From mikes@bioch.ox.ac.uk Wed Jun 29 11:04:13 1994 Received: from oxmail.ox.ac.uk for mikes@bioch.ox.ac.uk by www.ccl.net (8.6.9/930601.1506) id KAA10362; Wed, 29 Jun 1994 10:27:38 -0400 From: Received: from bioch.ox.ac.uk by oxmail.ox.ac.uk with SMTP (PP) id <21645-0@oxmail.ox.ac.uk>; Wed, 29 Jun 1994 15:25:46 +0100 Received: from ocms.ox.ac.uk (nmrpcd.ocms) by bioch.ox.ac.uk (5.0/SMI-SVR4) id AA04760; Wed, 29 Jun 1994 15:24:38 +0000 Received: by ocms.ox.ac.uk (931110.SGI/bioch3.0) id AA16532; Wed, 29 Jun 94 15:27:19 +0100 Date: Wed, 29 Jun 94 15:27:19 +0100 Message-Id: <9406291427.AA16532@nmrpcd.ocms.ocms.ox.ac.uk> To: chemistry@ccl.net Subject: rmsds between different structures. content-length: 643 Dear All, I am looking for a software package which will enable me to least-squares-fit and find the rmsds between two structures. The complicating factor is that I want to do it on structures of different amino acid sequences, to fit on the backbone and all relevent atoms, and give an rmsd based on this. I have tried XPLOR but it seems to insist the molecules are identical. I would also like to have the backbone rmsd printed out on a residue-by-residue basis. I can if necessary write a script to extract the relevant coordinates from the pdb files. I appreciate any help anyone may be able to give me. Thanks Mike Smith From C1790@SLVAXA.UMSL.EDU Wed Jun 29 12:04:12 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.9/930601.1506) id LAA10828; Wed, 29 Jun 1994 11:20:16 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HE409K4HW08ZDV7I@SLVAXA.UMSL.EDU>; Wed, 29 Jun 1994 10:21:24 CST Date: Wed, 29 Jun 1994 10:21:23 -0600 (CST) From: BILL WELSH Subject: OPEN POSTDOCTORAL POSITION To: chemistry@ccl.net Message-id: <01HE409K5ATE8ZDV7I@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 I would like to post an opening in my lab for a Postdoctoral Research Fellow in the application of computational neural networks to analytical/pharmaceutical chemistry. Salary is $25,000+ plus full benefits for first year with possible extension to a 2nd year. This is a part of a large FDA-funded project to create a National Drug Database containing "scientific fingerprints" of all over-the-counter and prescription drugs sold in the USA. A related project involves the molecular simulation of chromatographic separations. Some expertise in chemometrics and neural networks is required, but experience in computational chemistry, commercial molecular-modeling software, unix-based and PC-based operating systems, and QSAR/COMFA methods is desirable. Position requires good oral/written communication skills and is open immediately. Applications will be accepted until position is filled. I expect that the postion will be filled very soon, so please do not hesitate if interested. Please mail or fax (314-553-5342) your CV including list of publications and research experience, along with at least one letter of reference, to Prof. Wiliam Welsh, Dept. of Chemistry, University of Missouri-St. Louis, 8001 Natural Bridge Rd., St. Louis, MO 63121. My office phone number is 314-553- 5318. The University of Missouri-St. Louis is an AA/EOE employer committed to excellence through diversity. From brian@bert.chem.wsu.edu Wed Jun 29 13:04:13 1994 Received: from serval.net.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.6.9/930601.1506) id MAA11669; Wed, 29 Jun 1994 12:09:09 -0400 Received: by serval.net.wsu.edu; id AA04417; Wed, 29 Jun 1994 09:09:04 -0700 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA20607; Wed, 29 Jun 1994 09:09:27 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9406291609.AA20607@bert.chem.wsu.edu> Subject: Re: CCL:rmsds between different structures. To: mikes@bioch.ox.ac.uk Date: Wed, 29 Jun 1994 09:09:27 -0800 (PDT) Cc: CHEMISTRY@ccl.net In-Reply-To: <9406291427.AA16532@nmrpcd.ocms.ocms.ox.ac.uk> from "mikes@bioch.ox.ac.uk" at Jun 29, 94 03:27:19 pm X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1658 mikes@bioch.ox.ac.uk wrote: : : Dear All, : : I am looking for a software package which will enable me to : least-squares-fit and find the rmsds between two structures. The : complicating factor is that I want to do it on structures of different : amino acid sequences, to fit on the backbone and all relevent atoms, and : give an rmsd based on this. : : I have tried XPLOR but it seems to insist the molecules are : identical. I would also like to have the backbone rmsd printed out on a : residue-by-residue basis. : : I can if necessary write a script to extract the relevant coordinates from : the pdb files. : : I appreciate any help anyone may be able to give me. : : Thanks : : Mike Smith Mike: I've run into the same problem with the proteins I work with. Since you seem to be primarily interested in the backbone RMSD (as I was), then why don't you edit out all the side chains (i.e. make all the side chains =GLY). If you have access to QUANTA, it will align non-identical structures. -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | ||--------------------| INTERNET brian@bert.chem.wsu.edu | || \\ WSU || Biochem/Biophysics | BITNET F0388913@WSUVMS1 | |\ - *|| WSU , 261 Fulmer | DECNET JAGUAR::F0388913 | | | || Pullman, WA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From rhanselm@acs.ucalgary.ca Wed Jun 29 17:04:15 1994 Received: from acs7.acs.ucalgary.ca for rhanselm@acs.ucalgary.ca by www.ccl.net (8.6.9/930601.1506) id QAA14635; Wed, 29 Jun 1994 16:22:48 -0400 From: Received: from acs6.acs.ucalgary.ca by acs7.acs.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA22822; Wed, 29 Jun 1994 14:25:51 -0600 Received: by acs6.acs.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA55064; Wed, 29 Jun 1994 14:25:51 -0600 Date: Wed, 29 Jun 1994 14:25:51 -0600 Message-Id: <9406292025.AA55064@acs6.acs.ucalgary.ca> To: chemistry@ccl.net Subject: Re: MSDS >To all, >Does anyone know how to access/obtain Material Safety Data Sheets(MSDS) to >obtain info on the safe handling of chemicals/or any equivalent >information? If so can you please send the info >ad219@leo.nmc.edu >Thanks much. >Karl Jalkanen Dear Karl, You can obtain MSDS sheets very easily through the University of Utha gopher. Just follow the following hierarchy: -> University of Utah 3. Academic Organizations/ 2. Chemistry/ 8. Material Safety Data Sheets/ Cheers Roger From flbdsilv@fox.cce.usp.br Wed Jun 29 20:04:18 1994 Received: from bee08.uspnet.usp.br for flbdsilv@fox.cce.usp.br by www.ccl.net (8.6.9/930601.1506) id TAA16250; Wed, 29 Jun 1994 19:19:26 -0400 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee08.uspnet.usp.br (8.6.8.1/RISC-CCE2.0) id UAA33296 Received: from localhost (flbdsilv@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id UAA22366 Date: Wed, 29 Jun 1994 20:12:10 -0300 (BDT) From: Fernando Luis Barroso da Silva Subject: Molecular Modeling - Brazil - 1994 To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +---------------------------------------+ | | | 2nd. CONFERENCE ON MOLECULAR MODELING | | | +---------------------------------------+ october 26-28, 1994 Rio de Janeiro, BRAZIL First Announcement ORGANIZER Mar