From owner-molec-model@net.bio.net Mon May 03 07:09:00 1999 Path: biosci!WSUNIX.WSU.EDU!arthurr From: arthurr@WSUNIX.WSU.EDU (art roberts) Newsgroups: bionet.molec-model Subject: A great site of molecular modeling Date: 3 May 1999 01:09:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <372D5965.4E4B3EDA@wsunix.wsu.edu> NNTP-Posting-Host: net.bio.net http://biotech.isCool.net This site allows easy access to hyperlinks and free software for the biochemist, biophysicist and molecular biologist. This site is constantly evolving and expanding, so it can be easy to use, reliable, and comprehensive. This is purely a non-profit site for your enjoyment. Sincerely, Art Roberts From owner-molec-model@net.bio.net Mon May 03 15:36:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.amsterdam.nl.net!sun4nl!uunet!ams.uu.net!ffx.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!not-for-mail From: William Guilford Newsgroups: bionet.molec-model Subject: Re: A great site of molecular modeling Date: Mon, 03 May 1999 12:29:08 -0400 Organization: University of Virginia Lines: 30 Message-ID: <372DCED3.CE3D353C@virginia.edu> References: <372D5965.4E4B3EDA@wsunix.wsu.edu> NNTP-Posting-Host: bootp-4-104.bootp.virginia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 [en] (Win95; I) X-Accept-Language: en > http://biotech.isCool.net > > This site allows easy access to hyperlinks and free software for the > biochemist, biophysicist and molecular biologist. This site is > constantly evolving and expanding, so it can be easy to use, reliable, > and comprehensive. This is purely a non-profit site for your enjoyment. I must admit, that's a pretty nice site! Good job. Visit this one, everybody! - Bill G. ------------------------------------------------- "Specialization is for insects" - Robert Heinlein William H.O. Guilford, Ph.D. Assistant Professor Department of Biomedical Engineering HSC Box 377 University of Virginia Charlottesville, Virginia 22908 Whg2n@virginia.edu http://yakko.bme.virginia.edu/ Phone: 804-243-2740 Fax: 804-982-3870 From owner-molec-model@net.bio.net Mon May 03 19:47:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!nf1.mgmt.sympatico.ca!news1.bellglobal.com!news21.bellglobal.com.POSTED!not-for-mail Message-ID: <372DC302.20CC85B8@sympatico.ca> From: "A. Khiat" X-Mailer: Mozilla 4.51 [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: InsightII problem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 17 Date: Mon, 03 May 1999 20:43:43 GMT NNTP-Posting-Host: 199.243.239.2 X-Trace: news21.bellglobal.com 925764223 199.243.239.2 (Mon, 03 May 1999 16:43:43 EDT) NNTP-Posting-Date: Mon, 03 May 1999 16:43:43 EDT Organization: Sympatico Hi, We have this message when we start Molecular simulations Inc (MSI) InsightII (version 970): killed...Loading InsightII using GL graphics...Killed. Even without the GL graphics loaded, the program gets killed. Moreover, the InsightII (version 400) is fully operational using the same license. Our system (Indigo 2) run on Irix 6.2 and all required patches are installed. How do we figure out what the problem is? Can it be related to the lmup command? Thank you very much. From owner-molec-model@net.bio.net Tue May 04 11:28:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-ge.switch.ch!news.bme.hu!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.molec-model Subject: Re: InsightII problem Date: 4 May 1999 12:23:25 GMT Organization: IIF Lines: 32 Message-ID: References: <372DC302.20CC85B8@sympatico.ca> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.3 UNIX) Hi, sometimes this is caused by the memory limit or other limits set in the shell to a too small a value. Look at what the "limit" shell command reports. Try to set all the settings to "unlimited" (e.g. "limit memoryuse unlimited", etc.). Then try running InsightII again. If this works, put the "limit ... unlimited" commands in your .cshrc file or in the /etc/cshrc file. I'm not sure this will work but give it a try. I don't think it is a license problem. Regards, Andras Szilagyi On Mon, 03 May 1999 20:43:43 GMT, A. Khiat wrote: >Hi, > >We have this message when we start Molecular simulations Inc (MSI) >InsightII (version 970): killed...Loading InsightII using GL >graphics...Killed. > >Even without the GL graphics loaded, the program gets killed. Moreover, >the InsightII (version 400) is fully operational using the same license. > >Our system (Indigo 2) run on Irix 6.2 and all required patches are >installed. How do we figure out what the problem is? Can it be related >to the lmup command? > >Thank you very much. > From owner-molec-model@net.bio.net Tue May 04 12:25:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!news.net.uni-c.dk!not-for-mail From: Mogens Kjaer Newsgroups: bionet.molec-model Subject: Re: InsightII problem Date: Tue, 04 May 1999 15:17:07 +0200 Organization: Carlsberg Laboratory Lines: 18 Message-ID: <372EF353.C0ED3698@crc.dk> References: <372DC302.20CC85B8@sympatico.ca> NNTP-Posting-Host: 130.226.182.195 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 925823828 34318 130.226.182.195 (4 May 1999 13:17:08 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 4 May 1999 13:17:08 GMT X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686) X-Accept-Language: en Andras Szilagyi wrote: > > Hi, > > sometimes this is caused by the memory limit or other limits set in the > shell to a too small a value. - or you could have run out of virtual memory. Does something get logged in /var/adm/SYSLOG ? Mogens -- Mogens Kjaer, Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark Phone: +45 33 27 53 25, Fax: +45 33 27 47 08 Email: mk@crc.dk Homepage: http://www.crc.dk From owner-molec-model@net.bio.net Tue May 04 13:19:00 1999 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!cyclone.bc.net!torn!news1.bellglobal.com!news20.bellglobal.com.POSTED!not-for-mail Message-ID: <372F0128.4CE5DB3B@sympatico.ca> From: "A. Khiat" X-Mailer: Mozilla 4.51 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Re: InsightII problem References: <372DC302.20CC85B8@sympatico.ca> <372EF353.C0ED3698@crc.dk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 30 Date: Tue, 04 May 1999 14:14:36 GMT NNTP-Posting-Host: 199.243.239.2 X-Trace: news20.bellglobal.com 925827276 199.243.239.2 (Tue, 04 May 1999 10:14:36 EDT) NNTP-Posting-Date: Tue, 04 May 1999 10:14:36 EDT Organization: Sympatico Hi Mr Kjaer, We entered the "limit memoryuse unlimited" command in the unix shell before starting InsightII and we still have the killed message. Nothing seems to be writen in the SYSLOG file. How can we modify the virtual memory parameters? What other parameters should we make unlimited? Thank you. Mogens Kjaer wrote: > Andras Szilagyi wrote: > > > > Hi, > > > > sometimes this is caused by the memory limit or other limits set in the > > shell to a too small a value. > > - or you could have run out of virtual memory. > > Does something get logged in /var/adm/SYSLOG ? > > Mogens > > -- > Mogens Kjaer, Carlsberg Laboratory, Dept. of Chemistry > Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark > Phone: +45 33 27 53 25, Fax: +45 33 27 47 08 > Email: mk@crc.dk Homepage: http://www.crc.dk From owner-molec-model@net.bio.net Tue May 04 13:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!yellow.newsread.com!netaxs.com!newsread.com!news-peer.gip.net!news.gsl.net!gip.net!howland.erols.net!news.net.uni-c.dk!not-for-mail From: Mogens Kjaer Newsgroups: bionet.molec-model Subject: Re: InsightII problem Date: Tue, 04 May 1999 16:27:06 +0200 Organization: Carlsberg Laboratory Lines: 23 Message-ID: <372F03BA.ABF28179@crc.dk> References: <372DC302.20CC85B8@sympatico.ca> <372EF353.C0ED3698@crc.dk> <372F0128.4CE5DB3B@sympatico.ca> NNTP-Posting-Host: 130.226.182.195 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 925828026 12928 130.226.182.195 (4 May 1999 14:27:06 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 4 May 1999 14:27:06 GMT X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686) X-Accept-Language: en "A. Khiat" wrote: > > Hi Mr Kjaer, > > We entered the "limit memoryuse unlimited" command in the unix shell before > starting InsightII and we still have the killed message. Nothing seems to be > writen in the SYSLOG file. How can we modify the virtual memory parameters? > What other parameters should we make unlimited? If nothing relevant is logged in SYSLOG, then virtual memory is not the problem... What is the output, if you just write "limit" ? Mogens PS: Don't send me cc's of usenet postings... -- Mogens Kjaer, Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark Phone: +45 33 27 53 25, Fax: +45 33 27 47 08 Email: mk@crc.dk Homepage: http://www.crc.dk From owner-molec-model@net.bio.net Tue May 04 13:40:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.belnet.be!news-ge.switch.ch!news.bme.hu!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.molec-model Subject: Re: InsightII problem Date: 4 May 1999 14:35:37 GMT Organization: IIF Lines: 22 Message-ID: References: <372DC302.20CC85B8@sympatico.ca> <372EF353.C0ED3698@crc.dk> <372F0128.4CE5DB3B@sympatico.ca> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.3 UNIX) On Tue, 04 May 1999 14:14:36 GMT, A. Khiat wrote: >Hi Mr Kjaer, > >We entered the "limit memoryuse unlimited" command in the unix shell before >starting InsightII and we still have the killed message. Nothing seems to be >writen in the SYSLOG file. How can we modify the virtual memory parameters? >What other parameters should we make unlimited? > >Thank you. It was me who suggested this, not Mr Kjaer. As I wrote earlier, try to set all the parameters to "unlimited" that is reported by the "limit" command alone. This includes cputime, filesize, datasize, stacksize, coredumpsize, memoryuse, vmemoryuse and descriptors. As far as the virtual memory parameters are concerned, this is a bit tricky. You should read the appropriate man pages and documentation. As far as I can remember, the MSI documentation describes this as well. Andras From owner-molec-model@net.bio.net Tue May 04 14:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!torn!news1.bellglobal.com!news20.bellglobal.com.POSTED!not-for-mail Message-ID: <372F0AB1.83257829@sympatico.ca> From: "A. Khiat" X-Mailer: Mozilla 4.51 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Re: InsightII problem References: <372DC302.20CC85B8@sympatico.ca> <372EF353.C0ED3698@crc.dk> <372F0128.4CE5DB3B@sympatico.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 39 Date: Tue, 04 May 1999 14:55:16 GMT NNTP-Posting-Host: 199.243.239.2 X-Trace: news20.bellglobal.com 925829716 199.243.239.2 (Tue, 04 May 1999 10:55:16 EDT) NNTP-Posting-Date: Tue, 04 May 1999 10:55:16 EDT Organization: Sympatico Here are the parameters when the "limit" command is typed: cputime unlimited filesize unlimited datasize 524288 kbytes stacksize 65536 kbytes coredumpsize unlimited memoryuse 122308 kbytes descriptors 200 vmemoryuse 524288 kbytes memoryuse becomes 524288 when the unlimited command is typed. What really intrigues us is that the InsightII 400 version is fully operational. Are the requirements for the 970 version that different?? Andras Szilagyi wrote: > On Tue, 04 May 1999 14:14:36 GMT, A. Khiat wrote: > > >Hi Mr Kjaer, > > > >We entered the "limit memoryuse unlimited" command in the unix shell before > >starting InsightII and we still have the killed message. Nothing seems to be > >writen in the SYSLOG file. How can we modify the virtual memory parameters? > >What other parameters should we make unlimited? > > > >Thank you. > > It was me who suggested this, not Mr Kjaer. As I wrote earlier, try to > set all the parameters to "unlimited" that is reported by the "limit" > command alone. This includes cputime, filesize, datasize, stacksize, > coredumpsize, memoryuse, vmemoryuse and descriptors. > > As far as the virtual memory parameters are concerned, this is a bit > tricky. You should read the appropriate man pages and documentation. As > far as I can remember, the MSI documentation describes this as well. > > Andras From owner-molec-model@net.bio.net Tue May 04 18:38:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.belnet.be!news-ge.switch.ch!news.bme.hu!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.molec-model Subject: Re: InsightII problem Date: 4 May 1999 19:32:41 GMT Organization: IIF Lines: 37 Message-ID: References: <372DC302.20CC85B8@sympatico.ca> <372EF353.C0ED3698@crc.dk> <372F0128.4CE5DB3B@sympatico.ca> <372F0AB1.83257829@sympatico.ca> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.3 UNIX) On Tue, 04 May 1999 14:55:16 GMT, A. Khiat wrote: >Here are the parameters when the "limit" command is typed: >cputime unlimited >filesize unlimited >datasize 524288 kbytes >stacksize 65536 kbytes >coredumpsize unlimited >memoryuse 122308 kbytes >descriptors 200 >vmemoryuse 524288 kbytes > >memoryuse becomes 524288 when the unlimited command is typed. Please enter all the following commands: limit vmemoryuse unlimited limit memoryuse unlimited limit datasize unlimited limit stacksize unlimited and then try to run InsightII again. If it is killed again, the most likely cause is that the virtual memory is too small. Look at what the "limit" command reports for vmemoryuse (after setting it to "unlimited"). On our machine, it reports 2097152 kbytes, i.e. 2 gigabytes, and InsightII 97.0 works for us. You should configure the virtual memory as it is described in the Installation Guide that comes with InsightII. >What really intrigues us is that the InsightII 400 version is fully >operational. >Are the requirements for the 970 version that different?? I don't know but that is fairly possible. Andras From owner-molec-model@net.bio.net Wed May 05 12:33:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!130.185.14.36!torn!news1.bellglobal.com!news21.bellglobal.com.POSTED!not-for-mail Message-ID: <37300015.30470092@sympatico.ca> From: "A. Khiat" X-Mailer: Mozilla 4.51 [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Re: InsightII problem References: <372DC302.20CC85B8@sympatico.ca> <372EF353.C0ED3698@crc.dk> <372F0128.4CE5DB3B@sympatico.ca> <372F0AB1.83257829@sympatico.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 68 Date: Wed, 05 May 1999 13:29:13 GMT NNTP-Posting-Host: 199.243.239.2 X-Trace: news21.bellglobal.com 925910953 199.243.239.2 (Wed, 05 May 1999 09:29:13 EDT) NNTP-Posting-Date: Wed, 05 May 1999 09:29:13 EDT Organization: Sympatico Hi Mr Szilagyi Even when we put the vmemoryuse unlimited we get 524288, and here is the results of swap -l and swap -s. indigo% swap -l lswap path dev pri swaplo blocks free maxswap vswap 2 /.swap.virtual 128,16 2 0 0 0 0 600000 1 /dev/swap 128,17 0 0 260696 260696 260696 0 indigo% swap -s total: 0.00k allocated + 63.27m add'l reserved = 63.27m bytes used, 480.90m bytes available indigo% limit cputime unlimited filesize unlimited datasize 524288 kbytes stacksize 65536 kbytes coredumpsize unlimited memoryuse 122308 kbytes descriptors 200 vmemoryuse 524288 kbytes Thank you very much Andras Szilagyi wrote: > On Tue, 04 May 1999 14:55:16 GMT, A. Khiat wrote: > > >Here are the parameters when the "limit" command is typed: > >cputime unlimited > >filesize unlimited > >datasize 524288 kbytes > >stacksize 65536 kbytes > >coredumpsize unlimited > >memoryuse 122308 kbytes > >descriptors 200 > >vmemoryuse 524288 kbytes > > > >memoryuse becomes 524288 when the unlimited command is typed. > > Please enter all the following commands: > limit vmemoryuse unlimited > limit memoryuse unlimited > limit datasize unlimited > limit stacksize unlimited > > and then try to run InsightII again. > > If it is killed again, the most likely cause is that the virtual memory > is too small. Look at what the "limit" command reports for vmemoryuse > (after setting it to "unlimited"). On our machine, it reports 2097152 > kbytes, i.e. 2 gigabytes, and InsightII 97.0 works for us. You should > configure the virtual memory as it is described in the Installation Guide > that comes with InsightII. > > >What really intrigues us is that the InsightII 400 version is fully > >operational. > >Are the requirements for the 970 version that different?? > > I don't know but that is fairly possible. > > Andras From owner-molec-model@net.bio.net Tue May 11 18:04:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!128.174.5.49!vixen.cso.uiuc.edu!not-for-mail From: lu@ks.uiuc.edu (Hui Lu) Newsgroups: bionet.molec-model,pnet.jobs.available,comp.graphic.misc Subject: job opening: research programmer Date: 11 May 1999 18:58:48 GMT Organization: University of Illinois at Urbana-Champaign Lines: 33 Message-ID: <7h9ul8$msv$3@vixen.cso.uiuc.edu> NNTP-Posting-Host: monaco.ks.uiuc.edu X-Newsreader: Alexandra.app (Version 0.82) Position Announcement, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Title: Research Programmer The Theoretical Biophysics (TB) Group at the University of Illinois (http://www.ks.uiuc.edu/) at Urbana-Champaign (UIUC) is inviting applications for several research programmer positions. The group develops a collaborative software environment for structural biology, and MDScope, a set of molecular modeling tools for large-scale biological structures. The new positions will involve the integration of VMD, the visualization component, and of NAMD, the highly-parallel computational engine of MDScope within this environment. Tasks will include coupling of VMD and NAMD to other serial and parallel applications across a network, web-based collaboration tool development, and integration within metacomputing environments. Application information: available immediately. Minorities, women and other designated class members are encouraged to apply. Please send resume (e-mail in plain text preferred, no attached files) with cover letter and three references to: Dr. Gila Budescu Beckman Institute 405 N. Mathews Ave Urbana, IL 61801 gila@ks.uiuc.edu (217)244-6914 For a more detailed job description look at: http://www.ks.uiuc.edu/Services/Events/programmer_99.html The University Of Illinois is an AA-EOE. From owner-molec-model@net.bio.net Tue May 11 21:28:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!awabi.library.ucla.edu!134.139.1.31!csulb.edu!usenet From: "Jeffrey A. Cohlberg" Newsgroups: bionet.molec-model Subject: Biochemistry lecturer position Date: Tue, 11 May 1999 14:25:36 -0700 Organization: Cal. State Univ. Long Beach Lines: 31 Message-ID: <3738A050.1BD1@csulb.edu> NNTP-Posting-Host: 134.139.180.141 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Opening for a Full-Time Lecturer, 1999-2001 California State University, Long Beach Department of Chemistry and Biochemistry Duties: Lecturing in introductory and intermediate biochemistry courses and supervision of biochemistry laboratory courses. Opportunities may also be available for lecturing in graduate level biochemistry courses and supervision of biochemistry colloquia for senior undergraduate and MS students. Fall 1999 classes begin on August 30. Salary commensurate with qualifications and experience. Qualifications: Ph. D. in Chemistry or Biochemistry or a closely related field. Ability to communicate effectively with a diverse campus community. Prior successful teaching experience preferred. Required Documentation: Letter of application; resume; three letters of recommendation; official transcript from institution awarding highest degree. Position open until filled (or recruitment canceled). Review of applications to begin May 15. Applications and required documentation should be addressed to: Dr. N. M. Senozan, Chair, Department of Chemistry and Biochemistry, 1250 Bellflower Blvd, Long Beach, CA 90840-3903. For more information contact Dr. Nail Sezozan (nsenozan@csulb.edu) or Dr. Jeffrey Cohlberg (cohlberg@csulb.edu). Equal Opportunity/Affirmative Action/Title IX Employer From owner-molec-model@net.bio.net Tue May 11 23:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: Willy Wriggers Newsgroups: bionet.molec-model Subject: update: multi-res. docking w/ Situs 1.1 Date: Wed, 12 May 1999 00:18:38 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 34 Message-ID: <7hahcs$tg3$1@nnrp1.deja.com> NNTP-Posting-Host: 132.239.156.46 X-Article-Creation-Date: Wed May 12 00:18:38 1999 GMT X-Http-User-Agent: Mozilla/4.51 [en] (X11; I; Linux 2.2.6 i686) X-Http-Proxy: 1.0 x35.deja.com:80 (Squid/1.1.22) for client 132.239.156.46 Hi all, A new version (1.1) of the free single-molecule, multi-resolution docking package went online at URL http://chemcca10.ucsd.edu/~situs Some of the new features are: - A more powerful and more accurate clustering algorithm to correlate features within structural data sets. - Electron microscopy: support of ASCII, CCP4, SPIDER, and MRC file formats, map file export in CCP4 format for visualization e.g. with Swiss PDB Viewer - Small-angle X-ray scattering: Support for docking of crystal structures to bead models from SAXS refinements (Chacon et al., Biophys. J. 74:2760-2775, 1998) More info can be found online and in the current issue of J. Structural Biology (1999) 125:185-195, URL http://www.academicpress.com/jsb Cheers, Willy -- Willy Wriggers, Ph.D. -- URL http://chemcca10.ucsd.edu/~wriggers Tel: (619)534-2913. Fax: (619)534-7042. E-mail: wriggers@ucsd.edu --== Sent via Deja.com http://www.deja.com/ ==-- ---Share what you know. Learn what you don't.--- From owner-molec-model@net.bio.net Wed May 12 13:28:00 1999 Path: biosci!KAC.COM.KW!wie69 From: wie69@KAC.COM.KW (yiopski) Newsgroups: bionet.molec-model Subject: Your ad to Millions Date: 12 May 1999 07:28:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: <199905124259BAA27679@deflopster.nchulc.edu.tw> NNTP-Posting-Host: net.bio.net F R E E ADS IN THE NEW "PICK-A-BARGAIN"! ============================================== "PICK-A-BARGAIN", a unique mailer, delivers your ad to 1 Million internet people's mailboxes! 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ASK FOR REMOVAL! 31974j919-2rw54 uenticat From owner-molec-model@net.bio.net Thu May 13 14:45:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!logbridge.uoregon.edu!newsswitch.lcs.mit.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!diablo.theplanet.net!diablo.dera.gov.uk!server2.netnews.ja.net!news.reading.ac.uk!suma3!ssr97lrc From: "l.r.cooper" Newsgroups: bionet.molec-model Subject: PDB superposition and RMSD Date: Thu, 13 May 1999 14:27:10 +0100 Organization: University of Reading Lines: 32 Message-ID: NNTP-Posting-Host: suma3.reading.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8BIT dear all, does anyone have a piece of code which superimposes two PDB files then reports their RMSD in angstroms? will summarize °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` //=\Mr. Lee R. Cooper Bsc(Hons) MSc, Parallel, Emergent//=\evolution, \=//& Distributed Architechture Laboratory, Dept. of \=//creationists //=\Comp. Science, University of Reading, Whiteknights //=\have argued, \=//PoBox 225, Reading, Berkshire. RG6 6AY (UK) \=/was as likely //=\Tel +44 (0)118 987 5123 x7645 (0915-1700)|Fax //=to have made \=//Tel +44 (0)118 931 8188 x7817 (1900-2300)|0118 975 \=//man as a //=\http://www.rdg.ac.uk/~ssr97lrc/ 1994 //=\monkey..., °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` randomly typing the bible without error. with natural selection acting as an eraser of mistakes; assuming thirteen mistakes for every correct character & a rate of 1 keystroke per second, the 6 million characters of the holy script could be typed in 13x6e6 s, or <3 yrs. From owner-molec-model@net.bio.net Thu May 13 15:12:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!feeder.qis.net.MISMATCH!feeder.qis.net!news.maxwell.syr.edu!easynet-tele!easynet.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!biosci From: mh270@bioc.cam.ac.uk (Miriam Hirshberg) Newsgroups: bionet.molec-model Subject: PDB superposition and RMSD Date: 13 May 1999 17:07:01 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 28 Message-ID: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 926611622 22932 193.62.192.80 (13 May 1999 16:07:02 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 13 May 1999 16:07:02 GMT X-Received: from mole.bio.cam.ac.uk (exim@mole.bio.cam.ac.uk [131.111.36.9]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA12871 for ; Thu, 13 May 1999 17:06:59 +0100 (BST) X-Received: from [131.111.36.28] (helo=babylon.bioc.cam.ac.uk) by mole.bio.cam.ac.uk with smtp (Exim 1.92 #3) id 10hy0c-0002Yb-00; Thu, 13 May 1999 17:06:54 +0100 X-Received: from mh270 by babylon.bioc.cam.ac.uk with local (Exim 1.651 #3) id 10hy0f-0007mW-00; Thu, 13 May 1999 17:06:57 +0100 X-To: molmodel@hgmp.mrc.ac.uk, ssr97lrc@reading.ac.uk X-Reply-To: m.hirshberg@mole.bio.cam.ac.uk There are many programs try http://www.biochem.ucl.ac.uk/~martin/swreg.html = FroFit v1.8 Miri >dear all, > >does anyone have a piece of code which superimposes two PDB files then >reports their RMSD in angstroms? > >will summarize > Mr. Lee R. Cooper ====================================================================== Miriam (Miri) Hirshberg e-mail: m.hirshberg@mole.bio.cam.ac.uk Department of Biochemistry Tel : (+44) 01223 766018 University of Cambridge Tel : (+44) 01223 333600 (switch board) 80 Tennis Court Road Fax : (+44) 01223 766002 Old Addenbrooke's Site Cambridge CB2 1GA, UK ======================================================================= --- From owner-molec-model@net.bio.net Fri May 14 05:40:00 1999 Path: biosci!BGUMAIL.BGU.AC.IL!aflaloc From: aflaloc@BGUMAIL.BGU.AC.IL (claude aflalo) Newsgroups: bionet.molec-model Subject: Re: PDB superposition and RMSD Date: 13 May 1999 23:40:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Thu, 13 May 1999, l.r.cooper wrote: > > dear all, > > does anyone have a piece of code which superimposes two PDB files then > reports their RMSD in angstroms? > > will summarize Try SwissPDB viewer Claude Aflalo ######################## Phones: Office 972-7-6472118 #### Dept. of Life Sciences Lab 972-7-6472119 Ben Gurion University of the Negev Fax 972-7-6472890 P.O.Box 653 email: aflaloc@bgumail.bgu.ac.il Beer Sheva 84105 Israel URL: http://www.bgu.ac.il/life/aflalo.html From owner-molec-model@net.bio.net Fri May 14 06:57:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!oleane!pasteur.fr!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.molec-model Subject: Re: PDB superposition and RMSD Date: 14 May 1999 09:52:19 +0200 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 16 Message-ID: <7hgknj$hu6@moka.ccr.jussieu.fr> NNTP-Posting-Host: moka.ccr.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: vishnu.jussieu.fr 926668285 26638 134.157.1.23 (14 May 1999 07:51:25 GMT) X-Complaints-To: Newsmaster@jussieu.fr@vishnu.jussieu.fr NNTP-Posting-Date: 14 May 1999 07:51:25 GMT In article "l.r.cooper" wrote: >dear all, > >does anyone have a piece of code which superimposes two PDB files then >reports their RMSD in angstroms? > >will summarize The CSR algorithm computes the common 3D motif then reports the RMSD of the common motif pair. I can email you the code for DEC-alpha, SGI, RS6000, CRAY (indicate the exact platform and system version). Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr From owner-molec-model@net.bio.net Fri May 14 09:49:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!newscore.univie.ac.at!news-ge.switch.ch!diablo.dera.gov.uk!server1.netnews.ja.net!server2.netnews.ja.net!news.reading.ac.uk!suma3!ssr97lrc From: "l.r.cooper" Newsgroups: bionet.molec-model Subject: summary PDB superposition & RMSD Date: Fri, 14 May 1999 11:36:33 +0100 Organization: University of Reading Lines: 147 Message-ID: Reply-To: "l.r.cooper" NNTP-Posting-Host: suma3.reading.ac.uk Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-559023410-758783491-926678193=:28574" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---559023410-758783491-926678193=:28574 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8BIT °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` //=\Mr. Lee R. Cooper Bsc(Hons) MSc, Parallel, Emergent//=\evolution, \=//& Distributed Architechture Laboratory, Dept. of \=//creationists //=\Comp. Science, University of Reading, Whiteknights //=\have argued, \=//PoBox 225, Reading, Berkshire. RG6 6AY (UK) \=/was as likely //=\Tel +44 (0)118 987 5123 x7645 (0915-1700)|Fax //=to have made \=//Tel +44 (0)118 931 8188 x7817 (1900-2300)|0118 975 \=//man as a //=\http://www.rdg.ac.uk/~ssr97lrc/ 1994 //=\monkey..., °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` randomly typing the bible without error. with natural selection acting as an eraser of mistakes; assuming thirteen mistakes for every correct character & a rate of 1 keystroke per second, the 6 million characters of the holy script could be typed in 13x6e6 s, or <3 yrs. ---559023410-758783491-926678193=:28574 Content-Type: TEXT/PLAIN; name="RMSD.txt" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: replies & code DQpGcm9tIGwuci5jb29wZXJAcmVhZGluZy5hYy51ayBGcmkgTWF5IDE0IDEx OjM1OjE4IDE5OTkNCkRhdGU6IEZyaSwgMTQgTWF5IDE5OTkgMTE6MzY6MjAg KzAxMDANCkZyb206ICJsLnIuY29vcGVyIiA8bC5yLmNvb3BlckByZWFkaW5n LmFjLnVrPg0KVG86IENIRU1JU1RSWUBjY2wubmV0DQpDYzogc3NyOTdscmNA 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ZCwgdGhlIDYgbWlsbGlvbiBjaGFyYWN0ZXJzDQpvZiB0aGUgaG9seSBzY3Jp cHQgY291bGQgYmUgdHlwZWQgaW4gMTN4NmU2IHMsIG9yIDwzIHlycy4NCg0K ICBbUGFydCAyLCBUZXh0L1BMQUlOICA2MjEgbGluZXNdDQogIFtVbmFibGUg dG8gcHJpbnQgdGhpcyBwYXJ0XQ0KDQo= ---559023410-758783491-926678193=:28574-- From owner-molec-model@net.bio.net Fri May 14 12:17:00 1999 Path: biosci!biosci!not-for-mail From: Craig M Sager Newsgroups: bionet.molec-model Subject: WORKSHOP: DEVELOPING AND USING PC CLUSTERS AS A BIOMEDICAL RESEARCH TOOL Date: 14 May 1999 06:17:13 -0700 Organization: Pittsburgh Supercomputing Center Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <373B267E.8E8C5F1B@psc.edu> NNTP-Posting-Host: net.bio.net The Pittsburgh Supercomputing Center's Biomedical Initiative will be offering the following NIH-sponsored training workshop: DEVELOPING AND USING PC CLUSTERS AS A BIOMEDICAL RESEARCH TOOL Workshop Dates: June 17-19, 1999. Application deadline: May 20, 1999 This workshop is designed to assist biomedical researchers who are interested in establishing a PC cluster for use by their laboratory. The workshop will address software and hardware topics encountered in the process of building, operating and managing a PC cluster. In addition, software development issues will also be described. Topics of discussion will include: "What do you need to consider when creating an operating environment?" "How to select System Software?" "How to Administer the Cluster?" "What applications are appropriate?" and "How to get the best performance for your money?" Full details, including on-line applications and financial support, may be found on the PSC Web site: http://www.psc.edu/biomed/workshops/workshops.html The Pittsburgh Supercomputing Center's Biomedical Initiative is an NIH Supported Resource Center. From owner-molec-model@net.bio.net Sat May 15 03:21:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail From: amartin@stagleys.demon.co.uk (Andrew Martin) Newsgroups: bionet.molec-model Subject: Re: PDB superposition and RMSD Date: Fri, 14 May 1999 09:03:46 GMT Organization: Private Address Message-ID: References: X-Trace: mail2news.demon.co.uk 926741747 mail2news:621 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!finch-post-11.mail.demon.net![194.222.20.72]!stagleys.demon.co.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 27 Miriam Hirshberg (mh270@bioc.cam.ac.uk) wrote: : There are many programs try : http://www.biochem.ucl.ac.uk/~martin/swreg.html = FroFit v1.8 ^^^^^^ ProFit : Miri Thanks for the recommendation Miri! Strangely that's the one I'd have recommended too :-) For more info on what it can do, take a look at: http://www.biochem.ucl.ac.uk/~martin/text/ProFit.readme Best wishes, Andrew -- Dr. Andrew C.R. Martin UCL and Inpharmatica From owner-molec-model@net.bio.net Sun May 16 20:45:00 1999 Path: biosci!INAME.COM!tmspro1 From: tmspro1@INAME.COM Newsgroups: bionet.molec-model Subject: Does your business need to accept Credit Cards? Date: 16 May 1999 14:45:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: tmspro1@iname.com NNTP-Posting-Host: net.bio.net DOES YOUR BUSINESS ACCEPT CREDIT CARDS?? ******************************************************************* We provide businesses of ALL types, with a 99% approval rate, an opportunity to have their own NO HASSLE CREDIT CARD MERCHANT ACCOUNT. Good credit, bad credit, no credit--not a problem. 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Thank you very much, Merchant Services ************************************************************************* This is a one time mailing, you will not received this email again. From owner-molec-model@net.bio.net Mon May 17 20:05:00 1999 Path: biosci!BIO.ORNL.GOV!beh From: beh@BIO.ORNL.GOV (Brian Hingerty) Newsgroups: bionet.molec-model Subject: superposition and RMSD's Date: 17 May 1999 14:05:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net The question about superposition and RMSDs can be handled with the program molmol ftp://ftp.mol.biol.ethz.ch/pub/software/MOLMOL Brian Hingerty -------------------------------------------------------------------------------- Brian E. Hingerty Life Sciences Division Oak Ridge National Laboratory 1060 Commerce Park, Room 243 P.O. Box 2008, MS-6480 Oak Ridge, TN 37831-6480 tel: 423-574-0844 fax: 423-574-0004 e-mail: beh@ornl.gov private e-mail: behingerty@worldnet.att.net From owner-molec-model@net.bio.net Wed May 19 01:57:00 1999 Path: biosci!KRYTEN.CMS.LIVJM.AC.UK!juusoi64 From: juusoi64@KRYTEN.CMS.LIVJM.AC.UK (Vipserd) Newsgroups: bionet.molec-model Subject: Your Ad to Millions (we do the work) Date: 18 May 1999 19:57:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 58 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990518216JAA22272@jouimep.khm.uni-koeln.de> NNTP-Posting-Host: net.bio.net **** EXPOSURE to YOUR MARKET **** Have you captured your Internet Market ? THE INTERNET There are currently over 100 million Internet users and thousands are joining each day. Currently, the Internet is experiencing both a phenomenal and exponential growth rate. Imagine the amount of prospects increasing daily. DO YOU HAVE A PRODUCT OR SERVICE ? 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We are OSD. ___________________________________________To be removed place (R) in the subject line at 2signup@gte.net Offer good only on United States Netwerks, we are planning to go to Europe next year. From owner-molec-model@net.bio.net Thu May 20 17:26:00 1999 Path: biosci!nih.knaw.nl!A.van.Ooyen From: A.van.Ooyen@nih.knaw.nl (Arjen van Ooyen) Newsgroups: bionet.molec-model Subject: Axonal Competition for Neurotrophins Date: 20 May 1999 11:26:10 -0700 Organization: Netherlands Institute for Brain Research Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: <37445208.A95@nih.knaw.nl> NNTP-Posting-Host: net.bio.net NEW PAPER: Competition for Neurotrophic Factor in the Development of Nerve Connections A. van Ooyen & D. J. Willshaw Proc. R. Soc. Lond. B Biol. Sci. (1999) 266: 883-892. Download full text from the following website: http://www.cns.ed.ac.uk/people/arjen/competition.html Or request a reprint of the paper version (don't forget to give your address): A.van.Ooyen@nih.knaw.nl ABSTRACT The development of nerve connections is thought to involve competition among axons for survival promoting factors, or neurotrophins, which are released by the cells that are innervated by the axons. Although the notion of competition is widely used within neurobiology, there is little understanding of the nature of the competitive process and the underlying mechanisms. We present a new theoretical model to analyse competition in the development of nerve connections. According to the model, the precise manner in which neurotrophins regulate the growth of axons, in particular the growth of the amount of neurotrophin receptor, determines what patterns of target innervation can develop. The regulation of neurotrophin receptors is also involved in the degeneration and regeneration of connections. Competition in our model can be influenced by factors dependent on and independent of neuronal electrical activity. Our results point to the need to measure directly the specific form of the regulation by neurotrophins of their receptors. -- Arjen van Ooyen, Netherlands Institute for Brain Research, Meibergdreef 33, 1105 AZ Amsterdam, The Netherlands. email: A.van.Ooyen@nih.knaw.nl website: http://www.cns.ed.ac.uk/people/arjen.html phone: +31.20.5665483 fax: +31.20.6961006 From owner-molec-model@net.bio.net Fri May 21 13:43:00 1999 Path: biosci!kfunigraz.ac.at!andreas.kungl From: andreas.kungl@kfunigraz.ac.at (andreas kungl) Newsgroups: bionet.molec-model Subject: 3rd International Conference on Molecular Structural Biology Date: 21 May 1999 07:43:13 -0700 Organization: Karl-Franzens-Universitaet Graz Lines: 326 Sender: daemon@net.bio.net Distribution: world Message-ID: <37456EE8.57425B6A@kfunigraz.ac.at> NNTP-Posting-Host: net.bio.net The Biochemistry Subgroup of the Austrian Chemical Society is pleased to announce the Third International Conference on Molecular Structural Biology which will take place in Vienna, Austria from September 8-12, 1999 FOR DETAILED INFORMATION, PLEASE SEE BELOW OR VISIT OUR HOMEPAGE AT http://www.kfunigraz.ac.at/ipcwww/icmsb99 ************************************************************************ Introduction to the ICMSB99 The First and the Second International Conference on Molecular Structural Biology (ICMSB) took place in Vienna in September 1995 and 1997. Both conferences were very well received by all who took part, including over 250 participants from more than 20 countries worldwide. The organisers are pleased to announce the Third ICMSB, which will take place from 8th to 12th September 1999, and which will, like the previous conferences, feature internationally renowned speakers. The ICMSB99 will focus on topics covering a number of the most exciting areas in the field, with the aim of bringing together specialised scientists from different areas. It will be opened by one of the most outstanding scientists in the field of structural biology, Robert Huber, and the following four days of sessions will include Folding and Function, Novel Structures, Advances in Microscopic Methods, Structural Molecular Biology, Structure-Based Drug Design, and Prediction and Simulation. ************************************************************************ Vienna - An Attractive Conference Location The ICMSB99 will be located at the Federal Chancellery in Vienna. The city is a particularly attractive location for a conference, with its combination of historical buildings, green parks, and modern architecture. Some of the most famous city sights include Schönbrunn Palace and the Hofburg, former homes of the Habsburgs, St. Stephans Cathedral, and the colourful Hundertwasser House. Also unique to Vienna is the Prater park, with its endless green avenues and its funfair, featuring the ´´Riesenrad´´ (ferris wheel). Of course, no trip to Vienna would be complete without a visit to one of the many traditional Viennese cafés, for a piece of the famous Sachertorte. An ´´Oldtimer-Tram´´tour around the Ringstraße will take participants past many of the finest sights. ************************************************************************ Organising Committee A. Kungl, P. Andrew, A. Binder, S. Kristl, A. Schilk ************************************************************************ Scientific Committee C. Kratky, M. Sippl, A. Kungl, P. Andrew ************************************************************************ In Cooperation With Austrian Academy of Sciences Austrian Federal Chancellery ************************************************************************ Sponsored By Austrian Airlines Novartis Forschungsinstitut ************************************************************************ Scientific Programme The six sessions of the conference cover a wide range of topics and experimental methods, which will be presented in the form of plenary lectures, selected short oral communications, and posters. Wednesday 8th: Registration from 2 p.m. onwards Evening: Honorary Lecture (followed by a welcome drink and snack) Robert Huber (Max-Planck-Institute, Martinsried): Diversity and Conservation in Proteolytic Enzymes and their Inhibitors Thursday 9th: Morning Session: Advances in Microscopic Methods Werner Kühlbrandt (Max-Planck-Institute, Frankfurt): Two Conformations of Membrane Ion Pumps Hansgeorg Schindler (Linz University): Single Molecule Microscopy Methods for Structural Biology Helen Hansma (University of California, Santa Barbara): Probing Biomaterials with the Atomic Force Microscope Afternoon Session: Folding and Function Alan Fersht (Cambridge University): Minichaperones: Practical and Mechanistic Tools Thomas Kiefhaber (Biozentrum Basel): Speed Limit for Protein Folding Peter Wright (Scripps Institute): Structure and Dynamics of Unfolded Proteins and Protein Folding Intermediates Friday 10th: Morning Session: Novel Structures Michael Rossmann (Purdue University): The Assembly of Viruses Examined by Combining Crystallography and Cryo-electron Microscopy Don Wiley (Harvard University): Structural Studies of Viral Entry Mechanisms in Influenza, HIV-1 and bola Viruses Kurt Wüthrich (ETH Zürich): TROSY and BSE - Recent Progress with NMR in Structural Biology Afternoon Session: Structure-Based Drug Design Siegfried Reich (Agouron Pharmaceuticals): The Use of Protein Structural Information in Drug Design and Development: Some Examples Keith Wilson (Vertex Pharmaceuticals): Structure-Based Drug Design: Reality over Hype Poster Session I Saturday 11th: Morning Session: Structural Molecular Biology Stephen Cusack (EMBL Grenoble): tRNA and Amino Acid Recognition by Aminoacyl-tRNA Synthetases Robert Kaptein (Utrecht University): Allosteric Interactions in Protein-DNA Recognition Christoph Kratky (Graz University): Structure and Mechanism of Enzymes with a B12 Cofactor Paul Sigler (Yale University): Structure and Function in Chaperonin-Assisted Protein Folding Afternoon: Poster Session II (followed by the ´´Oldtimer-Tram´´ tour) Sunday 12th: Morning Session: Structural Genomics David Eisenberg (UCLA): Protein-Protein Interactions Terry Gaasterland (Rockefeller University): Using Patterns of Evolution Across Whole Genomes to Support Structural Genomics Target Selection John Moult (University of Maryland): The Past, Present, and Future of Protein Structure Prediction Wayne Hendrickson (Columbia University): Prospects of High-Throughput Crystallographic Structure Determination Approx. 1 p.m.: End of Conference with Farewell Drink and Snack ************************************************************************ Call for Posters Interested participants are invited to submit abstracts describing original work which has not been presented elsewhere. Abstracts should arrive no later than July 10th, 1999. Authors will be informed about the provisional acceptance of the abstract by the end of July. The presentation of the abstract as a poster will be confirmed, and included in the Book of Abstracts when one or more of the authors registers for the conference. Contributors of outstanding abstracts will be chosen by the Scientific Committee to give a 15 minute oral presentation. Poster Prize A prize of ATS 2,000 will be awarded for the best poster contribution i n terms of innovative results and presentation. ************************************************************************ Abstract Submission Camera-ready abstracts should be printed in good quality on a single (A4) sheet of paper, within the area 16 cm wide and 24 cm long. The title should be followed by the author(s) name(s), affiliation(s), and address(es). Text should be in a 12 point font with maximum 1.5 line spacing. Please send two unfolded copies of the abstract to the conference secretariat. ************************************************************************ Posters The poster boards will be 100 cm (width) x 200 cm (height). Materials for poster mounting will be provided. ************************************************************************ Conference Proceedings The lectures and poster presentations will be published by the Austrian Chemical Society in book form (with an ISBN number), and will be distributed to the participants upon arrival at the conference. Additional copies of the Conference Proceedings can be purchased for ATS 300,-. ************************************************************************ General Information Exhibition: An exhibition of instruments, accessories, software, literature, and other items is planned. Companies interested in displaying their products are kindly requested to contact the conference secretariat. Social Events: The conference will be opened by a welcome drink f ollowing the honorary lecture in the Federal Chancellery on the evening of Wednesday, September 8th. On Saturday afternoon, the conference participants will be taken on a tram tour of the city centre. Following this, all participants are encouraged to visit a typical Viennese Heurigen (wine cellar) to enjoy the local food and wine (not included in the registration fee). A further social event will be arranged for one other evening, leaving one evening free to explore Vienna. In addition, half day tours to some of Vienna´s best known sights will be organised for accompanying people (dependent on participant number). Registration (please contact the Conference Secretariat or our homepage): Registration Fee Before August 1 After August 1 Regular Participant 5.000 ATS 5.500 ATS GÖCH Member* 4.000 ATS 4.500 ATS Student** 2.500 ATS 3.000 ATS GÖCH-Students*/** 1.750 ATS 2.000 ATS Accompanying Person 500 ATS 600 ATS *Payment must be accompanied by proof of the remittance of the ´99-GÖCH membership fee **Payment must be accompanied by proof of student status The registration desk will be open from 2 p.m. on Wednesday, September 8th. The registration fee includes the Conference Proceedings and participation in all scientific sessions, the welcome and farewell drinks, lunch from Thursday to Saturday, coffee breaks, and participation in the social programme (please note: the Heurigen visit is not included). Accompanying people attend only the social programme (welcome drink, tram tour, additional evening). Accomodation is not included in the registration fee! For accomodation, to register for the Heurigen evening, and to book social events for accompanying people, please ask for the flyer of the travel agency MONDIAL CONGRESS (at the conference secretariat or at our homepage). Remittance of Fees: Remittance must be made in Austrian Schillings (ATS) payable to the Gesellschaft Österreichischer Chemiker, Arbeitsgruppe Biochemie, Account Number 0043-19265/04 at Bank Creditanstalt, Bank Code 11000. Payment is also accepted by sending a (Euro-)Cheque to the conference secretariat or by filling in the credit card form (Visa, Euro/Mastercard, Diners Club, and American Express are accepted). All charges due to bank transfer have to be paid by the sender. The sender´s name and address have to be clearly marked on every remittance. Cancellation: Applications may be cancelled up to August 1st, in which case 85% refund of fees already paid will be made. It will not be possible to offer any refunds if cancellations are made after that date. ************************************************************************ Conference Homepage Please visit our homepage at http://www.kfunigraz.ac.at/ipcwww/icmsb99 for the latest update of the programme plus further information. ************************************************************************ Key Dates July 10, deadline for submitting poster abstracts August 1, deadline for early registration fee August 1, deadline for cancellation ************************************************************************ Location Austrian Federal Chancellery (Bundeskanzleramt) Festsaal Radetzkystraße 2 A-1031 Vienna ************************************************************************ Conference Secretariat Dr. Andreas Kungl Austrian Chemical Society (GÖCH), Biochemistry Subgroupc/o Institute of Pharmaceutical Chemistry University of Graz, Universitätsplatz 1, A-8010 Graz Tel.: +43 316 380 5373, Fax: +43 316 382541 E-Mail: andreas.kungl@kfunigraz.ac.at From owner-molec-model@net.bio.net Wed May 26 02:29:00 1999 Path: biosci!MINDSPRING.COM!grizzlyan From: grizzlyan@MINDSPRING.COM (Michael Sherrell) Newsgroups: bionet.molec-model Subject: MS, seqs, synths, NMRs for sale Date: 25 May 1999 20:29:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BEA6EC.EE9B4B40@user-33qsohi.dialup.mindspring.com> NNTP-Posting-Host: net.bio.net Mass spectrometers, sequencers, synthesizers, NMRs for sale: LC/Mass spectrometers: Sciex API III+ LC/MS/MS $ 69,000 ES, APCI, under PE service contract HP 1100 benchtop LC/MSD, APCI & API-electrospray, autosampler, DAD detector, < 1 year old, $130,000 Finnigan Navigator benchtop LC/MS: $ 75,000; 18 mos. old; factory refurb, install & 90-day warr. included Finnigan TSQ 7000 LC+GC/MS/MS: $ 97,500; current software; API-1 source; under Finnigan service contract Sciex 150 benchtop LC/MS: $ 98,000; 2 yrs old; includes Gilson 215 liquid handler, ELSD detector & HP 1100 HPLC. 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Michael Sherrell Grizzly Analytical 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com From owner-molec-model@net.bio.net Wed May 26 16:21:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.amsterdam.nl.net!sun4nl!uunet!ams.uu.net!ffx.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!not-for-mail From: eperozo@virginia.edu Newsgroups: bionet.molec-model Subject: Postdoctoral Position Available Date: Wed, 26 May 1999 13:09:54 -0400 Organization: University of Virginia Lines: 34 Message-ID: <374C2AE2.10F0@virginia.edu> NNTP-Posting-Host: spin.med.virginia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Computational Membrane Protein Structure A postdoctoral position is open immediately at The University of Virginia Medical Center for a computationally oriented molecular biologist. 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Applications including a CV, a description of research experience, and the addresses and telephone numbers of three references should be sent to: Dr Eduardo Perozo Department of Molecular physiology and Biological physics University of Virginia Health Science Center 1300 Jefferson Park Ave Charlottesville VA 22906 Email: eperozo@virginia.edu Ph: (804) 243-6580 Fax: (804) 982-1616 From owner-molec-model@net.bio.net Thu May 27 06:22:00 1999 Path: biosci!rutgers!nntp.upenn.edu!dsinc!newsserver.jvnc.net!198.138.0.5!newshub.northeast.verio.net!howland.erols.net!newsfeed.cwix.com!202.54.1.25!news.vsnl.net.in!not-for-mail From: "Anisha" Newsgroups: bionet.molec-model Subject: YOUNG BEAUTIFUL MODEL AVAILABLE Date: Thu, 27 May 1999 12:37:50 +0530 Organization: VSNL Lines: 175 Message-ID: <7ijuvp$isp$1@news.vsnl.net.in> NNTP-Posting-Host: ppp-185-221.bng.vsnl.net.in Mime-Version: 1.0 Content-Type: multipart/related; boundary="----=_NextPart_000_007C_01BEA83D.BBC9F980"; type="multipart/alternative" X-Trace: news.vsnl.net.in 927825721 19353 203.197.185.221 (27 May 1999 17:22:01 GMT) X-Complaints-To: postmaster@news.vsnl.net.in NNTP-Posting-Date: 27 May 1999 17:22:01 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_007C_01BEA83D.BBC9F980 Content-Type: multipart/alternative; boundary="----=_NextPart_001_007D_01BEA83D.BBC9F980" ------=_NextPart_001_007D_01BEA83D.BBC9F980 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi!=20 My name is Anisha.=20 I am 24 yrs old beautiful model from Paris, I would like to accompany you (discerning gentlemen) for dining, entertainment and pleasure in Europe.=20 I've long black hair and dark eyes,a slim good figure with beautiful = face=20 I am well educated, sociable, polite and fun to be with.=20 If you'd like to arrange a liaison, you can contact me at : =20 ------=_NextPart_001_007D_01BEA83D.BBC9F980 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 

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If you'd like to arrange a liaison, you can contact me at :

=20

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AFFFFABRRRQB/9k= ------=_NextPart_000_007C_01BEA83D.BBC9F980-- From owner-molec-model@net.bio.net Thu May 27 08:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 May 1999 02:00:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199905270900.CAA17682@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-molec-model@net.bio.net Fri May 28 14:13:00 1999 Path: biosci!unq.edu.ar!gustavo From: gustavo@unq.edu.ar (Gustavo Parisi) Newsgroups: bionet.molec-model Subject: alignment Date: 28 May 1999 08:13:52 -0700 Organization: CEI Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <374EAFCC.1DB902D9@unq.edu.ar> Reply-To: gustavo@unq.edu.ar NNTP-Posting-Host: net.bio.net I'm looking for a software to obtain an alignment between several sequences and a protein structure. Thanks in advance. 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CALL NOW!!! 1-937-586-9313 From owner-molec-model@net.bio.net Mon May 31 08:48:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!dispose.news.demon.net!demon!newspeer.clara.net!news.clara.net!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci From: 13453136@compuserve.com Newsgroups: bionet.molec-model Subject: INTERNATIONAL DRIVERS LICENCE Date: 31 May 1999 10:42:13 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: <09425720372146@compuserve.com> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 928143733 2398 193.62.192.80 (31 May 1999 09:42:13 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 31 May 1999 09:42:13 GMT X-Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA16720 for ; Mon, 31 May 1999 10:42:11 +0100 (BST) X-Received: from mcsnt2.mcs.co.uk (mcsgate.mcs.co.uk [193.32.81.102]) by mserv1.dl.ac.uk with ESMTP id KAA19254 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from 13453136@compuserve.com); Mon, 31 May 1999 10:42:16 +0100 (BST) X-Precedence: first-class X-Received: from [193.32.50.165] by mcsnt2.admin.mcs.co.uk (NTMail 4.20.0009/NU3554.00.ef18afcd) with ESMTP id lwzbaaaa for ; Mon, 31 May 1999 10:42:57 +0100 X-Received: FROM hyh BY mcsnt2.mcs.co.uk ; Mon May 31 10:42:45 1999 X-To: guy22@aol.com X-Info: Evaluation version of NTMail at mcsnt2.mcs.co.uk Lines: 35 INTERNATIONAL DRIVER'S LICENSE Need a new driver's license? 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