From wolpert@neon.chem.utk.edu Mon Sep 20 06:11:01 1993 Date: Mon, 20 Sep 93 13:11:01 PDT From: wolpert@neon.chem.utk.edu (Edward Wolpert) Message-Id: <9309202011.AA21868@neon.chem.utk.edu> To: CHEMISTRY@ccl.net Subject: MM3 useful for Sugars? (The following letter is forwarded to the list by me. Please send replies to me, and I will re-direct them. Thanks.) -------------- Netters- Is MM3 useful to describe properly the anomeric effect in sugars? Are there better programs out there to describe this effect? We would like to know before we spend the money and time getting the program. Thanks for your help. -E. Gakh --------------- Forward by: E.G. Wolpert wolpert@neon.chem.utk.edu From mwitten@hermes.chpc.utexas.edu Mon Sep 20 12:35:00 1993 From: mwitten@hermes.chpc.utexas.edu Message-Id: <9309202235.AA14933@morpheus.chpc.utexas.edu> Subject: WORLD CONGRESS ANNOUNCEMENT To: CHEMISTRY@ccl.net Date: Mon, 20 Sep 93 17:35:00 CDT FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE, PUBLIC HEALTH AND BIOTECHNOLOGY 24-28 April 1994 Hyatt Regency Hotel Austin, Texas ----- (Feel Free To Cross Post This Announcement) ---- 1.0 CONFERENCE OVERVIEW: With increasing frequency, computational sciences are being exploited as a means with which to investigate biomedical processes at all levels of complexity; from molecular to systemic to demographic. Computational instruments are now used, not only as exploratory tools but also as diagnostic and prognostic tools. The appearance of high performance computing environments has, to a great extent, removed the problem of increasing the biological reality of the mathematical models. For the first time in the history of the field, practical biological reality is finally within the grasp of the biomedical modeler. Mathematical complexity is no longer as serious an issue as speeds of computation are now of the order necessary to allow extremely large and complex computational models to be analyzed. Large memory machines are now routinely available. Additionally, high speed, efficient, highly optimized numerical algorithms are under constant development. As these algorithms are understood and improved upon, many of them are transferred from software implementation to an implementation in the hardware itself; thereby further enhancing the available computational speed of current hardware. The purpose of this congress is to bring together a transdisciplinary group of researchers in medicine, public health, computer science, mathematics, nursing, veterinary medicine, ecology, allied health, as well as numerous other disciplines, for the purposes of examining the grand challenge problems of the next decades. This will be a definitive meeting in that it will be the first World Congress of its type and will be held as a follow-up to the very well received Workshop On High Performance Computing In The Life Sciences and Medicine held by the University of Texas System Center For High Performance Computing in 1990. Young scientists (graduate students, postdocs, etc.) are encouraged to attend and to present their work in this increasingly interesting discipline. Funding is being solicited from NSF, NIH, DOE, Darpa, EPA, and private foundations, as well as other sources to assist in travel support and in the offsetting of expenses for those unable to attend otherwise. Papers, poster presentations, tutorials, focused topic workshops, birds of a feather groups, demonstrations, and other suggestions are also solicited. 2.0 CONFERENCE SCOPE AND TOPIC AREAS: The Congress has a broad scope. If you are not sure whether or not your subject fits the Congress scope, contact the conference organizers at one of the addresses below. Subject areas include but are not limited to: *Visualization/Sonification --- medical imaging --- molecular visualization as a clinical research tool --- simulation visualization --- microscopy --- visualization as applied to problems arising in computational molecular biology and genetics or other non-traditional disciplines --- telemedicine *Computational Molecular Biology and Genetics --- computational ramifications of clinical needs in the Human Genome, Plant Genome, and Animal Genome Projects --- computational and grand challenge problems in molecular biology and genetics --- algorithms and methodologies --- issues of multiple datatype databases *Computational Pharmacology, Pharmacodynamics, Drug Design *Computational Chemistry as Applied to Clinical Issues *Computational Cell Biology, Physiology, and Metabolism --- Single cell metabolic models (red blood cell) --- Cancer models --- Transport models --- Single cell interaction with external factors models (laser, ultrasound, electrical stimulus) *Computational Physiology and Metabolism --- Renal System --- Cardiovascular dynamics --- Liver function --- Pulmonary dynamics --- Auditory function, coclear dynamics, hearing --- Reproductive modeling: ovarian dynamics, reproductive ecotoxicology, modeling the hormonal cycle --- Metabolic Databases and metabolic models *Computational Demography, Epidemiology, and Statistics/Biostatistics --- Classical demographic, epidemiologic, and biostatistical modeling --- Modeling of the role of culture, poverty, and other sociological issues as they impact healthcare --- Morphometrics *Computational Disease Modeling --- AIDS --- TB --- Influenza --- Statistical Population Genetics Of Disease Processes --- Other *Computational Biofluids --- Blood flow --- Sperm dynamics --- Modeling of arteriosclerosis and related processes *Computational Dentistry, Orthodontics, and Prosthetics *Computational Veterinary Medicine --- Computational issues in modeling non-human dynamics such as equine, feline, canine dynamics (physiological/biomechanical) *Computational Allied Health Sciences --- Physical Therapy --- Neuromusic Therapy --- Respiratory Therapy *Computational Radiology --- Dose modeling --- Treatment planning *Computational Surgery --- Simulation of surgical procedures in VR worlds --- Surgical simulation as a precursor to surgical intervention --- The Visible Human *Computational Cardiology *Computational Nursing *Computational Models In Chiropractice *Computational Neurobiology and Neurophysiology --- Brain modeling --- Single neuron models --- Neural nets and clinical applications --- Neurophysiological dynamics --- Neurotransmitter modeling --- Neurological disorder modeling (Alzheimer's Disease, for example) --- The Human Brain Project *Computational Models of Psychiatric and Psychological Processes *Computational Biomechanics --- Bone Modeling --- Joint Modeling *Computational Models of Non-traditional Medicine --- Acupuncture --- Other *Computational Issues In Medical Instrumentation Design and Simulation --- Scanner Design --- Optical Instrumentation *Ethical issues arising in the use of computational technology in medical diagnosis and simulation *The role of alternate reality methodologies and high performance environments in the medical and public health disciplines *Issues in the use of high performance computing environments in the teaching of health science curricula *The role of high performance environments for the handling of large medical datasets (high performance storage environments, high performance networking, high performance medical records manipulation and management, metadata structures and definitions) *Federal and private support for transdisciplinary research in computational medicine and public health 3.0 CONFERENCE COMMITTEE *CONFERENCE CHAIR: Matthew Witten, UT System Center For High Performance Computing, Austin, Texas m.witten@chpc.utexas.edu *CURRENT CONFERENCE DIRECTORATE: Regina Monaco, Mt. Sinai Medical Center Dan Davison, University of Houston Chris Johnson, University of Utah Lisa Fauci, Tulane University Daniel Zelterman, University of Minnesota Minneapolis James Hyman, Los Alamos National Laboratory Richard Hart, Tulane University Dennis Duke, SCRI-Florida State University Sharon Meintz, University of Nevada Los Vegas Dean Sittig, Vanderbilt University Dick Tsur, UT System CHPC Dan Deerfield, Pittsburgh Supercomputing Center Istvan Gyori, University of Veszprem (Hungary) Don Fussell, University of Texas at Austin Ken Goodman, University Of Miami School of Medicine Martin Hugh-Jones, Louisiana State University Stuart Zimmerman, MD Anderson Cancer Research Center John Wooley, DOE Sylvia Spengler, University of California Berkeley Robert Blystone, Trinity University Gregory Kramer, Santa Fe Institute Franco Celada, NYU Medical Center David Robinson, NIH, NHLBI Jane Preson, MCC Peter Petropoulos, Brooks Air Force Base Marcus Pandy, University of Texas at Austin George Bekey, University of Southern California Stephen Koslow, NIH, NIMH Fred Bookstein, University of Michigan Ann Arbor Dan Levine, University of Texas at Arlington Richard Gordon, University of Manitoba (Canada) Stan Zeitz, Drexel University Marcia McClure, University of Nevada Las Vegas Renato Sabbatini, UNICAMP/Brazil (Brazil) Hiroshi Tanaka, Tokyo Medical and Dental University (Japan) Shusaku Tsumoto, Tokyo Medical and Dental University (Japan) Additional conference directorate members are being added and will be updated on the anonymous ftp list as they agree. 4.0 CONTACTING THE CONFERENCE COMMITTEE: To contact the congress organizers for any reason use any of the following pathways: ELECTRONIC MAIL - compmed94@chpc.utexas.edu FAX (USA) - (512) 471-2445 PHONE (USA) - (512) 471-2472 GOPHER: log into the University of Texas System-CHPC select the Computational Medicine and Allied Health menu choice ANONYMOUS FTP: ftp.chpc.utexas.edu cd /pub/compmed94 POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 5.0 SUBMISSION PROCEDURES: Authors must submit 5 copies of a single-page 50-100 word abstract clearly discussing the topic of their presentation. In addition, authors must clearly state their choice of poster, contributed paper, tutorial, exhibit, focused workshop or birds of a feather group along with a discussion of their presentation. Abstracts will be published as part of the preliminary conference material. To notify the congress organizing committee that you would like to participate and to be put on the congress mailing list, please fill out and return the form that follows this announcement. You may use any of the contact methods above. If you wish to organize a contributed paper session, tutorial session, focused workshop, or birds of a feather group, please contact the conference director at mwitten@chpc.utexas.edu . The abstract may be submitted electronically to compmed94@chpc.utexas.edu or by mail or fax. There is no official format. 6.0 CONFERENCE DEADLINES AND FEES: The following deadlines should be noted: 1 November 1993 - Notification of intent to organize a special session 15 December 1993 - Abstracts for talks/posters/ workshops/birds of a feather sessions/demonstrations 15 January 1994 - Notification of acceptance of abstract 15 February 1994 - Application for financial aid 1 April 1994 - Registration deadline (includes payment of all fees) Fees include lunches for three days, all conference registration materials, the reception, and the sit down banquet: $400.00 Corporate $250.00 Academic $150.00 Student Students are required to submit verification of student status. The verification of academic status form appears appended to the registration form in this announcement. Because financial aid may be available for minority students, faculty, and for individuals from declared minority institutions, you may indicate that you are requesting financial aid as a minority individual. Additionally, we anticipate some support for women to attend. Application for financial aid is also appended to the attached form. 7.0 CONFERENCE PRELIMINARY DETAILS AND ENVIRONMENT LOCATION: Hyatt Regency Hotel, Austin, Texas, USA DATES: 24-28 April 1994 The 1st World Congress On Computational Medicine, Public Health, and Biotechnology will be held at the Hyatt Regency Hotel, Austin, Texas located in downtown Austin on the shores of Town Lake, also known as the Colorado River. The Hyatt Regency has rooms available for the conference participants at a special rate of $79.00/night for single or double occupancy, with a hotel tax of 13%. The Hyatt accepts American Express, Diner's Club, Visa, MasterCard, Carte Blanche, and Discover credit cards. This room rate will be in effect until 9 April 1994 or until the block of rooms is full. We recommend that you make your reservations as soon as possible. You may make your reservations by calling (512) 477-1234 or by returning the enclosed reservation form. Be certain to mention that you are attending the First World Congress On Computational Medicine, Public Health, and Biotechnology if you make your reservations by telephone. The hotel is approximately, five miles (15 minutes >from Robert Mueller Airport). The Hyatt offers courtesy limousine service to and from the airport between the hours of 6:00am and 11:00pm. You may call them from the airport when you arrive. If you choose to use a taxi, expect to pay approximately $8.00. Automobiles may be rented, at the airport, from most of the major car rental agencies. However, because of the downtown location of the Congress and access to taxis and to bus service, we do not recommend that you rent an auto unless you are planning to drive outside of the city. Should you not be able to find an available room at the Hyatt Regency, we have scheduled an "overflow" hotel, the Embassy Suites, which is located directly across the street from the Hyatt Regency. If, due to travel expense restrictions, you are unable to stay at either of these two hotels, please contact the conference board directly and we will be more than happy to find a hotel near the conference site that should accommodate your needs. Austin, the state capital, is renowned for its natural hill-country beauty and an active cultural scene. Several hiking and jogging trails are within walking distance of the hotel, as well as opportunities for a variety of aquatic sports. From the Hyatt, you can "Catch a Dillo" downtown, taking a ride on our delightful inner-city, rubber-wheeled trolley system. In Austin's historic downtown area, you can take a free guided tour through the State Capitol Building, constructed in 1888. Or, you can visit the Governor's Mansion, recognized as one of the finest examples of 19th Century Greek Revival architecture and housing every Texas governor since 1856. Downtown you will find the Old Bakery and Emporium, built by Swedish immigrant Charles Lundberg in 1876 and the Sixth Street/Old Pecan Street Historical District - a seven-block renovation of Victorian and native stone buildings, now a National Registered Historic District containing more than 60 restaurants, clubs, and shops to enjoy. The Laguna Gloria Art Museum, the Archer M. Huntington Art Gallery, the LBJ Library and Museum, the Neill-Cochran Museum House, and the Texas Memorial Museum are among Austin's finest museums. The Umlauf Sculpture Garden, has become a major artistic attraction. Charles Umlauf's sculptured works are placed in a variety of elegant settings under a canopy of trees. The Zilker Gardens contains many botanical highlights such as the Rose Garden, Oriental Garden, Garden of the Blind, Water Garden and more. Unique to Austin is a large population of Mexican free-tailed bats which resides beneath the Congress Avenue Bridge. During the month of April, the Highland Lakes Bluebonnet Trail celebrates spring's wildflowers (a major attraction) as this self-guided tour winds through the surrounding region of Austin and nearby towns (you will need to rent a car for this one). Austin offers a number of indoor shopping malls in every part of the city; The Arboretum, Barton Creek Square, Dobie Mall, and Highland Mall, to name a few. Capital Metro, Austin's mass transit system, offers low cost transportation throughout Austin. Specialty shops, offering a wide variety of handmade crafts and merchandise crafted by native Texans, are scattered throughout the city and surrounding areas. Dining out in Austin, you will have choices of American, Chinese, Authentic Mexican, Tex-Mex, Italian, Japanese, or nearly any other type of cuisine you might wish to experience, with price ranges that will suit anyone's budget. Live bands perform in various nightclubs around the city and at night spots along Sixth Street, offering a range of jazz, blues, country/Western, reggae, swing, and rock music. Day temperatures will be in the 80-90(degrees F) range and fairly humid. Evening temperatures have been known to drop down into the 50's (degrees F). Cold weather is not expected so be sure to bring lightweight clothing with you. Congress exhibitor and vendor presentations are also being planned. 8.0 CONFERENCE ENDORSEMENTS AND SPONSORSHIPS: Numerous potential academic sponsors have been contacted. Currently negotiations are underway for sponsorship with SIAM, AMS, MAA, IEEE, FASEB, and IMACS. Additionally AMA and ANA continuing medical education support is being sought. Information will be updated regularly on the anonymous ftp site for the conference (see above). Currently, funding has been generously supplied by the following agencies: University of Texas System - CHPC U.S. Department of Energy ================== REGISTRATION FORM =============== (Please list your name below as it will appear on badge.) First Name : Middle Initial (if available): Family Name: Your Professional Title: [ ]Dr. [ ]Professor [ ]Mr. [ ]Mrs. [ ]Ms. [ ]Other:__________________ Office Phone (desk): Home/Evening Phone (for emergency contact): Fax: Electronic Mail (Bitnet): Electronic Mail (Internet): Postal Address: Institution or Center: Building Code: Mail Stop: Street Address1: Street Address2: City: State: Zip or Country Code: Country: Please list your three major interest areas: Interest1: Interest2: Interest3: Registration fee: $____________ Late fee $50 (if after April 1, 1994) $____________ **IF UT AUSTIN, PLEASE PROVIDE YOUR: UNIVERSITY ACCT. #: ______________________ UNIVERSITY ACCT. TITLE: ______________________ NAME OF ACCT. SIGNER: ______________________ ===================================================== VERIFICATION OF STUDENT STATUS Name: Mailing Address: University at which you are a student: What level student(year): Your student id number: Name of your graduate or postdoctoral advisor: Telephone number for your advisor: By filling in this section, I agree that I am electronically signing my signature to the statement that I am currently a student at the above university. ======================================================= REQUEST FOR FINANCIAL AID Name: Mailing Address: I request financial assistance under one or more of the following categories: [ ] Student (You must fill out the Verification of Student Status Section in order to be considered for financial aid under this category) [ ] Academic [ ] Minority [ ] Female [ ] Black [ ] Hispanic [ ] Native American Indian [ ] Other This form is not meant to invade your personal privacy in any fashion. However, some of the grant funds are targeted at specific ethnic/minority groups and need to be expended appropriately. None of these forms will be in any way released to the public. And, after the congress, all of the financial aid forms will be destroyed. No records will be kept of ethnic or racial backgrounds. If you have any questions concerning financial aid support, please contact Matthew Witten at the above addresses. ============================================================== From ngo@interval.com Mon Sep 20 08:33:18 1993 Message-Id: <9309202331.AA29927@interval.interval.com> Date: Mon, 20 Sep 1993 16:33:18 -0800 To: GKING@arserrc.gov From: ngo@interval.com (Tom Ngo) Subject: Re: C++ compiler >Hello chem netters. I was wondering if there is such a thing as a public >domain C++ compiler. I would be using it on an SGI Iris 4D/35 running >IRIX 4.0.1 with the R2000A/R3000 processor chip. Thanks in advance. Yessir. Not public domain, but copyright (copyleft, actually) and freely distributable. Get GCC from prep.ai.mit.edu. It is the GNU compiler, which includes front ends for C, C++ and Objective C. I do not currently use it, but I have used it intensively in the past, and I do recommend it. You have to compile the compiler yourself. SGI is one platform for which this should be relatively easy. The compiler is probably not bug-free, but it is also incorrect to think that "you get (only) what you pay for." --Tom ============================================================================= Tom Ngo 415/354-3616 (Voice) Interval Research Corporation 415/354-0872 (FAX) 1801-C Page Mill Rd Palo Alto, CA 94304 ngo@interval.com From JKONG@ac.dal.ca Mon Sep 20 17:37:33 1993 Date: Mon, 20 Sep 1993 20:37:33 -0300 From: JKONG@ac.dal.ca Subject: Help wanted: file system consistancy To: chemistry@ccl.net Message-Id: <01H36NKOZIRM000C1Z@AC.DAL.CA> Dear netters, We have a filesystem consistancy problem. The free space shown by "df /tmp" is much less (400mb) than total(2gb) minus the number shown by "du -k /tmp". The problem appeared after I moved several files(one of them is really big, 340mb) to another machine through NFS, i.e. "mv /tmp/g92* /linus/tmp". /linus/tmp is a file system on another machine(Steller). /tmp is on an ibm rs6k/580. I tried "smit - filesystem - verify" and "fsck" command and they failed. I would very appreciated your any help. Regards, Jing Kong Department of Chemistry Dalhousie University Hfx, NS, Canada From xu@lisboa.ks.uiuc.edu Mon Sep 20 15:05:55 1993 From: Dong Xu Message-Id: <9309210105.AA09646@lisboa.ks.uiuc.edu> Date: Mon, 20 Sep 93 20:05:55 -0500 To: chemistry@ccl.net Subject: How to join the Biophysical Society Dear netters, Some of our members in our research group would like to participate in next year's Biophysical Society meeting in New Orleans around March. This requires that we become a student/postdoc member of the Biophysical Society. Could someone tell me how we can join it? Thanks a lot! -Dong Xu xu@lisboa.ks.uiuc.edu From bayly@merck.com Mon Sep 20 10:39:07 1993 Message-Id: <199309201438.AA02769@oscsunb.ccl.net> Date: Mon, 20 Sep 93 10:37:52 -0400 From: bayly@merck.com To: CHEMISTRY@ccl.net Subject: Re: quaternion algorithm for overlap Carlos Simmerling writes: > Does anyone have a reference for a quaternion-based algorithm > for overlapping two structures to minimize rms? I have one reference > to J. Mol. Sim. but I am having trouble locating the journal. I would > appreciate any help. I think you will find the following reference will fill the bill: S.K. Kearsley, Acta Cryst., A45, pp.208-210 (1989) Christopher Bayly bayly@merck.com From NEELY@DUCVAX.AUBURN.EDU Mon Sep 20 10:49:12 1993 Date: Mon, 20 Sep 1993 09:47 CST From: NEELY@DUCVAX.AUBURN.EDU Subject: transition states for Cl containing compounds To: chemistry@ccl.net Message-Id: <01H360WR7UE8001IOE@DUCVAX.AUBURN.EDU> I've been trying to use AMPAC/MOPAC to locate transition states for the reaction of O and OH with trichloroethylene, and am having trouble getting the gradient norm down to something rea- sonable. I've tried 2 different definitions of the molecule, and constraining the 2 Cl's bound to one of the carbons to having the same bondlength & angle, none of which has done the trick. Any hints would be welcome! Thanks, Irene Newhouse From Enrico.Purisima@BRI.NRC.CA Mon Sep 20 12:34:21 1993 Message-Id: <9309201633.AA02780@bobino.BRI.NRC.CA> Date: Mon, 20 Sep 93 12:33:30 -0400 From: Enrico.Purisima@BRI.NRC.CA (Enrico Purisima) To: chemistry@ccl.net Subject: quaternion reference Re Carlos Simmerling's request: There is a paper by A. L. Mackay in Acta Cryst A40:156-166 (1984) called "Quaternion transformation of molecular orientation." This uses a quaternion-based method for superposing two structures. ============================================================================== Enrico O. Purisima Biotechnology Research Institute e-mail: rico@bri.nrc.ca National Research Council of Canada phone : (514) 496-6343 Montreal, Quebec H4P 2R2 fax : (514) 496-5143 Canada ============================================================================== From carlos@pap.chem.uic.edu Mon Sep 20 13:11:30 1993 Date: Mon, 20 Sep 93 11:52:37 CDT From: Carlos Simmerling Message-Id: <9309201652.AA19104@pap.chem.uic.edu> To: CHEMISTRY@ccl.net Subject: overlap algorithm summary I want to thank everyone who responded to my request for overlap algorithms. I was able to find one that met my needs. Since many people also sent requests to me for the information, I will just summarize the responses here. Again, thanks to those who helped. Carlos Simmerling ******************************************************************************* look in /pub/chemistry/quatfit directory @ www.ccl.net There you will find a program (quatfit.c) and a readme with the details. The program is a version of Kearley algorithm (Kearley, S.K., J. Comput. Chem, 11, 1187-1192 (1990)). R.E.Cachau _______________________________________________________________________________ Raul E. Cachau, National Cancer Institute, Frederick Cancer Research and Development Center, PRI/DynCorp, Structural Biochemistry Program and Frederick Biomedical Supercomputer Center, Building 322, Room 19, P.O.Box B, Frederick, MD 21702-1201, USA. Phone: +1-(301)-846-6062; Fax: +1-(301)-846-6066; e-Mail: cachau@ncifcrf.gov _______________________________________________________________________________ ******************************************************************************* look at this: %A R. Diamond %T On the multiple simultaneous superposition of molecular structures by rigid body transformations %J Prot. Sci. %V 1 %P 1279-1287 %D 1992 plus references in there to one of Diamond's earlier papers. ...good luck ...dave case ******************************************************************************* >From @s.ms.uky.edu:proctor!mvl.pg.com!LAIDIG_WD@ms.uky.edu Sat Sep 18 12:15:12 1993 Try this reference - Quaternion Transformation of Molecular Orientation by A. L. Mackay, Acta Cryst. A40, 165-166 (1984). Bill. ******************************************************************************* Oops, that was long ago. I don't have the references near here, but I think something like Acta Cryst 1984, "Kabsch"?? I hope you get better replies than this one.... Regards, -- Rob W. W. Hooft, European Molecular Biology Laboratory, Meyerhofstr. 1, D-69117 Heidelberg, BRD. ============= E-mail: hooft@EMBL-Heidelberg.de ======= Use a Real Operating System on your 386: Linux is FREE! ======= ******************************************************************************* I don't have the quaternion reference, but there are two papers by Kabsch in Acta. Cryst. which give a matrix method that is excellent. This is an exact (ie, non-iterative) method. The references are: . W. Kabsch, Acta Cryst., A32, 922 (1976) . W. Kabsch, Acta Cryst., A34, 827 (1978) Hope this helps, -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ********************** Wagner, Beame, Screvane in '93! ********************** ******************************************************************************* A recent reference on this subjet is: R. Diamond (1992). "On the multiple simultaneaous superposition of molecular structures by rigid body transformations". Protein Science 1, 1279-1287. _________________________________________________________________________ Alexandre Bonvin Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 Tel. : int+31.30.533959 CH 3584 Utrecht Fax. : int+31.30.537623 The Netherlands Email: albo@nmr.chem.ruu.nl _________________________________________________________________________ ******************************************************************************* Simon K. Kearsley published the stuff you require in 1988 - I remember J.Comp.Chem. but unfortunateley I don't have the full reference. C Charles Marais Department of Chemistry University of Cape Town Private Bag Rondebosch chuck@uctvax.uct.ac.za South Africa 7700 chuck@psipsy.uct.ac.za ------------------------------------------------------------------ ******************************************************************************* From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Ask jkl@ccl.net ( jan Labanowski - list coordinator) ( the name of program is "quatfit") Best regards G.B. ******************************************************************************* I am responding to your request for an quaternion-based algorithm for overlapping two structures. A very good algorithm is reported in: "The alignment of protein structures in three dimensions", M. Zuker and R.L. Somorjai, Bulletin of Mathematical Biology 51(1), 1989, pp55-78. I believe that either of the authors will make code (FORTRAN) available. Try Michael Zuker - I am not sure of his e-mail, but I think is zuker@nrcbsa.bio.nrc.ca or Ray Somorjai at somorjai@bolyai.ibd.nrc.ca Heather Gordon Chemical Physics Theory Group Department of Chemistry University of Toronto, Canada From hogue@canada.den.mmc.com Mon Sep 20 13:28:23 1993 Date: Mon, 20 Sep 93 11:28:24 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9309201728.AA00920@canada.den.mmc.com> To: chemistry@ccl.net Subject: Triple defluorination on iron Calling all fluorine chemists: I need your opinion on a triple defluorination mechanism I am proposing in my MSthesis. I think three fluorines can be transferred to a bare metal atom like iron from one terminal F3CO- group of a perfluoropolyether (PFPE) molecule whichhas been activated by the loss of a fluorine anion elsewhere in the molecule. The two pieces of evidence leading me to this conclusion are shown below. First, XPS analyses by people other than myself have shown AlF3 and AlF6-3 species on atomically clean Al surfaces exposed to PFPE at room temperature under UHV conditions. Atomically clean iron also receives at least one fluorineand possible three under UHV conditions at cryogenic temperatures. Second, my AM1 model of a simple 30 atom PFPE indicates that the three terminal fluorines at one end of the molecule become activated (have high HOMO coefficients) after a fluorine anion is abstracted from the original HOMO located near the center of the molecule. Thank you in advance for your help. If you want to call: (303) 971-2543. From raman@bioc01.uthscsa.edu Mon Sep 20 14:09:42 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9309201810.AA24745@bioc01.uthscsa.edu> Subject: U1 SNRP coordinates ... To: shenkin@still3.chem.columbia.edu (Peter Shenkin) Date: Mon, 20 Sep 1993 13:10:08 -0500 (CDT) Peter: Here is the header from the pre-release corresponding to SNRNP U1, deposited by Phil Evans and colleagues. The pdb code is "1nrc" and I had no trouble finding the same. Hope this helps. Cheers -raman ******************************************************************** HEADER PRELIMINARY 12-MAR-92 P1NRC COMPND N-TERMINAL FRAGMENT (RESIDUES 1-95) OF A PROTEIN FROM U1 COMPND 2 SMALL NUCLEAR RIBONUCLEOPROTEIN (SNRNP U1) MUTANT WITH COMPND 3 GLN 85 REPLACED BY CYS (/Q85C$) SOURCE HUMAN (HOMO $SAPIENS) GENE EXPRESSED IN (ESCHERICHIA $COLI) AUTHOR K.NAGAI,P.R.EVANS 1 1 REFERENCE 1 1 AUTH K.NAGAI,C.OUBRIDGE,T.H.JENSEN,J.LI,P.R.EVANS 1 TITL CRYSTAL STRUCTURE OF THE /RNA$-BINDING DOMAIN OF 1 TITL 2 THE U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 1 REF NATURE V. 348 515 1990 1 REFN ASTM NATUAS UK ISSN 0028-0836 006 2 2 RESOLUTION. 2.8 ANGSTROMS. 3 3 REFINEMENT. 3 PROGRAM XPLOR PROLSQ 3 R VALUE 0.022 4 5 5 RESIDUES 1 - 5 AND 91 - 95 OF CHAIN A WERE NOT LOCATED IN 5 THE ELECTRON DENSITY MAPS. RESIDUES 1 - 5, 50 - 52, AND 5 89 - 95 OF CHAIN B WERE NOT LOCATED IN THE ELECTRON DENSITY 5 MAPS. CRYST1 148.100 148.100 148.100 90.00 90.00 90.00 I 41 3 2 96 -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From TS4327@OHSTMVSA.ACS.OHIO-STATE.EDU Mon Sep 20 15:39:07 1993 Message-Id: <199309201939.AB09287@oscsunb.ccl.net> Date: Mon, 20 Sep 93 15:36 EDT To: CHEMISTRY@ccl.net From: TS4327@OHSTMVSA.ACS.OHIO-STATE.EDU Subject: Need information on molecule drawing program. Dear Netter, I need information on any molecule drawing program which can be used on a 486 PC or a HP-730 workstation. This program should be able to accept Z matrix or Cartesian Coordinate inputs for molecules and has ability for user to rotate a molecule about any axis. In addition, I need the program to produce publishing quality pictues on a HP Laser Jet series II and/or a HP-GL file for later use. The price of such program should not be too expensive since the budget is very limited for this. If anyone has information, please send it to me. If there is such program on the public domain, please send me the FTP site address and login information. My e-mail address is TS4327@OHSTMVSA.ACS.OHIO-STATE.EDU. Best regards. Albert Chow. From prasad@chem.psu.edu Mon Sep 20 16:00:15 1993 Date: Mon, 20 Sep 1993 15:59:27 -0400 From: "Prasad B.S Kodali" Message-Id: <9309201959.AA25269@galilei> To: chemistry@ccl.net Subject: MM3 parameters Hello, I am planning to do MD simulations of solid naphthalene using MM3 force field. 1). Can this force field be used to simulate naphthalene crystal? 2). Can someone give me the references to find the parameters for the potential energy function? Thank You Prasad prasad@chem.psu.edu