) lecture material. I am particularly interested in audio/visual materials for presenting lectures on neural nets and chemometrics. I would like to hear of any source (e.g., company, organization, WWW source) that might provide/sell audio/visual presentation materials for lectures on any aspect of these topics. Thanks, and best wishes to all during the holday season. Bill Welsh Dept. of Chemistry Univ. of Missouri-St. Louis