From Gerald.Loeffler@univie.ac.at Thu Jun 12 07:04:38 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id GAA20171; Thu, 12 Jun 1997 06:36:56 -0400 (EDT) Received: from gerilap.imp.univie.ac.at (gerilap.imp.univie.ac.at [131.130.80.125]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id MAA11650 for ; Thu, 12 Jun 1997 12:36:55 +0200 Message-ID: <339FD0DC.4043@univie.ac.at> Date: Thu, 12 Jun 1997 12:35:08 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@univie.ac.at Organization: I.M.P. X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: Computational Chemistry List Subject: Removing Translation and Rotation after MD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings! I would very much appreciate your comments to the following problem: I need to remove the translational and rotational motion of a protein after a Molecular Dynamics simulation. I know, this is a seemingly trivial problem. A) Up to now I didn't care much about the details and just fitted all protein structures along the MD trajectory to the start structure such that the C-alpha atoms are optimally (i.e., minimal root-mean-square deviation) superimposed (e.g. using the excellent profit program). B) However, it may be that for my current problem the other alternative that came to my mind would be better suited, namely 1) removing translation by superimposing the centers of gravity of all structures and subsequently 2) removing rotation by superimposing the "principal axes of inertia" of all structures. Firstly, I'm not sure if the terminology of B)2) is correct. Secondly, I'm missing the formulas to do B)1) and B)2). Thridly, I'd like to know if there are cases where either method A) or method B) are definitely prefered. Fourthly, it may be that there are other methods of removing translation and rotation?! Fifthly, which free program implements method B) or other intersting methods? As always, I thank you very much in advance for your help, and I will summarize to the list if there is some interest in that. Cheers, gerald -- Gerald Loeffler PostDoc in Theoretical Biochemistry EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From ccl@www.ccl.net Thu Jun 12 10:48:28 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA21524; Thu, 12 Jun 1997 10:35:30 -0400 (EDT) Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA02080; Thu, 12 Jun 1997 10:35:31 -0400 (EDT) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id KAA38881 for ; Thu, 12 Jun 1997 10:35:31 -0400 Sender: richard@TC.Cornell.EDU Message-ID: <33A00933.5E65@tc.cornell.edu> Date: Thu, 12 Jun 1997 10:35:31 -0400 From: Richard Gillilan X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:more on animation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Since there has been recent interest in animation, I thought I'd throw in my 2c. We do quite a lot of general scientific animation here at the Cornell Theory Center. Our main tool is IBM Visualization Data Explorer (DX). I've written a few molecular graphics modules which create most of the constructs I need for biomolecular systems. Because DX is so general, it's not as easy to work with as a dedicated application program like VMD. Generality can be an advantage when you need to do unusual things like have a point moving on a colored potential energy surface while a corresponding molecular model changes its conformation. A video Paul Bash and I are about to finish has a ball-and-stick model, ribbon, electron density surfaces and a point on P.E. curve all moving while a photon excites the works to a higher state. DX, AVS and similar packages are good for this kind of thing. We use RenderMan to do high-quality rendering and special effects when needed. Anyone who already has DX can download these modules (no cost). http://www.tc.cornell.edu/Visualization/Staff/richard/CM/CM.html Art Olson's group at Scripps may also have some tools like this for AVS http://www.scripps.edu/pub/olson-web/ Also, I should mention VPLA, the Visual Programming Language for Animation. This was written by Wayne Lytle, a former staff member here and is also available at no cost: http://www.tc.cornell.edu/Visualization/Software/VPLA/ It is a VERY nice alternative to SoftImage, Alias and other unaffordable professional animation programs. I use it whenever I need nice choreography and special effects in a scene: like swimming bacteria with bumps and moving cilia and flagella or fly-though scenes with fancy camera angles and special lighting (like underwater). Richard Gillilan Cornell Theory Center http://www.tc.cornell.edu/~richard/ From ccl@www.ccl.net Thu Jun 12 14:48:29 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA23605; Thu, 12 Jun 1997 14:46:36 -0400 (EDT) Received: from po6.andrew.cmu.edu for hpaik+@andrew.cmu.edu by bedrock.ccl.net (8.8.3/950822.1) id OAA09221; Thu, 12 Jun 1997 14:46:35 -0400 (EDT) Received: (from postman@localhost) by po6.andrew.cmu.edu (8.8.2/8.8.2) id OAA04441 for CHEMISTRY@ccl.net; Thu, 12 Jun 1997 14:46:31 -0400 Received: via switchmail; Thu, 12 Jun 1997 14:46:29 -0400 (EDT) Received: from pcs35.andrew.cmu.edu via qmail ID ; Thu, 12 Jun 1997 14:45:50 -0400 (EDT) Received: from pcs35.andrew.cmu.edu via qmail ID ; Thu, 12 Jun 1997 14:45:49 -0400 (EDT) Received: from mms.4.170.Jun.27.1996.16.34.50.sun4.51.MacMail.5.2.CUILIB.3.45.SNAP.NOT.LINKED.pcs35.andrew.cmu.edu.sun4m.54 via MS.5.6.pcs35.andrew.cmu.edu.sun4_51; Thu, 12 Jun 1997 14:45:49 -0400 (EDT) Message-ID: <4nc4DRW00iWU058l40@andrew.cmu.edu> Date: Thu, 12 Jun 1997 14:45:49 -0400 (EDT) From: Hyun-Jong Paik To: CHEMISTRY@ccl.net Subject: Thermal Radical Initiator Hi, I need your help. I need spcecil thermal initiator for my research. I don't have exact sturcture in mind. I'd like to take a look at the catalogues of companies which provide special initiator. Could you recommend the companies? Thanks in advance. From polymer@rmit.EDU.AU Thu Jun 12 18:48:30 1997 Received: from rmit.EDU.AU for polymer@rmit.EDU.AU by www.ccl.net (8.8.3/950822.1) id SAA25116; Thu, 12 Jun 1997 18:34:01 -0400 (EDT) Received: from bunyip.ph.rmit.edu.au (bunyip.ph.rmit.EDU.AU [131.170.94.250]) by rmit.EDU.AU (8.8.5/8.7.3/voga/ram2) with ESMTP id IAA29797 for ; Fri, 13 Jun 1997 08:33:23 +1000 (EST) Received: from BUNYIP/SpoolDir by bunyip.ph.rmit.edu.au (Mercury 1.21); 13 Jun 97 08:34:12 +1000 Received: from SpoolDir by BUNYIP (Mercury 1.21); 13 Jun 97 08:33:46 +1000 From: "Prof. Robert Shanks" Organization: RMIT Applied Physics To: chemistry@www.ccl.net Date: Fri, 13 Jun 1997 8:34:01 EST-10ESUT Subject: CCL:Molecular modeling software for non-theorists? Reply-to: ShanksRA@rmit.EDU.AU Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.0, wide beta 6) Message-ID: <14F7D709BE@bunyip.ph.rmit.edu.au> To: Julius Su Molecular modeling software for non-theorists? We use: Chem3D (Macintosh) Hyperchem (MS Windows) CAChe (Macintosh) MSI Insight II Polymer (Silicon Graphics) Unichem (Silicon Graphics interface, Cray computations) I can reiterate your experience with Chem3D, in fact the Chem Office programs are well integrated and offer full scripting and web interaction. Hyperchem is similar, but a stand alone modelling program. It has more display facility than Chem3D in that it can display orbitals. It can also compute vibrational modes. It has similar ease of use to Chem3D. CAChe has more extensive computations than either of the above and it is property based. On the Macintosh it has an automatic spreadsheet type entry system (Project Leader) for molecules and properties - once this has been setup the program will automatically move through all the properties desired for each molecule and place the values in the cells. It has some QSPR type computations in addition to the quantum mechanical and molecular mechanics methods. MSI Insight we use onlt for polymers. It is a research tool which is not in the same category as the above programs. Unichem is a quantum mechanics program. It is only difficult to use in that it requires links with a Cray Supercomputer. Sincerely Robert Shanks From: jsu@ugcs.caltech.edu (Julius Su) Subject: CCL:Molecular modeling software for non-theorists? To: chemistry@www.ccl.net Date: Mon, 9 Jun 1997 21:40:42 -0700 (PDT) Hello, I work for a research group that uses laser spectroscopy to investigate the basic dynamics of chemical systems on a short time scale. Some members of our group have done fairly high level ab initio and molecular dynamics simulations in the past; however, the main focus of the group has definitely been experimental. Because of this, there has been no standard way to model chemical systems in our group. Individuals in the group have either written their own molecular dynamics routines or have had access to facilities where programs like Gaussian 92 could be run, but no convenient in-group facility to do simple molecular modeling has existed. We are currently seeking to change this. We would like to have some standard way of finding the geometries of small to medium molecules at a reasonable level of theory (semiemperical would be fine) and for doing molecular dynamics of photoexcited systems. This system would have to be accessible and easy enough to use that any experimentalist that wished to carry out an experiment would be able to quickly throw together a rough simulation of the system in question. Our group plans to purchase two fairly high end PCs to run the software that would be needed to do this. I have recently purchased a copy of Chem3D Pro with MOPAC for my personal use, and have found the interface for molecule building and geometry optimization to be intuitive and easy to use. We also have some simple code that was written within the group to do molecular dynamics on small clusters of rigid molecules. This code can be easily interfaced with Chem3D. Alternatively, we have found information on the Web about HyperChem, which appears to have the ability to do model building, geometry optimization, and a feature that would be especially useful to us, reactive molecular dynamics. It also appears to have facilities built in to visualize vibrational modes and molecular oribtals (althought the latter feature would not be nearly as important.) Since our group already has a copy of Gaussian 94, the added ab initio capabilities of the program are nice but not essential. The main concern at this point, however, is how easy HyperChem would be to use. Chem3D has impressed us with its intuitive interface and its tight integration with ChemDraw. We have not been able to find a demo of version of HyperChem with enabled building facilities to compare. Since 90% of the time will probably be spent doing simple model building and geometry optimization, this is particularly important to us. So, has anyone on this list had experience with HyperChem and Chem3D? How easy is it to build molecules in HyperChem? Does it have a reasonably useable interface? Can it generate publication quality graphics? Can experimentalists who don't want to spend too much time learning the nitty-gritty of semiemperical theory do simple calculations using it? Thank you very much for your help. Later, Julius Su jsu@cco.caltech.edu --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --- __________________________________ Prof. Robert A. Shanks Professor of Polymer Science Department of Applied Chemistry Royal Melbourne Institute of Technology Box 2476V GPO Melbourne Victoria 3001 Australia Telephone and Fax +61 3 6602122 Mobile Telephone +61 041 935 8001 WWW RMIT Polymer Science Page: http://www.rmit.edu.au/departments/cm/polymer/index.html __________________________________ From churca@opium.q1.fcen.uba.ar Thu Jun 12 19:48:32 1997 Received: from opium.q1.fcen.uba.ar for churca@opium.q1.fcen.uba.ar by www.ccl.net (8.8.3/950822.1) id TAA25240; Thu, 12 Jun 1997 19:21:28 -0400 (EDT) Received: from localhost (churca@localhost) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id UAA12102; Thu, 12 Jun 1997 20:10:30 -0300 Date: Thu, 12 Jun 1997 20:10:30 -0300 (ARST) From: Ojitos To: Andy Holder cc: chemistry@www.ccl.net Subject: Re: CCL:Qsar programs In-Reply-To: <9706111530.AA40193@134.193.11.2> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Thanks everybody for the help about QSAR program. It was really helpful to get all this information, i will try to make a resume and send it. Thanks, again Adrian Adrian Turjanski churca@q1.fcen.uba.ar