From Robert.Franke@ruhr-uni-bochum.de Tue Apr 7 09:22:51 1998 Received: from sunu450.rz.ruhr-uni-bochum.de for Robert.Franke@ruhr-uni-bochum.de by www.ccl.net (8.8.3/950822.1) id IAA02024; Tue, 7 Apr 1998 08:30:50 -0400 (EDT) From: Received: (qmail 26332 invoked from network); 7 Apr 1998 12:30:38 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.222.1) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 7 Apr 1998 12:30:38 -0000 Received: (qmail 10215 invoked by uid 10796); 7 Apr 1998 12:30:38 -0000 Date: Tue, 7 Apr 1998 14:30:38 +0200 (MSZ) To: ccl Subject: c++ class for linear algebra Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's, I would like to know if anyone has a source for a powerfull c++ class concerning linear algebra features like matrix multiplication etc. I will summarize for the net. Thanks in anticipation, your's robert /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ /\ /\ /\ Robert Franke /\ /\ Fakultaet fuer Chemie /\ /\ Lehrstuhl fuer Theoretische Chemie /\ /\ Ruhr-Universitaet Bochum /\ /\ D-44780 Bochum /\ /\ Phone: 049-234-7006751 or /\ /\ 049-234-7005294 /\ /\ Fax: 049-234-7094109 /\ /\ email: robert.franke@rz.ruhr-uni-bochum.de /\ /\ /\ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ From eugene@liposome.genebee.msu.su Tue Apr 7 11:22:59 1998 Received: from liposome.genebee.msu.su for eugene@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id KAA02678; Tue, 7 Apr 1998 10:41:47 -0400 (EDT) Received: (from eugene@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id SAA14249; Tue, 7 Apr 1998 18:41:46 +0400 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Date: Tue, 7 Apr 1998 18:41:45 +0400 (MSD) To: chemistry@www.ccl.net Subject: FYI:progress in water modelling (from SG News Day 4.6.98) In-Reply-To: <199804061702.VAA12150@liposome.genebee.msu.su> References: <199804061702.VAA12150@liposome.genebee.msu.su> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13610.14974.882923.607440@liposome.genebee.msu.su> rgeorgan writes: THE SCIENCE GUIDE DAILY NEWS UPDATE The Science News from 12:25 PM EST; Monday, April 06, 1998 [...] PHYSICS, ASTRONOMY & ASTROPHYSICS, SPACE, AERONAUTICS, AND AEROSPACE **** Why Is Ice So Slippery? Mysteries Of The "Invisible" Ice Surface - EurekAlert http://www.scienceguide.com/News/News_Articles/4698Article_3.html Physicists from the Max Planck Institute for Fluid Dynamics in G=F6ttingen have determined the molecular structure and vibrations of=20= the topmost layer of ice crystals. Their experiments provide the first=20= direct evidence for an unusual softness of the ice surface, as reported in Physical Review Letters [80, 2638 (1998)] [...] From mkh100@york.ac.uk Tue Apr 7 11:33:53 1998 Received: from pump2.york.ac.uk for mkh100@york.ac.uk by www.ccl.net (8.8.3/950822.1) id LAA02769; Tue, 7 Apr 1998 11:06:08 -0400 (EDT) Received: from ebor.york.ac.uk (mkh100@ebor.york.ac.uk [144.32.129.242]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id QAA28324 for ; Tue, 7 Apr 1998 16:05:48 +0100 (BST) Date: Tue, 7 Apr 1998 16:05:48 +0100 (BST) From: Michael Hodgson To: CCL Subject: Radial Plots of DNA torsion angles Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi... I am looking for a cheap/free program to compute the backbone torsion angles of a short oligonucletide, so I can plot them as a radial distribution. Does anyone know of any software (any OS) that will perform this task? Many thanks in advance. -Michael <\ ***** -==============+XXX) *****--------------------------------------- Michael Hodgson Protein Structure Group University of York, www : www.yorvic.york.ac.uk/~hodgson Heslington, YORK, YO1 5DD Those who live by the sword get shot by those who don't ----------------------------------------------------------------------***** From mattacf@mcmail.CIS.McMaster.CA Tue Apr 7 20:22:59 1998 Received: from mcmail.CIS.McMaster.CA for mattacf@mcmail.CIS.McMaster.CA by www.ccl.net (8.8.3/950822.1) id TAA06612; Tue, 7 Apr 1998 19:39:30 -0400 (EDT) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.5/8.8.5) with SMTP id TAA00702 for ; Tue, 7 Apr 1998 19:39:29 -0400 (EDT) Date: Tue, 7 Apr 1998 19:39:29 -0400 (EDT) From: "C.F. Matta" To: CCL Subject: Re: CCL:Radial Plots of DNA torsion angles Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Hodgson I think I have exactly what you need. I prepared a LOTUS123 spreadsheet program that could handle polypeptides of as many as 8100 atoms. The input is the coordinates in PDB format. The program then computes backbone bond angles, distances and ALL sorts of dihedrals that you may require (not only the usual phi, psi, and omega). Along a properly labeled list of dihedral, you get the number of residues per turn, the height in A of each turn, the delta (twist) angle (twist between each residue as you look along the axis of the polypeptide, the N and t parameters. In addition, if you input the helix type (e.g. 3-10 helix, pi-helix, etc.) it will provide you with a list of hydrogen bond distances and angles along the backbone. The program can also compute the full distance matrix for peptides that are smaller than 250 atoms (but can be modified for larger ons up to 8100). After each calculation, it will automatically provide you with a labelled Ramachandran plot as well as averages of all the computed parameters. All what you need is to input the pdb info and familiarize yourself with the package. For the latter purpose, it comes with some test data. System requirement: any PC with any version of LOTUS123 Version 4 (or later) running under Windows. (This program is totally free of charge. I take no responsibility for any outcome of its use). Cheers. Cherif Matta Graduate Student Chemistry Department McMaster University Hamilton, Ontario Canada, L8S 4M1 From mattacf@mcmail.CIS.McMaster.CA Tue Apr 7 20:41:20 1998 Received: from mcmail.CIS.McMaster.CA for mattacf@mcmail.CIS.McMaster.CA by www.ccl.net (8.8.3/950822.1) id TAA06597; Tue, 7 Apr 1998 19:35:11 -0400 (EDT) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.5/8.8.5) with SMTP id TAA29904; Tue, 7 Apr 1998 19:35:05 -0400 (EDT) Date: Tue, 7 Apr 1998 19:35:05 -0400 (EDT) From: "C.F. Matta" To: Michael Hodgson cc: CCL Subject: Re: CCL:Radial Plots of DNA torsion angles In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Hodgson I think I have exactly what you need. I prepared a LOTUS123 spreadsheet program that could handle polypeptides of as many as 8100 atoms. The input is the coordinates in PDB format. The program then computes backbone bond angles, distances and ALL sorts of dihedrals that you may require (not only the usual phi, psi, and omega). Along a properly labeled list of dihedral, you get the number of residues per turn, the height in A of each turn, the delta (twist) angle (twist between each residue as you look along the axis of the polypeptide, the N and t parameters. In addition, if you input the helix type (e.g. 3-10 helix, pi-helix, etc.) it will provide you with a list of hydrogen bond distances and angles along the backbone. The program can also compute the full distance matrix for peptides that are smaller than 250 atoms (but can be modified for larger ons up to 8100). After each calculation, it will automatically provide you with a labelled Ramachandran plot as well as averages of all the computed parameters. All what you need is to input the pdb info and familiarize yourself with the package. For the latter purpose, it comes with some test data. System requirement: any PC with any version of LOTUS123 Version 4 (or later) running under Windows. (This program is totally free of charge. I take no responsibility for any outcome of its use). Cheers. Cherif Matta Graduate Student Chemistry Department McMaster University Hamilton, Ontario Canada, L8S 4M1