From comartin@wicc.weizmann.ac.il Mon Nov 18 03:46:26 1996 Received: from theochem.weizmann.ac.il for comartin@wicc.weizmann.ac.il by www.ccl.net (8.8.2/950822.1) id CAA03251; Mon, 18 Nov 1996 02:47:38 -0500 (EST) Received: from [132.76.57.106] by theochem.weizmann.ac.il with ESMTP (Apple Internet Mail Server 1.1.1); Mon, 18 Nov 1996 09:45:38 +0200 X-Sender: comartin@theochem.weizmann.ac.il Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Wisdom: Language Can Kill Date: Mon, 18 Nov 1996 09:28:54 +0200 To: chemistry@www.ccl.net From: "Jan M.L. Martin" Subject: apologies Dear subscribers, a number of people complained about my posting an entire program to CCL, and suggested that I give an ftp URL instead of wasting precious bandwidth. Let me point out in my defense that I checked the list WWW pages for submission instructions and that what I came up with was the following: http://www.ccl.net/ccl/welcome.html > > > Topics which may appear on the list include: > >[...] > *Programs and utilities > [...] > If you are posting a long file (e.g. a program), please split it into > chunks which are smaller than 50 KBytes. Always identify the part number > and total number of parts in the Subject line (e.g. NiceDraw Part 2 of > 5). > [...] So I just did what it *says* in these pages. Nevertheless, I apologize for any long downloads and aggravation I may have caused people who do not receive their mail on Unix boxes and had their modems clogged up by my "garbage". The package is now up for download by FTP at: ftp://www.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/gar2ped Future updates and/or corrections will be made to the FTP file *only*, and only announcements will sent out to the list. As a final note, I would respectfully suggest that the moderator update the above submission information. Sincerely, Jan Martin ---------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** temporary WWW home page http://theochem.weizmann.ac.il/ *** ------ kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo lefached k'lal ----- From psto@xs4all.nl Mon Nov 18 06:42:47 1996 Received: from magigimmix.xs4all.nl for psto@xs4all.nl by www.ccl.net (8.8.2/950822.1) id GAA08298; Mon, 18 Nov 1996 06:05:02 -0500 (EST) Received: from xs2.xs4all.nl (xs2.xs4all.nl [194.109.6.43]) by magigimmix.xs4all.nl (8.7.5/XS4ALL) with ESMTP id MAA13021 for ; Mon, 18 Nov 1996 12:04:18 +0100 (MET) Received: from [194.109.44.87] (asd03-22.dial.xs4all.nl [194.109.44.87]) by xs2.xs4all.nl (8.7.6/XS4ALL) with SMTP id MAA11642 for ; Mon, 18 Nov 1996 12:04:13 +0100 (MET) Date: Mon, 18 Nov 1996 12:04:13 +0100 (MET) Message-Id: <199611181104.MAA11642@xs2.xs4all.nl> X-Sender: psto@xs4all.nl (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: psto@xs4all.nl (Peter Stone) Subject: Gene processing toolbox for the Mac Hi, I'm not a chemist but a programmer, and I've written several hundred general-purpose algorithms that might be useful for you. The algorithms let you generate and process rna and turn the results into amino acids. Let me know if such program is needed, and what other features it should have. I'm not a regular on this list and would appreciate answers directly to my email. Peter psto@xs4all.nl --- Here is an example of how a recursive van kock gene can be constructed. Implement it in an organism and we might get interesting new properties, designed with mathematical perfection from the algorithm library of: - fractals - chaos - lsystems - fourier synthesis - autocatalysis - neurons - energy fields - fibonacci numbers - loops - morphs - transforms - interpolations - palindromes - variations - divisions - primes - solar systems - rna - clusters - proportions - permutations - rotations You can also process existing genes with the above. Morph eye to ear, or permute hiv hxb2 env gene, experiment if a rotated fibonacci neuron structure performs better than non-rotated, loop genes for better beef productivity, etc. ; define recursive kock-curve (def-grammar 'koch-curve axiom (f + f + f + f) f (f + f - f - f f + f + f - f) - (-) + (+) < (<) > (>) ) ; define neuron to convert linear symbols to rna symbols (def-neuron symbols-to-rna (in 1 'a) 'u (in 1 'b) 'g (in 1 'c) 't (in 1 'd) 'a ) ; generate master-rna from kock-curve in 3 recursion levels, and scale the ; symbols into rna symbols (setq master-rna (run-neuron 'symbols-to-rna (symbol-scale '(a d) (gen-lsystem axiom 3 '(f + - < >) 'koch-curve)))) ; compile rna into aminoacids (rna-compile master-rna) --> (gly leu gly trp gly gly val gly cys phe val val leu trp val gly val gly trp gly trp gly gly val phe gly leu trp gly gly val gly gly leu gly trp gly val trp phe val gly cys leu val leu phe tyr phe gly leu trp gly gly gly val phe gly phe ile leu phe trp phe tyr phe ile asn stp ile phe tyr phe gly phe leu val leu phe tyr lys leu asn ile leu) From HILAL2@FRCU.EUN.EG Mon Nov 18 10:38:32 1996 Received: from FRCU.EUN.EG for HILAL2@FRCU.EUN.EG by www.ccl.net (8.8.2/950822.1) id KAA09976; Mon, 18 Nov 1996 10:06:11 -0500 (EST) From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01IBZYM9XFN8000L0I@FRCU.EUN.EG>; Mon, 18 Nov 1996 17:05:43 O Date: Mon, 18 Nov 1996 17:05:42 +0000 (O) Subject: new user "Ahmad Omar" To: chemistry@www.ccl.net Message-id: <01IBZYM9XFNA000L0I@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear sir; I would like to add my name to your list with very best wishes, yours sincerely Ahmad Omar your sincerly From jaw@camsoft.com Mon Nov 18 16:38:35 1996 Received: from camsoft.com for jaw@camsoft.com by www.ccl.net (8.8.2/950822.1) id PAA12957; Mon, 18 Nov 1996 15:42:57 -0500 (EST) Received: from lutetium (lutetium.camsoft.com) by camsoft.com (4.1/3.1.090690-CambridgeSoft Corp.) id AA28336; Mon, 18 Nov 96 15:42:43 EST Message-Id: <2.2.32.19961118204350.00726c64@helium.camsoft.com> X-Sender: jaw@helium.camsoft.com X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 18 Nov 1996 15:43:50 -0500 To: janet.cicariello-cook@roche.com From: Joel Wolff Subject: Re: CCL:Getting structures from SYBYL to FMPro Cc: CHEMISTRY@www.ccl.net At 10:30 AM 11/18/96 -0500, you wrote: >Hi All, > >I am trying to put together an automated (semi-automated?) procedure for our >chemists to get their structures from SYBYL (3D-structure, on the SGI) into >FileMaker Pro v3.0 (2D-structures, on their Macintoshes). They are currently >re-drawing their structures (you can imagine the problem this is, especially >with the CombiChem folks) > Janet, The makers of ChemDraw can probably help you here. I can think of several easier ways to deal with this problem: 1. Export from SYBYL and open in Chem3D. Then export from Chem3D to ChemDraw format. 2. Contact us about our upcoming support of SMILES in ChemDraw 4.0. This would remove several steps in your process. 3. Move the files through ChemFinder, which already has links between Chem3D, ChemDraw and FileMaker. Everything can be done via AppleScript once the files are moved to the Macintosh. Let me know how I can help. Joel Wolff, Ph.D. Director, Technical Services CambridgeSoft Corporation 875 Massachusetts Avenue Cambridge, MA 02139 jaw@camsoft.com From darryl@om3.ch.umist.ac.uk Mon Nov 18 23:38:35 1996 Received: from nessie.mcc.ac.uk for darryl@om3.ch.umist.ac.uk by www.ccl.net (8.8.2/950822.1) id WAA15681; Mon, 18 Nov 1996 22:40:10 -0500 (EST) Received: from om3.ch.umist.ac.uk (actually trigger.ch.umist.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Mon, 18 Nov 1996 13:14:48 +0000 Received: by om3.ch.umist.ac.uk (940406.SGI/) for chemistry%www.ccl.net@nessie.mcc.ac.uk id AA08182; Mon, 18 Nov 96 13:40:39 GMT Date: Mon, 18 Nov 1996 13:40:38 +0000 (GMT) From: Darryl Ellson Subject: Computational studies of histidine radicals. To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am looking for any computational studies (particularly, but not necesssarily, DFT )which have been carried out on histidine radicals (neutral, cationic and +2 charged) or on related truncated species, such as 4Me-Imidazole. I am particularly interested in calculated vibrational frequencies and/or mode assignments for these species. If anyone could point me in a useful direction I would be most grateful. Regards. Darryl A. Ellson Darryl A. Ellson - Molecular Design & Simulation Laboratory. Dept. Chemistry, UMIST, Manchester. UK. M60 1QD Tel: 0161-236-3311 x4476 Fax: 0161-236-7677 |_o_| "Unless I am very much mistaken... I AM very much mistaken !" []=(_)=[] (M.Walker)