From owner-molec-model@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!redstone.interpath.net!mercury.interpath.net!not-for-mail From: morgan@mercury.interpath.net (Morgan Ryan) Newsgroups: bionet.molec-model Subject: modelling on Power Mac? Date: 2 Dec 1994 08:54:59 -0500 Organization: Interpath -- Public Access UNIX for North Carolina Lines: 16 Message-ID: <3bn8vj$g3u@mercury.interpath.net> NNTP-Posting-Host: mercury.interpath.net I just traded up my Mac to a 6100 PowerPC. Nice! But suddenly I have only one working molecular graphics program, RasMol, which has a native PPC version. MolView and MacMolecule are amazingly slow in emulation on the PPC (The PPC has its own math coprocessor, but it doesn't coprocess when emulating 68k...even speedy little MacMolecule takes minutes to come up). Do I have any other options? Has anyone ported MolScript to PPC? Are there any other programs available that I don't know about? (I've read the faq's and gone to NIH etc. I'm wondering if there is something newer around that hasn't been inserted in the usual online guides.) Also, is there a freeware modeller in existence that works like Ball-and-Stick? I'm just a hobbyist--can't afford lots of money for molecular software. What do people put on the well-equipped freeware Mac molecular graphics machine besides RasMol, MolView, MacMolecule and MacBabel? Anything? Thanks. Morgan Ryan / morgan@mercury.interpath.net From owner-molec-model@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!rutgers!csn!ub!library.erc.clarkson.edu!rpi!rebecca!tethys.ph.albany.edu!TIVOL From: tivol@tethys.ph.albany.edu Newsgroups: bionet.molec-model Subject: Re: cis-trans Pro and better substrates Date: 2 Dec 1994 23:14:39 GMT Organization: SUNYA School of Public Health, Albany, NY Lines: 21 Distribution: world Message-ID: <3bo9ov$rko@rebecca.albany.edu> References: <9411291932.AA16099@spartan.ac.BrockU.CA> Reply-To: tivol@tethys.ph.albany.edu NNTP-Posting-Host: tethys.ph.albany.edu In article <9411291932.AA16099@spartan.ac.BrockU.CA>, jatkin@SPARTAN.AC.BROCKU.CA writes: > How then can we speak of either the cis or the trans-Pro conformer >as being a preferred substrate? It is the peptide that is the substrate. >One may only suppose that one solution form reacts preferentially to >another. > If the transition from cis to trans (& trans->cis) is slow compared to binding, cleavage, etc., then it makes sense to treat the cis form and the trans form as different substrates--you would certainly treat a peptide containing a d- amino acid and an l-a.a. as different even though there is a finite rate for rascimization (sp?). > Can anyone comment on the ease with which the equilibrium is >established for small peptides? Clearly the key point. If equilibrium is established only slowly, then adding only one conformer to the reaction mix gives a situation which is not at equi- librium (as is the case with many biochemical reactions). Yours, Bill Tivol From owner-molec-model@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.molec-model Subject: [ANNOUNCE] Principles of Protein Structure Date: 03 Dec 1994 23:12:46 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 64 Distribution: world Message-ID: NNTP-Posting-Host: s-crim1.dl.ac.uk A Virtual Course PRINCIPLES OF PROTEIN STRUCTURE INVITATIONS for STUDENT REGISTRATION This is an interactive multimedia Internet course covering the basic principles of protein structure and related function. It is sponsored by: Birkbeck College, University of London and The Virtual School of Natural Sciences (Globewide Network Academy). Since the initial announcement 6 weeks ago, about 30 consultants worldwide have volunteered to help in various ways, and have already contributed extremely impressive material. There are many completely novel methods of learning in this course and it has already received much interest. WE ARE NOW INVITING APPLICATIONS FOR STUDENTS ON THE COURSE. There are no fees or formal qualifications required but there ARE a number of other requirements and all students MUST READ THE INSTRUCTIONS CAREFULLY before applying. Registration will ONLY BE ACCEPTED (OR EVEN ACKNOWLEDGED) VIA THE FORMS PROTOCOL UNDER HTML/CGI. (Most browsers such as Netscape, Mosaic and lynx (text-only) support this). ALL MATERIAL RELATING TO THE COURSE IS UNDER THE URL: http://www.cryst.bbk.ac.uk/PPS/index.html Please read this before mailing us with additional questions. There are also HTML/CGI forms for adding your comments, and this is a more efficient method than e-mail. All correspondence should go to the addresses given under the course URL and no longer to me. In this way we can record and manage your mail more efficiently. I am sorry that there has been a slight delay in registration, (due to technical server problems), but we don't expect it to delay the start of the course. We expect a heavy application, but it is NOT first-come-first-served, so please make sure you read the material carefully. Peter Murray-Rust December 3 1994 BTW The WWW pages at Daresbury (http://seqnet.dl.ac.uk:8000/vsns-pps) will remain as a mirror of the Birkbeck pages, but BBK is now the primary site. I believe that all the static documents link correctly, and we also believe that the forms and scripts work - use the bugs form for any problems. I am extremely grateful to several people for their technical help with the servers (Alan Bleasby, Dave Houldershaw, Alan Mills, Marcus Speh, and Richard Westlake). If there are technical problems with the DL material, mail me. P. Peter Murray-Rust (pmr1716@ggr.co.uk) Glaxo Research & Development, Greenford, UK mbglx@seqnet.dl.ac.uk, http://www.dl.ac.uk/CBMT/pmr.html (Thanks to Alan Bleasby) From owner-molec-model@net.bio.net Tue Dec 06 22:00:00 1994 Newsgroups: bionet.molec-model,bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!arris!diachun From: diachun@arris.com (Justin Diachun) Subject: Re: modelling on Power Mac? Message-ID: Sender: usenet@arris.com Nntp-Posting-Host: oyster.arris.com Organization: Arris Pharmaceutical Corp. References: <3bn8vj$g3u@mercury.interpath.net> Date: Wed, 7 Dec 1994 02:34:21 GMT Lines: 45 Xref: biosci bionet.molec-model:180 bionet.software:10275 In article <3bn8vj$g3u@mercury.interpath.net> morgan@mercury.interpath.net (Morgan Ryan) writes: > >I just traded up my Mac to a 6100 PowerPC. Nice! But suddenly I have only >one working molecular graphics program, RasMol, which has a native PPC >version. MolView and MacMolecule are amazingly slow in emulation on the >PPC (The PPC has its own math coprocessor, but it doesn't coprocess when >emulating 68k...even speedy little MacMolecule takes minutes to come up). > Do I have any other options? Has anyone ported MolScript to PPC? >Are there any other programs available that I don't know about? (I've >read the faq's and gone to NIH etc. I'm wondering if there is something >newer around that hasn't been inserted in the usual online guides.) > Also, is there a freeware modeller in existence that works like >Ball-and-Stick? I'm just a hobbyist--can't afford lots of money for >molecular software. What do people put on the well-equipped freeware Mac >molecular graphics machine besides RasMol, MolView, MacMolecule and >MacBabel? Anything? Thanks. Morgan Ryan / morgan@mercury.interpath.net I have almost the exact same question, and a flyer on a new product. Has anyone gotten anything from the Molecular Applications Group? They list packages called Look (proteins), SegMod (homology), and MacImdad. The MacImdad product looks interesting. It claims to have a compressed PDB database that can be searched to pull up structures. It is also available on PowerPC and other Mac systems. They offer a free demo disk that I have asked for. The ad reads "Display - Analyze - Print" so I guess it is in the RasMol field of applications. I would like to hear how this product compares to anything else on the market. I have the following contact information on the flyer: Molecular Applications Group 445 Sherman Avenue, Suite T Palo Alto, Ca 94306 toll free: 1-800-229-7382 (USA only) phone: 415-473-3030 fax: 415-473-1795 email: info@mag.com disclaimer: I have no affiliation with MAG or knowledge of the product. I am simply looking for unbiased 3rd party opinions. -- Justin Diachun diachun@arris.com System Administrator Arris Pharmaceutical From owner-molec-model@net.bio.net Tue Dec 06 22:00:00 1994 Newsgroups: bionet.molec-model,bionet.software Path: biosci!ns1.faseb.org!darwin.sura.net!fconvx.ncifcrf.gov!reming From: reming@ncifcrf.gov (Mary Remington) Subject: Palindrome search software Message-ID: Organization: Frederick Cancer Research and Development Center References: <3bn8vj$g3u@mercury.interpath.net> Date: Wed, 7 Dec 1994 12:42:33 GMT Lines: 4 Xref: biosci bionet.molec-model:182 bionet.software:10282 Does anyone know of a software program that will search DNA sequences for palindromes? Thanks, Mary From owner-molec-model@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!nntp.crl.com!crl8.crl.com!not-for-mail From: sunger@crl.com (Stefan Unger) Newsgroups: bionet.molec-model,bionet.software Subject: Re: modelling on Power Mac? Followup-To: bionet.molec-model,bionet.software Date: 6 Dec 1994 21:16:21 -0800 Organization: CRL Dialup Internet Access (415) 705-6060 [Login: guest] Lines: 61 Message-ID: <3c3gf5$4u1@crl8.crl.com> References: <3bn8vj$g3u@mercury.interpath.net> NNTP-Posting-Host: crl8.crl.com X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molec-model:181 bionet.software:10278 There is a new MAC visualization and analysis package called Protein Expert that is currently being ported to Power MAC. e-mail me for more information. I am the distributor. Biosoftware Marketing 4151 Middlefield Rd, Ste 109 Palo Alto, CA 94303 415-858-0522 fax: 415-858-0521 sunger@crl.com current version 680xx with math-coprocessor. Justin Diachun (diachun@arris.com) wrote: : In article <3bn8vj$g3u@mercury.interpath.net> morgan@mercury.interpath.net (Morgan Ryan) writes: : > : >I just traded up my Mac to a 6100 PowerPC. Nice! But suddenly I have only : >one working molecular graphics program, RasMol, which has a native PPC : >version. MolView and MacMolecule are amazingly slow in emulation on the : >PPC (The PPC has its own math coprocessor, but it doesn't coprocess when : >emulating 68k...even speedy little MacMolecule takes minutes to come up). : > Do I have any other options? Has anyone ported MolScript to PPC? : >Are there any other programs available that I don't know about? (I've : >read the faq's and gone to NIH etc. I'm wondering if there is something : >newer around that hasn't been inserted in the usual online guides.) : > Also, is there a freeware modeller in existence that works like : >Ball-and-Stick? I'm just a hobbyist--can't afford lots of money for : >molecular software. What do people put on the well-equipped freeware Mac : >molecular graphics machine besides RasMol, MolView, MacMolecule and : >MacBabel? Anything? Thanks. Morgan Ryan / morgan@mercury.interpath.net : I have almost the exact same question, and a flyer on a new product. : Has anyone gotten anything from the Molecular Applications Group? : They list packages called Look (proteins), SegMod (homology), and : MacImdad. The MacImdad product looks interesting. It claims to have : a compressed PDB database that can be searched to pull up structures. : It is also available on PowerPC and other Mac systems. They offer a : free demo disk that I have asked for. The ad reads "Display - Analyze : - Print" so I guess it is in the RasMol field of applications. I : would like to hear how this product compares to anything else on the : market. : I have the following contact information on the flyer: : Molecular Applications Group : 445 Sherman Avenue, Suite T : Palo Alto, Ca 94306 : toll free: 1-800-229-7382 (USA only) : phone: 415-473-3030 : fax: 415-473-1795 : email: info@mag.com : disclaimer: I have no affiliation with MAG or knowledge of the product. : I am simply looking for unbiased 3rd party opinions. : -- : Justin Diachun : diachun@arris.com : System Administrator : Arris Pharmaceutical From owner-molec-model@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!cc.UManitoba.CA!gordonr From: gordonr@cc.UManitoba.CA (Richard Gordon) Newsgroups: bionet.molec-model Subject: theoretical biology Date: 7 Dec 1994 05:57:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3bvk3j$o3n@erinews.ericsson.se> NNTP-Posting-Host: net.bio.net International organization of theoretical biologists? Dear Colleague: We have been running a small Canadian Society for Theoretical Biology (CSTB) for the past decade which has been attracting 1/3 international memberships. We charge only Can$25/yr for membership. We are at a critical juncture, needing new people to take active participation. With the cost of international travel and the lure of specialty conferences, it is difficult for us to get together physically. Yet there is a need for developing an intellectual community of like-minded scientists. Theoretical biologists are in a difficult position right now, perhaps analogous to theoretical physicists before quantum mechanics. There is great potential; we know the experimentalists need us; but in general they don't know that, and we have no niche. We think it is time to rethink whether the CSTB should continue to identify itself as a Canadian organisation, or whether we should become more explicitly international. It seems that our common bond is not Canadian residency, but rather a common international interest in theoretical biology and a desire to communicate. The services we have been able to offer to our members include a Newsletter, reduced rate subscriptions to the Journal of Biological Systems, and an Email network. We need to redefine our role, keeping in mind that there already exist several other organisations with overlapping interests, such as the SMB (Society for Mathematical Biology). The distinction between theoretical biology and mathematical biology is discussed in: Gordon, R. (1993). Careers in theoretical biology. Carolina Tips 56(3), 9-11. which might be a good point for beginning our deliberations. If you would like a copy of this just send a request to Dick Gordon at GordonR@cc.UManitoba.ca You are all encouraged to contribute to our discussion, whether or not you are a member of CSTB at the present time. Please send your comments to CSTB@biome.bio.ns.ca so that we can continue this discussion. To join, send the message subscribe cstb to Majordomo@biome.bio.ns.ca Dick Gordon, CSTB President Department of Radiology, University of Manitoba Room ON104, Health Sciences Centre, 820 Sherbrook Street Winnipeg, MB R3A 1R9 Canada Phone: (204) 787-1076, Fax: (204) 783-8565, E-mail: GordonR@cc.UManitoba.ca Bill Silvert, CSTB Secretary/Treasurer Habitat Ecology Division (HED), Bedford Inst. of Oceanography P. O. Box 1006, Dartmouth, Nova Scotia, CANADA B2Y 4A2. Tel. (902)426-1577 InterNet Address: silvert@biome.bio.ns.ca Fax (902)426-2256 HED runs a WWW server at URL=http://biome.bio.dfo.ca From owner-molec-model@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!rutgers!csn!yuma!purdue!mozo.cc.purdue.edu!darwin2.bio.purdue.edu!user From: flip@bogie2.bio.purdue.edu (Phillip D. Russell) Newsgroups: bionet.molec-model,bionet.software Subject: Re: modelling on Power Mac? Date: Wed, 07 Dec 1994 18:59:24 -0600 Organization: Purdue University Lines: 39 Message-ID: References: <3bn8vj$g3u@mercury.interpath.net> NNTP-Posting-Host: darwin2.bio.purdue.edu Xref: biosci bionet.molec-model:184 bionet.software:10293 In article , diachun@arris.com (Justin Diachun) wrote: > In article <3bn8vj$g3u@mercury.interpath.net> morgan@mercury.interpath.net (Morgan Ryan) writes: > > > >I just traded up my Mac to a 6100 PowerPC. Nice! But suddenly I have only > >one working molecular graphics program, RasMol, which has a native PPC > >version. MolView and MacMolecule are amazingly slow in emulation on the > >PPC (The PPC has its own math coprocessor, but it doesn't coprocess when > >emulating 68k...even speedy little MacMolecule takes minutes to come up). > > Do I have any other options? Has anyone ported MolScript to PPC? > >Are there any other programs available that I don't know about? (I've > >read the faq's and gone to NIH etc. I'm wondering if there is something > >newer around that hasn't been inserted in the usual online guides.) > I have almost the exact same question, and a flyer on a new product. > Has anyone gotten anything from the Molecular Applications Group? > They list packages called Look (proteins), SegMod (homology), and > MacImdad. The MacImdad product looks interesting. It claims to have > a compressed PDB database that can be searched to pull up structures. > It is also available on PowerPC and other Mac systems. They offer a > free demo disk that I have asked for. The ad reads "Display - Analyze > - Print" so I guess it is in the RasMol field of applications. I > would like to hear how this product compares to anything else on the > market. We have a FREE program that runs native on the PowerMac and blows the commercial programs away. It's called MolView and you can get it from: http://www.bio.purdue.edu/MolView/MolView.html Flip -- __@ Phillip "Flip" Russell | Purdue University __@ _ -_,_-\<,_flip@bogie2.bio.purdue.edu | West Lafayette, IN _ -\<,_ (_)-----/-(_) The important things... (_)-/-(_) My bikes and my Macintosh From owner-molec-model@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!news.dfn.de!scsing.switch.ch!elna.ethz.ch!smac.ethz.ch!user From: tan@mol.biol.ethz.ch (Song Tan) Newsgroups: bionet.molec-model,bionet.software Subject: Re: Palindrome search software Date: Wed, 07 Dec 1994 19:27:53 +0100 Organization: ETH-Honggerberg (Swiss Federal Institute of Technology) Lines: 14 Message-ID: References: <3bn8vj$g3u@mercury.interpath.net> NNTP-Posting-Host: smac.ethz.ch Xref: biosci bionet.molec-model:185 bionet.software:10295 > Does anyone know of a software program that will search DNA sequences for > palindromes? Thanks, Mary Programs that analyze sequences for possible RNA stemloop structures should do the trick. STEMLOOP in the GCG package is one example. Hope this helps. -- Song Tan Institute for Molecular Biology and Biophysics ETH-Honggerberg (Swiss Federal Institute of Technology) 8093 Zurich, Switzerland email: tan@mol.biol.ethz.ch From owner-molec-model@net.bio.net Thu Dec 08 22:00:00 1994 Newsgroups: bionet.molec-model Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uunet!zib-berlin.de!uni-paderborn.de!urmel.informatik.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!yorvic.york.ac.uk!priest From: priest@yorvic.york.ac.uk (Stuart Priest) Subject: Re: FDIV bug in Pentium chips!!! Message-ID: <1994Dec8.120715.20654@newsserver.rrzn.uni-hannover.de> Sender: news@newsserver.rrzn.uni-hannover.de (News Service) Reply-To: priest@yorvic.york.ac.uk Organization: Department of Chemistry, University of York References: <3b2msv$10pj@quartz.ucs.ualberta.ca> <3bl9af$jlp@xap.xyplex.com> <3bo1qf$3j2@news.iastate.edu> Date: Thu, 8 Dec 1994 12:07:15 GMT Lines: 88 In article <3bo1qf$3j2@news.iastate.edu>, kurtg@iastate.edu (Kurt R Glaesemann) writes: |> In article <3bl9af$jlp@xap.xyplex.com>, wrote: |> >By the way...If you do any serious number crunching and use 256 in your |> >calculations such as cell A1 (4195835 * 256) |> > cell A2 (3145727 / 256) |> > cell A3 =a1/a2 |> >You are boned. The Pentium will give the result 87407.92362 |> >Acual answer is 87413.2569 |> > |> >Hmmmmmm The error is to the LEFT of the decimal point. These Chips Suck! |> |> You really didn't need more than three significant figures ;-) |> |> >Have fun doing taxes...remember calculations done on a Pentium are still your |> >responsibility. You will be liable for all interest and penalties! |> |> I wonder if water comes out linear using quantum mechanics programs on |> pentiums. :-( |> |> |> -- |> kurtg@iastate.edu (For those of you not up on the latest.... a bug was found in the Pentium's math coprocessor a week ago. Intel acknowledged that it knew about it for a long time.) Q&A: THE PENTIUM FDIV BUG Q: How many Pentium designers does it take to screw in a light bulb? A: 1.99904274017, but that's close enough for non-technical people. Q: What do you get when you cross a Pentium PC with a research grant? A: A mad scientist. Q: What's another name for the "Intel Inside" sticker they put on Pentiums? A: The warning label. Q: What do you call a series of FDIV instructions on a Pentium? A: Successive approximations. Q: Complete the following word analogy: Add is to Subtract as Multiply is to: 1) Divide 2) ROUND 3) RANDOM 4) On a Pentium, all of the above A: Number 4. Q: What algorithm did Intel use in the Pentium's floating point divider? A: "Life is like a box of chocolates." (Source: F. Gump of Intel) Q: Why didn't Intel call the Pentium the 586? A: Because they added 486 and 100 on the first Pentium and got 585.999983605. Q: According to Intel, the Pentium conforms to the IEEE standards 754 and 854 for floating point arithmetic. If you fly in aircraft designed using a Pentium, what is the correct pronunciation of "IEEE"? A: Aaaaaaaiiiiiiiiieeeeeeeeeeeee! TOP TEN NEW INTEL SLOGANS FOR THE PENTIUM - -------------------------------------------------------------------------- 9.9999973251 It's a FLAW, Dammit, not a Bug 8.9999163362 It's Close Enough, We Say So 7.9999414610 Nearly 300 Correct Opcodes 6.9999831538 You Don't Need to Know What's Inside 5.9999835137 Redefining the PC -- and Mathematics As Well 4.9999999021 We Fixed It, Really 3.9998245917 Division Considered Harmful 2.9991523619 Why Do You Think They Call It *Floating* Point? 1.9999103517 We're Looking for a Few Good Flaws 0.9999999998 The Errata Inside -- #### (o o) +------------------------oooO---(__)---Oooo-----------------------------+ | Stuart Priest, Computer Manager priest@yorvic.york.ac.uk | | Protein Structure Group http://www.yorvic.york.ac.uk/~priest/ | ! Department of Chemistry | | University of York Telephone : 44 1904 432592 | | Heslington, York YO1 5DD, U.K. Fax : 44 1904 410519 | +-----------------------------------------------------------------------+ || || (__) (__) From owner-molec-model@net.bio.net Sat Dec 10 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!panix!not-for-mail From: jnr@panix.com (Josh Rubin) Newsgroups: bionet.molec-model Subject: Structure of DNA Date: 11 Dec 1994 16:41:59 -0500 Organization: PANIX Public Access Internet and Unix, NYC Lines: 14 Message-ID: <3cfrn7$ik6@panix.com> NNTP-Posting-Host: panix.com I would appreciate it if anyone would email me the basic physical dimensions of a DNA molecule, e.g., how many pairs of bases make one complete 360-degree turn, how far from one base pair to the next, and (if this makes sense) how far from the center of the spiral are the base pairs. TIA Josh Joshua N. Rubin (jnr@panix.com) 31 East 31st Street, Apt. 2E New York, NY 10016 (212) 213-5569 From owner-molec-model@net.bio.net Sat Dec 10 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!news.alpha.net!solaris.cc.vt.edu!swiss.ans.net!newstf01.news.aol.com!newsbf01.news.aol.com!not-for-mail From: loppen@aol.com (LOPPEN) Newsgroups: bionet.molec-model Subject: Structure Files Date: 11 Dec 1994 08:05:03 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 4 Sender: news@newsbf01.news.aol.com Message-ID: <3cetdv$lks@newsbf01.news.aol.com> NNTP-Posting-Host: newsbf01.news.aol.com I'm interested in obtaining structure files of simple molecules for use in RasMol. I understand they exist in the Cambridge Structural Database. Can they be accessed by FTP? If so how? Thanks........Larry From owner-molec-model@net.bio.net Sun Dec 11 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uxa.cso.uiuc.edu!dalke From: dalke@uxa.cso.uiuc.edu (Andrew Dalke) Newsgroups: bionet.molec-model Subject: Re: Structure of DNA Date: 12 Dec 1994 03:48:52 GMT Organization: University of Illinois at Urbana Lines: 13 Message-ID: <3cgh74$31g@vixen.cso.uiuc.edu> References: <3cfrn7$ik6@panix.com> NNTP-Posting-Host: uxa.cso.uiuc.edu In article <3cfrn7$ik6@panix.com> jnr@panix.com (Josh Rubin) writes: >I would appreciate it if anyone would email me the basic physical >dimensions of a DNA molecule, e.g., how many pairs of bases >make one complete 360-degree turn, >[...] Not meaning disrespect or anything but ... Are you asking us to do your homework? Andrew dalke@uiuc.edu From owner-molec-model@net.bio.net Sun Dec 11 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!swrinde!pipex!uunet!comp.vuw.ac.nz!canterbury.ac.nz!chmeds.ac.nz!gjacobs From: gjacobs@chmeds.ac.nz Newsgroups: bionet.molec-model Subject: Machines for 3D modelling... which??? Message-ID: <1994Dec12.143156.772@chmeds.ac.nz> Date: 12 Dec 94 14:31:56 +1200 References: Lines: 19 Q: Does anyone what machines are worth investigating (beyond SGIs, that is) for molecular modelling? What are their (comparative) performances for 3D work? Note that some other companies do have the licence for the Silicon Graphics (SGI) graphics language (GL) - but I don't know which! Any ideas?? In particular, is there anyway to have top-end 3D grpahics on a DEC Alpha? Grant Jacobs ---------------------------------------------------------------- Dr. Grant Jacobs Dept. Pathology email: GJacobs@chmeds.ac.nz Christchurch Medical School, or: G.Jacobs@chmeds.ac.nz Chrischurch, P.O. Box 4345, phone: (03) 364 0579 NEW ZEALAND. or: (03) 364 0009 (formerly, MRC Laboratory of FAX: (03) 364 0525 Molecular Biology, Cambridge, UK) From owner-molec-model@net.bio.net Sun Dec 11 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!swrinde!pipex!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molec-model Subject: Re: Structure Files Date: 12 Dec 1994 21:24:27 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 13 Message-ID: <3cif2b$2pbd@sat.ipp-garching.mpg.de> References: <3cetdv$lks@newsbf01.news.aol.com> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] LOPPEN (loppen@aol.com) wrote: > I'm interested in obtaining structure files of simple molecules for use in > RasMol. I understand they exist in the Cambridge Structural Database. Can > they be accessed by FTP? If so how? AFAIK the CSD cannot be by FTP. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-molec-model@net.bio.net Sun Dec 11 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!sol.ctr.columbia.edu!news.columbia.edu!konichiwa.cc.columbia.edu!hcb8 From: "Eluemuno R. Blyden" Newsgroups: bionet.molec-model Subject: Re: theoretical biology Date: Mon, 12 Dec 1994 00:19:28 -0500 Organization: Columbia University Lines: 22 Message-ID: References: <3bvk3j$o3n@erinews.ericsson.se> NNTP-Posting-Host: konichiwa.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: hcb8@konichiwa.cc.columbia.edu In-Reply-To: In reply to your posting I would like to say that You ARE needed on an international level. I particularly identified with your comparison to the evolution of physics. Please count me in as an enthusiastic supporter of your accession to global networkdom and add me to any mailing lists that you now have. I am interested in the area of sequence structure relations and also have a small software company that has developed medical imaging software for PCs and is working on visualisation programs for gene sequence analysis. Please send me information about how to join your society to: dr. Eluemuno R. Blyden Khepera Group, LLC 220 Manhattan Ave #5R New York City, NY 10025 blyden@bio.vu.nl hcb8@columbia.edu erb From owner-molec-model@net.bio.net Mon Dec 12 22:00:00 1994 Newsgroups: bionet.molec-model Path: biosci!newshost.lanl.gov!news.ttu.edu!aurora.LaTech.edu!darwin.sura.net!nih-csl!rvenable From: rvenable@deimos.cber.nih.gov (Rick Venable) Subject: Re: Machines for 3D modelling... which??? Message-ID: <1994Dec13.030754.17280@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: FDA/CBER Biophysics Lab X-Newsreader: TIN [version 1.2 PL2] References: <1994Dec12.143156.772@chmeds.ac.nz> Date: Tue, 13 Dec 1994 03:07:54 GMT Lines: 38 On 12 Dec 94 14:31:56 +1200 gjacobs@chmeds.ac.nz pontificated: > Q: Does anyone what machines are worth investigating (beyond SGIs, that is) > for molecular modelling? What are their (comparative) performances for > 3D work? HP 9000/7?5, DEC Alpha, IBM RS6000/5?? at least; both SGI and some IBMs have *hardware* to do GL quickly, while HP and DEC machines have better raw number crunching power. For software using X windows, especially PEX, GL hardware may not offer much advantage to SGI and IBM machines. Your relative performance may also be depend a good deal on the size ot the molecular system, who wrote the software you are using, how well tuned and/or busy the machine is, and not necessarily depend solely on who made the machine. You may wish to consider the ease of obtaining service and/or replacement parts and peripheral devices in your locale, as well as performance. You may wish to evaluate software first, then get the machine it runs best on. > Note that some other companies do have the licence for the Silicon Graphics > (SGI) graphics language (GL) - but I don't know which! Any ideas?? There is also a freely distributed software package for X11 which emulates the GL calls on *any* X windows system, but possibly not with anything close to the speed of hardware GL. If the rate limiting factor is floating point calculation speed, graphics rendering speed doesn't matter so much, though. > In particular, is there anyway to have top-end 3D grpahics on a DEC Alpha? Kubota makes an add-on graphics engine for DEC Alpha, especially for rendering volumetric surfaces rapidly. Contact Kubota or your DEC salesperson. > Grant Jacobs > ---------------------------------------------------------------- -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| / Not an official statement \ rvenable@deimos.cber.nih.gov \/ |=| \ or position of the FDA. / From owner-molec-model@net.bio.net Mon Dec 12 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!not-for-mail From: jnr@panix.com (Josh Rubin) Newsgroups: bionet.molec-model Subject: Re: Structure of DNA Date: 12 Dec 1994 19:09:53 -0500 Organization: PANIX Public Access Internet and Unix, NYC Lines: 25 Message-ID: <3ciooh$kb9@panix.com> References: <3cfrn7$ik6@panix.com> <3cgh74$31g@vixen.cso.uiuc.edu> NNTP-Posting-Host: panix.com Andrew Dalke writes: >In article <3cfrn7$ik6@panix.com> jnr@panix.com (Josh Rubin) writes: >>I would appreciate it if anyone would email me the basic physical >>dimensions of a DNA molecule, e.g., how many pairs of bases >>make one complete 360-degree turn, > Not meaning disrespect or anything but ... > Are you asking us to do your homework? Well, no . . . I want to model the molecule for fun using Alias Sketch!, a computer graphics program that runs on a Mac. It's not my day job and it's not homework. I've created a reasonable facsimile using dimensions from illustrations, but I don't know if these are accurate. Josh Joshua N. Rubin (jnr@panix.com) 31 East 31st Street, Apt. 2E New York, NY 10016 (212) 213-5569 From owner-molec-model@net.bio.net Mon Dec 12 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!laue.biochem.ubc.ca!ywchen From: ywchen@laue.biochem.ubc.ca (Y. W. Chen) Newsgroups: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Subject: BIOLOGICAL IMAGES NEWSGROUP? [Re: BIOLOGY IMAGES] Date: 13 Dec 1994 20:34:37 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 10 Distribution: world Message-ID: <3cl0gt$alv@nntp.ucs.ubc.ca> References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> NNTP-Posting-Host: laue.biochem.ubc.ca Xref: biosci bionet.software:10364 alt.binaries.pictures.d:10227 bionet.xtallography:1378 bionet.molec-model:198 Dear all, There are a whole gallery of biologically-related superb graphic images (eg. from structural works) scattered in various labs. Anyone vote for forming a new usenet news group collecting these pictures ? I am interested but I haven't got storage disk space and the expertise to run the newsgroup. Furthermore, I think a discussion group on how to generate these pictures will be helpful for communicating ideas as well. Yu Wai CHEN Department of Biochemistry & Molecular Biology University of British Columbia 2146 Health Sciences Mall Vancouver BC CANADA From owner-molec-model@net.bio.net Tue Dec 13 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!inherit.lmb.uni-muenchen.de!user From: Steipe@vms.biochem.mpg.de (Boris Steipe) Newsgroups: bionet.molec-model Subject: Re: Structure of DNA Followup-To: bionet.molec-model Date: 14 Dec 1994 10:42:52 GMT Organization: Genzentrum, biostructure lab Lines: 22 Distribution: world Message-ID: References: <3cfrn7$ik6@panix.com> NNTP-Posting-Host: 141.84.48.171 In article <3cfrn7$ik6@panix.com>, jnr@panix.com (Josh Rubin) wrote: > I would appreciate it if anyone would email me the basic physical > dimensions of a DNA molecule, e.g., how many pairs of bases > make one complete 360-degree turn, how far from one base pair to > the next, and (if this makes sense) how far from the center > of the spiral are the base pairs. Stryer BIOCEMISTRY (every biochemists basic text) gives: 10 base pairs per turn 34 A per turn, i.e. 3.4 A per base (1 Angstrom = 10^^-10m) diameter is given as 20 A, distance from center depends on what you mean: base ? phosphate ? closest some probe (e.g. a water molecule) can approach ? hydrogen furthest away from center ? etc. But: real DNA is somwhat bent and usually not exactly in the ideal B, A or Z conformation. If you need, I could mail you some real coordinates. Greetings Boris (steipe@vms.biochem.mpg.de) From owner-molec-model@net.bio.net Wed Dec 14 22:00:00 1994 Path: biosci!agate!news.duke.edu!usenet From: dpk@acpub.duke.edu (Dean Kanipe) Newsgroups: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [Re: BIOLOGY IMAGES] Date: 15 Dec 1994 08:52:54 GMT Organization: Duke University Lines: 12 Message-ID: <3cp056$11d@news.duke.edu> References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> <3cntjh$2anp@sat.ipp-garching.mpg.de> NNTP-Posting-Host: ddcd82196.mc.duke.edu X-Newsreader: WinVN 0.92.1 Xref: biosci bionet.software:10397 alt.binaries.pictures.d:10248 bionet.xtallography:1382 bionet.molec-model:201 In article <3cntjh$2anp@sat.ipp-garching.mpg.de>, krasel@alf.biochem.mpg.de (Cornelius Krasel) says: >I don't think a newsgroup would be appropriate. What about a centralized >ftp/gopher/www server? > >--Cornelius. I second this motion. A WWW page linking the existing resources would be a much more efficient way of doing it. I think that if you propose this to the Bio groups, you may find someone who can take it on as a project. dpk From owner-molec-model@net.bio.net Wed Dec 14 22:00:00 1994 Path: biosci!galaxy.ucr.edu!library.ucla.edu!europa.eng.gtefsd.com!gatech!newsfeed.pitt.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [Re: BIOLOGY IMAGES] Followup-To: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Date: 14 Dec 1994 23:03:13 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 16 Distribution: world Message-ID: <3cntjh$2anp@sat.ipp-garching.mpg.de> References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:10394 alt.binaries.pictures.d:10245 bionet.xtallography:1381 bionet.molec-model:200 Y. W. Chen (ywchen@laue.biochem.ubc.ca) wrote: > There are a whole gallery of biologically-related superb graphic images > (eg. from structural works) scattered in various labs. Anyone vote for > forming a new usenet news group collecting these pictures ? I am > interested but I haven't got storage disk space and the expertise to > run the newsgroup. I don't think a newsgroup would be appropriate. What about a centralized ftp/gopher/www server? --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-molec-model@net.bio.net Wed Dec 14 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!gumby!yale!yale!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Newsgroups: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [Re: BIOLOGY IMAGES] Date: 14 Dec 1994 15:59:28 GMT Organization: National Insts. of Health Lines: 43 Distribution: world Message-ID: <3cn4p0$ebr@babyblue.cs.yale.edu> References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) NNTP-Posting-Host: spasm.niddk.nih.gov Xref: biosci bionet.software:10398 alt.binaries.pictures.d:10251 bionet.xtallography:1383 bionet.molec-model:202 In article <3cl0gt$alv@nntp.ucs.ubc.ca>, ywchen@laue.biochem.ubc.ca (Y. W. Chen) writes: |> Dear all, |> |> There are a whole gallery of biologically-related superb graphic images (eg. from structural works) scattered in various labs. Anyone vote for forming a new usenet news group collecting these pictures ? I am interested but I haven't got storage disk spa|> ce and the expertise to run the newsgroup. Furthermore, I think a discussion group on how to generate these pictures will be helpful for communicating ideas as well. |> |> Yu Wai CHEN |> Department of Biochemistry & Molecular Biology |> University of British Columbia |> 2146 Health Sciences Mall |> Vancouver BC |> CANADA NO! This is entirely inappropriate for a newsgroup. These images are not constantly changing and, as you point out, are very large. Why should *thousands* of sites waste many many megabytes of disk space holding pictures that only a few people are interested in? If you're familiar with USENET, you'll realize that the local site administrators will delete the pictures posted to these groups as soon as they appear. Before proposing boneheaded things like this, PLEASE read news.announce.newusers like you're supposed to. An FTP or WWW site, where only one machine has to waste space on these pictures, is a far more appropriate way of distributing them. And by the way, several sites of this sort already exist (take a look at http:://www.nih.gov). Sheesh. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-molec-model@net.bio.net Wed Dec 14 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!hudson.lm.com!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!seqvax.caltech.edu!mathog From: mathog@seqvax.caltech.edu (David Mathog) Newsgroups: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [Re: BIOLOGY IMAGES] Date: 15 Dec 1994 09:30 PST Organization: Division of Biolgy, CALTECH Lines: 24 Distribution: world Message-ID: <15DEC199409303676@seqvax.caltech.edu> References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> NNTP-Posting-Host: seqvax.bio.caltech.edu News-Software: VAX/VMS VNEWS 1.41 Xref: biosci bionet.software:10404 alt.binaries.pictures.d:10255 bionet.xtallography:1385 bionet.molec-model:203 In article <3cl0gt$alv@nntp.ucs.ubc.ca>, ywchen@laue.biochem.ubc.ca (Y. W. Chen) writes... >There are a whole gallery of biologically-related superb graphic images >etc. > We don't really need to spray these all over the Internet, do we? Seems like a major waste of bandwidth and disk space. This isn't to say that biological images aren't valuable, just that a news group dedicated to them should probably restrict itself to notices of image availability, image content, and some technically related material. If mixed in with that were a steady stream of images it would dilute the information content and probably get the newsgroup restricted to a very short disk life. It *would* be nice if there were a definitive Biology Images Web page, especially one that had some way to search for images by content, something like "list all images of Drosophila wings." Regards, David Mathog mathog@seqvax.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-molec-model@net.bio.net Wed Dec 14 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!news2.near.net!satisfied.elf.com!rpi!rebecca!tethys.ph.albany.edu!TIVOL From: tivol@tethys.ph.albany.edu Newsgroups: bionet.molec-model Subject: Pentium haiku Date: 15 Dec 1994 15:58:48 GMT Organization: SUNYA School of Public Health, Albany, NY Lines: 3 Message-ID: <3cpp3o$j69@rebecca.albany.edu> Reply-To: tivol@tethys.ph.albany.edu NNTP-Posting-Host: tethys.ph.albany.edu Pi is equal to three In Tennessee And on a Pentium chip From owner-molec-model@net.bio.net Thu Dec 15 22:00:00 1994 Newsgroups: bionet.molec-model Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!news.doit.wisc.edu!decwrl!netcomsv!netcom.com!dougnb From: dougnb@netcom.com (Doug Neubauer) Subject: Molec. Dynamics Simulator Message-ID: Organization: NETCOM On-line Communication Services (408 261-4700 guest) Date: Fri, 16 Dec 1994 09:33:28 GMT Lines: 22 Hello. I have finished a molecular dynamics simulator for the SPC model of water. The core routines are essentially taken from: Allen-Tildesley, Computer Simulation of Liquids, and I added code for the coulomb force calculations, and the SPC model. It is, I think, more useful as a learning tool than a practical simulator, (although it does generate answers which match published data), for those like me, who are reading through Allen-Tildesley, and would like something which follows on from the Allen-Tildesley building blocks F.1-F.37, but not so complicated as a full-featured simulator such as Amber. If you are interested, send me email, and I will send you a copy. Regards. Doug Neubauer From owner-molec-model@net.bio.net Thu Dec 15 22:00:00 1994 Newsgroups: bionet.molec-model Path: biosci!agate!howland.reston.ans.net!news.starnet.net!wupost!uhog.mit.edu!bloom-beacon.mit.edu!world!chi From: chi@world.std.com (Cambridge Healthtech Institute) Subject: Small Molecule Mimetics Meeting Message-ID: Organization: The World Public Access UNIX, Brookline, MA X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 16 Dec 1994 13:39:13 GMT Lines: 7 Cambridge Healthtech Institute is organizing programs on Small Molecule Mimetics (April 10-11 1995) and Computer Aided Drug Development (April 12-13). Both will be held in San Francisco CA. Please submit poster titles and abstracts to chi@world.std.com. Inquiries are also welcome. From owner-molec-model@net.bio.net Thu Dec 15 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: dcarucci@hgmp.mrc.ac.uk (Dr. D.J. Carucci) Newsgroups: bionet.molec-model Subject: Predicted 3D structure Date: 16 Dec 1994 16:28:12 -0000 Lines: 23 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3csf6s$7th@mserv1.dl.ac.uk> Original-To: molmodel@dl.ac.uk Hi: I have cloned a new molecule that is structurally related to G-protein receptors. I would like to model the 3D structure of this new protein based on the 3D structure of other G-protein receptor molecules - to date bacteriorhodopsin. What computer programs are available to help me? I understand there is a program which "threads" a new protein primary structure through the 3D structure of another - It was in Science I believe. Thanks Dan _________________________________________________________________ Daniel J. Carucci, M.D. E-mail: d.carucci@lshtm.ac.uk Dept. of Medical Parasitology Tel: 44-71-927-2341 London School of Hygiene and Tropical Medicine FAX: 636-8739 Keppel Street London WC1E 7HT United Kingdom From owner-molec-model@net.bio.net Thu Dec 15 22:00:00 1994 Path: biosci!agate!spool.mu.edu!uwm.edu!news.doit.wisc.edu!ted.bocklabs.wisc.edu!user From: sspencer@rhino.bocklabs.wisc.edu (Stephan Spencer) Newsgroups: bionet.software,bionet.xtallography,bionet.molec-model Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [I'll provide the Web page] Date: 16 Dec 1994 15:28:51 GMT Organization: Institute for Molecular Virology, Univ of Wisconsin Lines: 33 Distribution: world Message-ID: References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> <15DEC199409303676@seqvax.caltech.edu> NNTP-Posting-Host: ted.bocklabs.wisc.edu Xref: biosci bionet.software:10421 bionet.xtallography:1387 bionet.molec-model:207 In article <15DEC199409303676@seqvax.caltech.edu>, mathog@seqvax.caltech.edu (David Mathog) wrote: > It *would* be nice if there were a definitive Biology Images Web page, > especially one that had some way to search for images by content, something > like "list all images of Drosophila wings." I agree. I'm surprised one is not already available, but if not, I will provide such a Web page on our (Institute for Molecular Virology) server (http://www.bocklabs.wisc.edu). I need people to help, however, in the form of emailing me links to sites that they know of. I can't do the research part, as I am writing my Master's thesis and looking for a job (in Australia or New Zealand, by the way, so if you know of any biocomputing/molecular visualization jobs "down under" please email me!). Our server is an excellent example of what's available in the area of biology images. We offer animations, interactive models, and high-resolution color-coded images of virus structures solved either by X-ray crystallography or by cryo-electron microscopy and image reconstruction. Many of these images/animations are *exclusively* available on our server. The URL (address of our server) is "http://www.bocklabs.wisc.edu". You need access to the World Wide Web to view these visualizations (more info on the World Wide Web is available in the bionet.software.www group, if you are unfamiliar with this Internet protocol). Cheers Stephan Spencer Institute for Molecular Virology University of Wisconsin-Madison sspencer@rhino.bocklabs.wisc.edu From owner-molec-model@net.bio.net Fri Dec 16 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!uxa.cso.uiuc.edu!pantazis From: dennis pantazis Newsgroups: bionet.molec-model Subject: Pentium Bug posting of Thurs. Dec. 8 (?) Date: Sat, 17 Dec 1994 01:24:19 -0600 Organization: University of Illinois at Urbana Lines: 13 Message-ID: NNTP-Posting-Host: uxa.cso.uiuc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I understand that someone posted an article about a short script about 'testing' your Pentium chip. I was unable to retrieve it. Could someone who has a copy of it, or the author please foreward it to me? Thanks in advance..... Dennis Pantazis pantazis@uxa.cso.uiuc.edu From owner-molec-model@net.bio.net Fri Dec 16 22:00:00 1994 Newsgroups: bionet.software,bionet.xtallography,bionet.molec-model Path: biosci!agate!ames!cnn.nas.nasa.gov!splatter.nas.nasa.gov!bross From: bross@splatter.nas.nasa.gov (Bill Ross) Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [I'll provide the Web page] Message-ID: Sender: news@cnn.nas.nasa.gov (News Administrator) Nntp-Posting-Host: splatter.nas.nasa.gov Organization: NAS/NASA Ames Research Center References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> <15DEC199409303676@seqvax.caltech.edu> Date: Sat, 17 Dec 1994 03:22:10 GMT Lines: 11 Xref: biosci bionet.software:10429 bionet.xtallography:1392 bionet.molec-model:209 For one list-of-lists collected from the point of view of molecular simulation, see http://www.amber.ucsf.edu/amber/0Net.html E.g. from that list, here are identical pages with "interactive chemistry" http://www.ch.ic.ac.uk/chemical_mime.html http://chem.leeds.ac.uk/Project/MIME.html Bill Ross From owner-molec-model@net.bio.net Fri Dec 16 22:00:00 1994 Newsgroups: bionet.molec-model,bionet.software,bionet.xtallography Path: biosci!agate!howland.reston.ans.net!swrinde!ihnp4.ucsd.edu!network.ucsd.edu!equalizer!timbuk.cray.com!walter.cray.com!mwd From: mwd@cray.com (Mark Dalton) Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [Re: BIOLOGY IMAGES] Message-ID: <1994Dec16.102646.11985@walter.cray.com> Followup-To: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Lines: 56 Nntp-Posting-Host: pajarito.cray.com X-Newsreader: TIN [version 1.2 021193BETA PL3-CRIb] References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> Date: 16 Dec 94 10:26:46 CST Xref: biosci bionet.molec-model:211 bionet.software:10431 bionet.xtallography:1393 > Y. W. Chen (ywchen@laue.biochem.ubc.ca) wrote: > Dear all, > There are a whole gallery of biologically-related superb graphic images > (eg. from structural works) scattered in various labs. Anyone vote for > forming a new usenet news group collecting these pictures ? I am > interested but I haven't got storage disk space and the expertise to > run the newsgroup. Furthermore, I think a discussion group on how to > generate these pictures will be helpful for communicating ideas as well. > Yu Wai CHEN Well I looked at the NIH site, has plenty of pointers to Crystal structures but lacks most things besides proteins (cells,membranes,oraganelles,etc). and I also agree that it sould not be done via listservers or usenet news. However, I did manage to find other sites that seem to have a similar idea. I would find these images very helpful also, since it his helpful to write WWW/Virtual courses that have images and even animations (like cell division). I have a list of all of the biology (and other) courses I have found: http://lenti.med.umn.edu/~mwd/courses.html The place to look would be (the page and their stated goal: Science and Mathematics Education Resources http://halcyon.com/cairns/science.html The goal of this page is to serve as an atlas of all the downloadable resources for good science and mathematics instruction and learning. It will also be a place where teachers can find materials to make the job of teaching easier and students can find materials to simplify learning. There will be pointers for teachers/learners of all ages. Your comments (good or bad) are most welcome! This page has grown so much that it has been be broken up by subject area to minimize the download time for the page. For Biology: Biological Sciences Educational Resources http://www.halcyon.com/cairns/bio.html I would like to see more of a effort. I am working on a Cell Biology course and I will make my images available (for non-profit use). I have been told by others I could not use their images due to Copyright reasons and deals they had with the publisher (so you may want to be a little careful). Thanks! Mark ----- Mark Dalton CH3-S-CH2 H H O H Cray Research,Inc. | | | \ | Los Alamos,NM 87544 CH2-C-COOH //\ ---C--CH2-C-COO C-CH2-C-COO mwd@cray.com | | || || | // | NH2 \\/ \ / CH NH3 O NH3 NH URL = http://lenti.med.umn.edu/~mwd/mwd.html From owner-molec-model@net.bio.net Thu Dec 22 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sun4nl!news.nic.surfnet.nl!highway.LeidenUniv.nl!rulglj!dirk From: dirk@rulglj (Dirk Huckriede) Newsgroups: bionet.molec-model Subject: newtest Date: 23 Dec 1994 09:06:16 GMT Organization: CCC group, Organic Chemistry, Leiden University, The Netherlands Lines: 19 Message-ID: <3de3u8$pn2@highway.LeidenUniv.nl> NNTP-Posting-Host: rulglj.leidenuniv.nl X-Newsreader: TIN [version 1.2 PL2] -- ------------------------------------------------------------------------------ Dirk Huckriede Computational Chemistry Courseware Gorlaeus Laboratories Leiden University P.O. Box 9502 Phone : +31 71 274505 2300 RA Leiden Fax : +31 71 274488 The Netherlands E-mail : dirk@rulglj.leidenuniv.nl ------------------------------------------------------------------------------ "to be or nut^H^H^H -- sh^Gt, how do I delete..^?^?^? Oh No Oh NO^D^D^D -- How do I get out of this thing anyway^C^C^C Kill it^Z^Z^Z (mumble mumble) Bus error (core dumped) ------------------------------------------------------------------------------ From owner-molec-model@net.bio.net Sat Dec 24 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!news.uiowa.edu!panda From: J. Monahan Newsgroups: bionet.software,alt.binaries.pictures.d,bionet.xtallography,bionet.molec-model Subject: Re: BIOLOGICAL IMAGES NEWSGROUP? [Re: BIOLOGY IMAGES] Date: 24 Dec 1994 23:31:08 GMT Organization: U of Iowa Panda System Lines: 47 Distribution: world Message-ID: <788312193-1-11819@blue.weeg.uiowa.edu> References: <3cik8e$ac6@sparc.occ.uky.edu> <3cken9$1h9@decaxp.harvard.edu> <3cl0gt$alv@nntp.ucs.ubc.ca> <15DEC199409303676@seqvax.caltech.edu> Reply-To: jmonahn@blue.weeg.uiowa.edu NNTP-Posting-Host: blue.weeg.uiowa.edu Xref: biosci bionet.software:10492 alt.binaries.pictures.d:10410 bionet.xtallography:1402 bionet.molec-model:213 It seems to me that this sort of project would be better undertaken by a.) gathering the images, 2.) Indexing them in a hypertext form, and 3.) distributing the product on CD-ROM. 3M in Minnesota duplicates CDs in quanities of 50+ for around $2.00 each. I began a searchable graphical database of human parasites for a parasitologist here- (at the University of Iowa) A total 0f some 2500 images of the species, the effected organs, the habitats and conditions that promote infection etc. All of this fits on a single CD. Joe Monahan jmonahn@blue.weeg.uiowa.edu In note <15DEC199409303676@seqvax.caltech.edu>, mathog@seqvax.caltech.edu (David Mathog) writes: >In article <3cl0gt$alv@nntp.ucs.ubc.ca>, ywchen@laue.biochem.ubc.ca (Y. W. >>Chen) writes...There are a whole gallery of biologically-related superb >>graphic imagesetc. >> > >We don't really need to spray these all over the Internet, do we? Seems >like a major waste of bandwidth and disk space. > >This isn't to say that biological images aren't valuable, just that a news >group dedicated to them should probably restrict itself to notices of image >availability, image content, and some technically related material. If >mixed in with that were a steady stream of images it would dilute the >information content and probably get the newsgroup restricted to a very >short disk life. > >It *would* be nice if there were a definitive Biology Images Web page, >especially one that had some way to search for images by content, something >like "list all images of Drosophila wings." > >Regards, > >David Mathog >mathog@seqvax.bio.caltech.edu >Manager, sequence analysis facility, biology division, Caltech --- Joe Monahan jmonahn@blue.weeg.uiowa.edu From owner-molec-model@net.bio.net Thu Dec 29 22:00:00 1994 Newsgroups: bionet.molec-model Path: biosci!agate!howland.reston.ans.net!pipex!uunet!newsflash.concordia.ca!CC.UMontreal.CA!charron From: charron@CHIMCN.UMontreal.CA (Charron Guy) Subject: jobs Message-ID: Sender: charron@chimcn.umontreal.ca Organization: Universite de Montreal Date: Fri, 30 Dec 1994 09:14:48 GMT Lines: 7 Hello everyone, I have just completed my bachelor degree in physics and now I want to do graduate studies in a computational physics subject. I already have an article published on finding eigenvalues of very large matrices. I would like to know what is your experience in relation to job market? Any clue on this subject will be greatly appreciated.