From owner-structural-nmr@net.bio.net Wed Jun 01 23:00:00 1994 Newsgroups: bionet.structural-nmr Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!uunet!nih-csl!rvenable From: rvenable@alw.nih.gov (Rick Venable) Subject: Re: What Macintosh to use? Message-ID: <1994Jun2.040920.11434@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: FDA Biophysics Lab References: <9405311750.AA22679@pines1.ljcrf.edu> <2shb1k$ick@ousrvr.oulu.fi> Date: Thu, 2 Jun 1994 04:09:20 GMT Lines: 27 In article <2shb1k$ick@ousrvr.oulu.fi> eha@phoenix.oulu.fi (Esa Haapaniemi) writes: >: Hi. What is a good, cheap Macintosh that I can buy that will allow >: me do relatively simple NMR calculations? This is going to be for >: my own personal use, but if it is going to cost $4K or more, I can >: get a sparc5 (which I am to do the calculations). > >I'm serious when I advice you to look at Amiga4000/40 w. Emplant. >It is upgradeable to 256 M of memory and all usable on Mac side >(Emplant emulates Quadra 900 in that configuration, except maths >is some 113 % of Quadra). For faster machine you could upgrade the >Amiga to 50 MHz 040, or hopefully some RISC, and then it could be >some 2x faster than ANY Mac. I'm not sure this is good advice; Commodore, the makers of the Amiga, have recently gone bankrupt, and are likely out of business for good. I'd say get a PowerPC based Mac, and get a native mode compiler (not 68040 emulation) or wait for native mode applications. They are not that much more expensive, and the speed increase (for native mode) is worth the cost difference. I believe a C compiler is out, and that Language Systems is working on a PowerPC native Fortran compiler. -- Rick Venable =====\ |=| "Eschew FDA/CBER Biophysics Lab |____/ |=| Obfuscation" Bethesda, MD U.S.A. | \ / |=| rvenable@helix.nih.gov \/ |=| -- the Phantom Nerd From owner-structural-nmr@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: salahub@ERE.UMontreal.CA (Salahub Dennis) Newsgroups: bionet.structural-nmr Subject: (temporary) unsubscribe Date: 3 Jun 1994 18:09:18 +0100 Lines: 18 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2sno3u$h3g@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk unsubscribe str-nmr If it is possible to start again on July 15, please set it up; otherwise I'll write again. Thank you Dennis Salahub -- ************************************************************ * Dennis Salahub SALAHUB@ERE.UMONTREAL.CA * * Departement de chimie Tel. (514) 343-6755 * * Universite de Montreal Fax (514) 343-2468 * * C.P. 6128, Succ. Centre-ville * * Montreal, Quebec H3C 3J7 * * Canada * ************************************************************ From owner-structural-nmr@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!news.cso.uiuc.edu!lwalsh From: lwalsh@nemo.life.uiuc.edu (Laura L. Walsh) Newsgroups: bionet.biophysics,bionet.structural-nmr,sci.bio,sci.bio.technology Subject: Annotated PDB Listing Date: 7 Jun 94 18:56:43 GMT Organization: University of Illinois at Urbana Lines: 62 Distribution: inet Message-ID: NNTP-Posting-Host: nemo.life.uiuc.edu Xref: biosci bionet.biophysics:296 bionet.structural-nmr:139 sci.bio:9387 sci.bio.technology:1258 Once again, I am making my "Annotated Guide to the Brookhaven Protein Data Bank" available. This file includes listings for all of the files in the January, 1994 release. The main additions this year are a complete listing of all of the lysozyme files, a better organization of the DNA files, and, most importantly, structure classifications for all of the protein chains in the data bank. There is also a companion file which lists all of the sequence relations among the individual protein chains. This file is called the "Sequence Relations" file. Most importantly, if there are errors, which there probably are, given that we are dealing with 2327 files, I would appreciate being informed of such. Please cite the work as suggested in the files if you use it in your own work. A write up of the work has been submitted for publication and may appear later this year. If so, the suggested citation will change. Laura Lynn Walsh ------------------- the retrieval instructions follow ------- e-mail) send a message: select chemistry cd documents/PDB/PDB_file_list limit 500kB size 70kB get pdb_annot_jan94.txt get pdb_annot_jan94 get pdb_seq_rel_jan94 quit to MAILSERV@osc.edu ftp) ftp infomeister.osc.edu (or ftp 128.146.36.5) Name: anonymous Passwd: YOUR_e-mail_address ftp> cd /pub/chemistry/documents/PDB/PDB_file_list ftp> get pdb_annot_jan94.txt ftp> get pdb_annot_jan94 ftp> get pdb_seq_rel_jan94 ftp> quit gopher) gopher infomeister.osc.edu 73 documents PDB PDB_file_list pdb_annot_jan94 pdb_annot_jan94.txt pdb_seq_rel_jan94 WWW) http://www.osc.edu/~ccl/documents.html Protein Data Bank PDB_file_list ------------------- end retrieval instructions -------------- Laura Walsh, Beckman Institute, University of Illinois 405 N. Mathews Ave., Urbana, IL 61801 (217) 244-2894 lwalsh@silibio.ncsa.uiuc.edu From owner-structural-nmr@net.bio.net Tue Jun 07 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!pipex!bt!uknet!daresbury!not-for-mail From: Serge Iourine Newsgroups: bionet.structural-nmr Subject: "spot" Date: 8 Jun 1994 06:50:28 +0100 Lines: 13 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2t3m74$ggh@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Dear netters, Recenly I've heard something about the program (I reckon it's called SPOT) to process the data from varian spectrometer on a normal pc, so that in fact you need spectrometer only to run the sample. Subsequent expantions, integrations, etc. you may do on your own computer. Where can I obtain full info about this program? Regards, s.i. From owner-structural-nmr@net.bio.net Tue Jun 07 23:00:00 1994 Path: biosci!RISVAX.ROWLAND.ORG!HOCH From: HOCH@RISVAX.ROWLAND.ORG (Jeffrey C. Hoch) Newsgroups: bionet.structural-nmr Subject: Used NMR for sale Date: 8 Jun 1994 08:12:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <940608111223.3e1@RISVAX.ROWLAND.ORG> NNTP-Posting-Host: net.bio.net We are upgrading our NMR spectrometer, and are offering for sale our used JEOL GX-400 NMR spectrometer. Proton sensitivity is 325:1, resolution is <0.1 Hz. It is equipped for fully multi- nuclear operation, and includes an indirect H(X) probe and a photo- CIDNP probe. We will price it aggressively, since we need the space it now occupies. It can perform a variety of multi-dimensional experiments. For more details, contact: Jeff Hoch (hoch@rowland.org) Rowland Institute Cambridge, MA (USA) (617) 497-4678 From owner-structural-nmr@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!CHEMF.RUTGERS.EDU!MARLA From: MARLA@CHEMF.RUTGERS.EDU (Marla Babcock) Newsgroups: bionet.structural-nmr Subject: Nucleic Acid Structure Analysis Program Release Date: 9 Jun 1994 13:41:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: <04C94B6F401F200536@chemf.rutgers.edu> NNTP-Posting-Host: net.bio.net ANNOUNCING THE RELEASE OF A PROGRAM WHICH ANALYSES NUCLEIC ACID CRYSTALLOGRAPHIC COORDINATE DATA ACCORDINATE TO THE EMBO GUIDELINES OF 1988. Several years ago, the European Molecular Biology Organization published guidelines defining how nucleic acid duplex structures can be examined. The guidelines defined three rotational and three translational parameters between the bases comprising a base pair as well as from one base pair to the next. There are five programs readily distributed in order to perform the calculations. We are releasing a sixth which was created to be able to handle not only the calculations of normal duplexes, but also comparably examine mispaired bases, hoogstein base pairs, looped out bases, a single base adjacent to a base pair, intercalated drugs for which a coordinate frame has been defined, etc. The nucleic acid structure analysis program is written in Fortran and runs in a UNIX or VMS environment (please specify preference). The program calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand. A simple interactive user interface allows for one to specify what file is examined and which parameters to calculate. The program was designed so that the user needs to spend a minimal time reading the documentation in order for the program to run. Full disclosure of the mathematics has been made and published so that the user can readily understand what their parameters mean. The mathematics are unique for this type of calculation and aviod many of the problems previously encountered. In particular, the calculations are performed by a single rotation not sequential rotations avoiding the use of a midway coordinate frame for rotational parameter calculations. This ensures that the magnitude of the rotational parameters is strand free and direction free. Because a single rotation is used, the equations for each rotational parameter are equivalent, therefore, a 5 degree rotation about the X axis is equivalent to a 5 degree rotation about either the Y or the Z axis. This is not always true of other mathematical formulations presently being used. The mathematics used for calculating the complementary base parameters is identical to the math used to calculate the neighboring base/base pair parameters except that different axes are involved. This is not generally the case of the other available programs. In addition, since the calculations are bases upon local considerations, the value of the parameter depends on only the bases involved and are independent of adjacent bases. This allows for more accurate comparison of parameters from one structure to another. Copies of the code can be acquired by e-mailing me at: Marla@Rutchm.Rutgers.edu. Dr. Marla Babcock Dept of Chemistry Rutgers University P.O. Box 939 Piscataway, N.J. U.S.A 08855 Useful References: A users guide to the programs is provided in the paper: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: A Users Guide to a Collection of New Analysis Programs," Journal of Biomolecular Structure and Dynamics, Vol. 11, No. 3, pp 597-628, 1993. The issues surrounding the definition of nucleic acid structure parameters and how we address these issues are discussed in: Babcock, M.S., and Olson, W.K., "A New Program for the Analysis of Nucleic Acid Structure Interpretation," in Computation of Biomolecular Structures: Achievements, Problems, and Perspectives, Soumpasis, D.M., and Jovin, T.M., Eds., Springer-Verlag, Heidelberg, pp 65-85, 1993. The mathematical definitions of the nucleic acid structure parameters and the methods used to calculate them are presented in: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and Helical Structure Parameters That are Truly Comparable Between Structures," Journal of Molecular Biology, Vol. 237, pp 125-156, 1994. In order to take into account base-stacking effects and other physical constraints, the mathematical definitions we have developed contain parameters called "pivot points", which are the points about which the bases in a structure buckle, propeller twist, and open. The statistical analyses that were performed to determine the optimum positions of the pivot points are presented in: Babcock, M.S., and Olson, W.K., "The Effect of Mathematics and Coordinate System on Comparability and 'Dependencies' of Nucleic Acid Structure Parameters," Journal of Molecular Biology, Vol. 237, pp 98-125, 1994. From owner-structural-nmr@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!IPACRES.CRES.IT!VLSIGROUP From: VLSIGROUP@IPACRES.CRES.IT Newsgroups: bionet.structural-nmr Subject: "Have you an NMR database?" Date: 10 Jun 1994 04:22:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HDDME90FO696W4KQ@ipacres.cres.it> NNTP-Posting-Host: net.bio.net Hi everybody! I'm a PHd student and I'm working on Neural Network classification capabilities. I'm interested in classification of molecules by NMR: there is the possibility to use a neural network, which is a classifier trained by examples, to individuate the chemical groups present in a unknown molecula simply presenting the NMR data as input to this classifier. It is due to the capability acquired by this network during the training phase: it consists on showing to the net the NMR data as input and indicate the groups that constitute that molecula; if the training set is sufficient large, the net will acquire a generalisation capabilities that will allow it to detect the groups present in a unknow molecula. Unfortunately I have not a NMR database in a magnetic support and it construction should require a lot of time. If anybody can help me can send an e-mail message to Alessandro Tarantino gentiltar@vlsipa.cres.it Thank you in advance for your help. From owner-structural-nmr@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!LILY.CHEM.WESLEYAN.EDU!phbolton From: phbolton@LILY.CHEM.WESLEYAN.EDU (Philip H. Bolton) Newsgroups: bionet.structural-nmr Subject: hpgl & postscript to a mac Date: 15 Jun 1994 07:15:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406151516.AA15427@lily.chem.wesleyan.edu> NNTP-Posting-Host: net.bio.net We like to be able to extensively annotate our spectra for publication and slides. The best program for doing this, in our opinion, is the Macintosh version of Adobe Illustrator. However, the plot output of Varian VNMR or Biosym FELIX can not be directly put into Adobe Illustrator format. Recently we have found a shareware program which does the conversion quite nicely in a single step as well as a commercial program which works even better. HPGL method. Save HPGL format plots from either VNMR or FELIX. These are then sent via ftp to a Macintosh. The shareware program EPSfilter2.1a1 (copyright by Bryce Fowler and available on any of the Merit Macintosh sites on the net- use Mosaic or its equivalent to go to University of Michigan GOpherBLUE [gopher.archive.merit.net/11/.software-archives/] and follow the links to the graphics section) converts HPGL to Adobe Illustrator. Conversion of a typical 2D spectrum requires a minute or two. The program claims to convert postscript to Illustrator but this feature does not work in our hands. Postscript method. Save postscript format plots and then ftp these over to the Macintosh. Adobe Acrobat Distiller converts the postscript files into "portable document format" which they call pdf. The pdf files can be opened and edited by Illustrator. This route eliminates the editing of the axis and so on required in the HPGL route. Distiller is supplied with Illustrator 5.5. We have also used IslandDraw on a SUN to do the annotations. In our opinion this program is slow and awkward compared to Illustrator. We also tried out Illustrator on the SUN but found this to be slow and awkward compared to the Macintosh verstion. ---------------------------------------------------------------------------- --------------------- Philip H. Bolton Professor of Chemistry Chemistry Department Wesleyan University Middletown, CT 06459 phbolton@lily.chem.wesleyan.edu ---------------------------------------------------------------------------- --------------------- From owner-structural-nmr@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!DGGPI2.CHEM.PURDUE.EDU!bruce From: bruce@DGGPI2.CHEM.PURDUE.EDU (Bruce Luxon) Newsgroups: bionet.structural-nmr Subject: HPGL to Mac NMR Spectra software Date: 15 Jun 1994 10:50:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406151751.AA03053@dggpi2.chem.purdue.edu> NNTP-Posting-Host: net.bio.net -=-=-=-=-=- PROGRAM ANNOUNCEMENT -=-=-=-=-=-=-= HPGLtoClipboard version 1.3a "HPGLtoClipboard" is a utility for converting HPGL files generated by VarianUs VNMR or Hare's FELIX into a spectrum drawn in PICT format that can be copied into the clipboard of a Macintosh. The PICT clipboard file can be copied into any program supporting PICT format. This program supports the HPGL commands PU, PD, LB and SC. All other HPGL commands are ignored. Currently "HPGLtoClipboard" reads only the maximum SC coordinates. Requirements: MacIntosh System 7.0 or above HOW TO GET: 1. FTP anonymous to dggpi2.chem.purdue.edu OR use one of the NMR GOPHERS: a. GOPHER to infomeister.osc.edu (Ohio Supercomputer Center, Ohio State U.) -> Software / Morass b. GOPHER to nmrfam.wisc.edu (Univ. of Wisconsin, Madison) -> Other NMR Gopher Servers and NMR Software Sites / Morass c. GOPHER to micro.ifas.ufl.edu (University of Florida, Gainsville) -> NMR Software / Morass 2. cd to pub/morass/hpgl 3. get (ascii) hpgl2clip1.3.sit.hqx 4. BinHex4.0 the .hqx file (upload -> application) 5. Stuffit1.5.1 the .sit file (open archive) 6. Try the sample files. You will have to 'pull' their windows open with the resize box to see the entire spectra. Written by Kevin H. Thornton while in the David G. Gorenstein Group at Purdue University (1992) Comments or Suggestions are welcome and should be sent to: Dr. Bruce A. Luxon Department of Chemistry Purdue University West Lafayette, IN 47907 (317) 494-5289 EMAIL bruce@dggpi2.chem.purdue.edu 6/15/94 ____________________________________________________________________________ | | | |"You can't always get what you want, | Dr. Bruce A. Luxon | | But if you try sometimes, | Chemistry Department | | You just might find | Purdue University | | You get what you need ..." | W. Lafayette, IN 47907 | | | (317)494-5289; Fax (317)494-0239 | | Mick Jagger | bruce@dggpi2.chem.purdue.edu | |______________________________________|___________________________________| From owner-structural-nmr@net.bio.net Sat Jun 18 23:00:00 1994 Newsgroups: bionet.genome.chromosomes,bionet.structural-nmr Path: biosci!agate!spool.mu.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!silver.ucs.indiana.edu!bhostetl From: bhostetl@silver.ucs.indiana.edu (Brian Hostetler) Subject: Needed: info on Protein <-> Nucleic Acid Interactions Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: silver.ucs.indiana.edu Organization: Indiana University, Bloomington IN Date: Sun, 19 Jun 1994 21:35:33 GMT Lines: 9 Xref: biosci bionet.genome.chromosomes:255 bionet.structural-nmr:146 I'm looking for information (databases, pages, etc) on Protein <-> Nucleic Acid interactions (databases, pages, etc). Please reply via e-mail. Thank you, -- Brian "Life is a sexually transmitted disease with a terminal prognosis." http://sparrow.bio.indiana.edu/brian/me From owner-structural-nmr@net.bio.net Sun Jun 19 23:00:00 1994 Path: biosci!NMR.UOREGON.EDU!STRAIN From: STRAIN@NMR.UOREGON.EDU (MIKE STRAIN) Newsgroups: bionet.structural-nmr Subject: any good pdb viewers for NMR... Date: 20 Jun 1994 11:37:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <940620113003.21000982@NMR.UOREGON.EDU> NNTP-Posting-Host: net.bio.net We use "molscript" and "RasMol" for viewing pdb files on our SGI systems. I think Sun versions of both programs are available. For more information: molscript: Per Kraulis pjk@oyster.csb.ki.se RasMol: rasmol@ggr.co.uk --Michael Strain strain@nmr.uoregon.edu Institute of Molecular Biology University of Oregon Eugene, OR 97403 From owner-structural-nmr@net.bio.net Sun Jun 19 23:00:00 1994 Path: biosci!PINES1.LJCRF.EDU!elya From: elya@PINES1.LJCRF.EDU (Elya S. Kurktchi) Newsgroups: bionet.structural-nmr Subject: any good pdb viewers for NMR files? Date: 20 Jun 1994 09:00:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406201558.AA14545@pines1.ljcrf.edu> NNTP-Posting-Host: net.bio.net Hi, Are there any PDB viewers that can be compiled on a sparc10 (4.1.3C, OW, no Motif/X11R5) and can all quick viewing of PDB files? Thanks. Elya. ---------------------------------------------------------------------------- | Elya S. Kurktchi Scientific Computing Center | | Network Systems Manager La Jolla Cancer Research Foundation | | Email: elya@ljcrf.edu 10901 North Torrey Pines Road | | Phone: (619) 455-6480 x631 La Jolla, CA 92037 | | Fax : (619) 450-3432 "X-Ray Protein Crystallography" | ---------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Sun Jun 19 23:00:00 1994 Path: biosci!CADMIUM.CSB.YALE.EDU!gardner From: gardner@CADMIUM.CSB.YALE.EDU (Kevin Gardner) Newsgroups: bionet.structural-nmr Subject: Re: hpgl & postscript to a mac Date: 20 Jun 1994 08:04:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406201504.AA06458@cadmium.csb.yale.edu> NNTP-Posting-Host: net.bio.net Sorry this is a bit tardy, but I think it's a valuable contribution to this discussion: Philip H. Bolton (phbolton@lily.chem.wesleyan.edu) wrote: > We like to be able to extensively annotate our spectra for > publication and slides. The best program for doing this, in our opinion, > is the Macintosh version of Adobe Illustrator. However, the plot output of > Varian VNMR or Biosym FELIX can not be directly put into Adobe Illustrator > format. Recently we have found a shareware > program which does the conversion quite nicely in a single step as well as > a commercial program which works even better. ... > Postscript method. Save postscript format plots and then ftp these > over to the Macintosh. Adobe Acrobat Distiller converts the postscript > files into "portable document format" which they call pdf. The pdf files > can be opened and edited by Illustrator. This route eliminates the editing > of the axis and so on required in the HPGL route. Distiller is supplied > with Illustrator 5.5. I wholeheartedly agree with the premise that transferring by way of a Postscript intermediate is preferable to HPGL, and that Illustrator provides one of the best (IMHO, the best) method for annotating/stylizing those files. Users who do not have access to the Illustrator 5.5/ Acrobat Distiller package that Phil describes may be interested in checking out a freeware alternative: aimaker, available by anon ftp to toby.princeton.edu in the pub/olszewsk directory. This is a nice set of Unix scripts that work in conjunction with ghostscript to convert just about any standard Postscript into an Adobe Illustrator format file (AI88 or AI3 styles are both supported). Once converted, I've been able to work with these files using either Illustrator or Canvas, amongst others. Just my $0.02, Kevin -- ************************************************************************* Kevin Gardner Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.csb.yale.edu Bitnet: gardner@yalemed From owner-structural-nmr@net.bio.net Sun Jun 19 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!moe.ksu.ksu.edu!matt.ksu.ksu.edu!not-for-mail From: jliu@ksu.ksu.edu (J.Liu~{6+MASfNL~}) Newsgroups: bionet.structural-nmr Subject: Pulse sequence for Varian unity plus, C-H NOE Date: 19 Jun 1994 21:42:17 -0500 Organization: Kansas State University Lines: 22 Message-ID: <2u2vm9$85s@matt.ksu.ksu.edu> NNTP-Posting-Host: matt.ksu.ksu.edu Keywords: Unity plus, NOE X-Newsreader: NN version 6.5.0 #1 (NOV) Dear netters: I am looking for a pulse sequence applicable to Varian's unity plus for measuring the NOE enhancement of a bonded C-H pair. It is not a HOESY sequence though. I am trying to do a model-free analysis of my protein and I already have T1 data and will get T2 soon. References for such a pulse sequence would be: a) L.E. Key, D.A. Torchia, A. Bax, Biochemistry 1989 28 8972-8979 b) A.G. Palmer III, M. Rance, P.E. Wright, JACS 1991 113 4371-4380 So if you have such a pulse sequence for either unity (plus) or Gemini or XVR system, please e-mail me the sequence code, preferably with the parlib, maclib and tablab files to jliu@ksu.ksu.edu Thanks in advance for your help. -- (__/_) J. Liu E-mail: jliu@ksu.ksu.edu __/ . Department of Biochemistry (CB453) (/(____(__(_(_ Kansas State University, Manhattan, KS 66506 From owner-structural-nmr@net.bio.net Mon Jun 20 23:00:00 1994 Path: biosci!DGGPI2.CHEM.PURDUE.EDU!bruce From: bruce@DGGPI2.CHEM.PURDUE.EDU (Bruce Luxon) Newsgroups: bionet.structural-nmr Subject: PDB VIEWERS Date: 21 Jun 1994 11:58:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406211859.AA07415@dggpi2.chem.purdue.edu> NNTP-Posting-Host: net.bio.net -> NMR NET Another 'PDB VIEWER' (though I hesitate to use the term because it is a lot more than that) that deserves a close look is GRASP from Anthony Nicholls in Barry Honig's group at Columbia. We use GRASP to view interproton constraints during NOESY restrained MD structural refinement by MORASS and find that it has become invaluable for this purpose. GRASP reads PBD files as well as others and offers a very wide array of choices on how to view and manipulate the files. The graphics are superb and can be saved as .rgb files on SGI boxes. Anthony's email address is: nicholls@cuhhca.hhmi.columbia.EDU Also, re. MIDAS, we find best results contacting the Computer Graphics Lab at UCSF. Try Prof. Tom Ferrin - tef@cgl.ucsf.edu. Ferrin et al wrote MIDAS. Bruce ____________________________________________________________________________ | | | |"You can't always get what you want, | Dr. Bruce A. Luxon | | But if you try sometimes, | Chemistry Department | | You just might find | Purdue University | | You get what you need ..." | W. Lafayette, IN 47907 | | | (317)494-5289; Fax (317)494-0239 | | Mick Jagger | bruce@dggpi2.chem.purdue.edu | |______________________________________|___________________________________| From owner-structural-nmr@net.bio.net Mon Jun 20 23:00:00 1994 Path: biosci!INDIANA.EDU!mpagel From: mpagel@INDIANA.EDU (Marty Pagel) Newsgroups: bionet.structural-nmr Subject: pdb viewers Date: 21 Jun 1994 08:10:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Macromodel version 4.5 requires an SGI or IBM/RS 6000, and is currently available from these sources: Academic Orders Joan Horgan (212)-854-8665 jqh@still3.chem.columbia.edu (212)-854-5429 (fax) Industrial Orders Dr. Dan Chodosh (215)-885-3706 (215)-355-0954 (fax) Technical Questions The Still Group (212)-854-5143 or 8402 mmod@still3.chem.columbia.edu (212)-678-9039 PCModel is written for the IBM PC, SGI, SUN, and a few other platforms. It's similar to Macromodel, but uses a better forcefield for organic chemistry. For more information, contact: Serena Software Chemistry Department Indiana University Bloomington, IN 47405-4001 Sybyl, from Tripos, and InsightII, from Biosym, are very nice biomolecular modeling and visualization programs, but they will cost you between $3,000-$10,000. In my opinion, InsightII is the best available program for biomolecular modeling. Tripos Associates 1699 South Hanley Road Suite 303 St. Louis, MO 63144 800-323-2960 Biosym Technologies, Inc. 9685 Scranton Road San Diego, CA 92121-3752 (619)-458-9990 (619)-458-0136 (fax) Cerius2, from MSI, is great for crystallographers, and also does a fine job for biomolecular and ploymer visualization. It will also cost thousands of $. Molecular Simulations Inc. 16 New England Executive Park Burlington, MA 01803-5297 (617)-229-9800 (617)-229-9899 (fax) Hyperchem, from AutoDesk, will no longer be supported (if the support hasn't already bee pulled). Lastly, for quick visualization (without any need for structural changes), Midas does a great job for proteins, and Ribbons handles nucleic acids equally well. Their "cartoon" features do a nice job highlighting helices and sheets. I've had trouble getting in touch with the Kuntz group at UCSF, which is understandable, since they are focused on research and not product distribution, so I don't know about the availability of Midas. I've listed the address from our old Midas documentation, but I apologize if it is incorrect. Midas Kuntz Group Department of Pharmaceutical Chemistry University of California, San Francisco 94143-0446 Ribbons 2.2 Mike Carson University of Alabama at Birmingham Center for Macromolecular Crystallography 252 BHS, 79 THT University Station Birmingham, AL 35294 carson@luna.cmc.uab.edu carson@uabcmc.bitnet ------------------------------------------------------- | Dr. Marty Pagel | | Senior NMR Spectroscopist | | Senior Molecular Modeler | | Chemistry Department mpagel@indiana.edu | | Indiana University (812)-855-6492 | | Bloomington, IN 47405-4001 (812)-855-8300 (fax) | ------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Jun 20 23:00:00 1994 Newsgroups: bionet.structural-nmr Path: biosci!agate!boulder!csn!ub!galileo.cc.rochester.edu!uhura.cc.rochester.edu!bmhn_cif From: bmhn_cif@uhura.cc.rochester.edu (Brian S. Meehan) Subject: Re: any good pdb viewers for NMR... Message-ID: <1994Jun21.130319.27374@galileo.cc.rochester.edu> Sender: news@galileo.cc.rochester.edu Nntp-Posting-Host: uhura.cc.rochester.edu Organization: University of Rochester - Rochester, New York References: <940620113003.21000982@NMR.UOREGON.EDU> <1994Jun21.084327.13470@nomina.lu.se> Date: Tue, 21 Jun 94 13:03:19 GMT Lines: 26 In <1994Jun21.084327.13470@nomina.lu.se> bryan@fkem2.lth.se (Bryan Finn) writes: >In article AA14545@pines1.ljcrf.edu, elya@PINES1.LJCRF.EDU (Elya S. Kurktchi) writes: >> >> Hi, >> >> Are there any PDB viewers that can be compiled on a sparc10 (4.1.3C, >> OW, no Motif/X11R5) and can all quick viewing of PDB files? > >and... Stuff Deleted... ave you tried MacroModel?? It can read PDB files as well as its own format. You can get to a PDB file non-trivially using the newzmat program from gaussian. Macromodel also will give you caculated spliting constants for certain atom - amd maybe chemical shifts but I am not certain - that wouold be complicated.. All and all it is a pretty good analysis program. I do not know about any recent verstions. Our is from about a year and a half ago. There is a mail group at Columbia that answers all of your macromodel questions. If interested. I will dig it up .. Peace Brian S. Meehan From owner-structural-nmr@net.bio.net Mon Jun 20 23:00:00 1994 Newsgroups: bionet.structural-nmr Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.lth.se!news.lu.se!heimdall!bryan From: bryan@fkem2.lth.se (Bryan Finn) Subject: Re: any good pdb viewers for NMR... Message-ID: <1994Jun21.084327.13470@nomina.lu.se> Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: heimdall.fkem2.lth.se Reply-To: bryan@fkem2.lth.se Organization: Physical Chemistry 2, Lund University, Sweden References: <940620113003.21000982@NMR.UOREGON.EDU> Date: Tue, 21 Jun 1994 08:43:27 GMT Lines: 45 In article AA14545@pines1.ljcrf.edu, elya@PINES1.LJCRF.EDU (Elya S. Kurktchi) writes: > > Hi, > > Are there any PDB viewers that can be compiled on a sparc10 (4.1.3C, > OW, no Motif/X11R5) and can all quick viewing of PDB files? and... In article 21000982@NMR.UOREGON.EDU, STRAIN@NMR.UOREGON.EDU (MIKE STRAIN) writes: > We use "molscript" and "RasMol" for viewing pdb files on our SGI > systems. I think Sun versions of both programs are available. > Molscript is very good and is portable to a number of systems but it should be mentioned that one needs a fortran compiler and, since the output is postscript, a postscript viewer such as Pageview or xpsview. I have also seen a program called Flex which is a good pdb viewer. I think that it is available from Michael Pique at Scripps Research Institute (mp@scripps.edu). There is a version for SunOS 4. Any others? Bryan ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-108254 | | Chemical Center Fax: +46-46-104543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | |_________________________________________________________________| | | | "It is unworthy of excellent men to lose hours like slaves in | | the labor of calculation." -- Leibniz | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Tue Jun 21 23:00:00 1994 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re:PDB Viewers.... Date: 22 Jun 1994 12:14:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 119 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406221915.AA02000@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Elya: >> >> Are there any PDB viewers that can be compiled on a sparc10 (4.1.3C, >> OW, no Motif/X11R5) and can all quick viewing of PDB files? > >and... I am in the process of writing a review of all the programs currently available for Molecular Structure Visualization and Dynamics. Here are some of the best ones suitable for your purpose: Most of the programs mentioned here are available at no cost to you. However, you must complete a license agreement prior to acquiring the package. You can also obtain these via FTP by arrangement with the parties involved. 1. SETOR by Stephen Evans, NRC, Canada This is an excellent structure visualization and manipulation software especially if you are interested in preparing slides for presentation. It is extremely easy to use. SETOR also comes with additional programs for preparing publication quality b/w figures. Color plates obtained by photographing the screen is quite good and publication quality. However, if you need high resolution color plates, there is an option to do this by sending the output to a dye-sublimation printer. An example of the latter can be found in Protein Science [1994] 3, p. 470 & 472. SETOR currently runs on SGI's and utilises the GL for graphics. The documentation which accompanies the program is quite good. Contact: elmo@nrcbsa.bio.nrc.ca ^^^^^^^ 2. GEMM by Joe Cammisa, Jong Ryul Kim & B.K. Lee, NIH GEMM stands for "Generate, Edit and Manipulate Molecules" and can do a lot more than just visualizing PDB files. It will accomodate a number of input formats (pdb, charmm, nih, etc.) and is very easy to use. There is no documentation accompanying the program, but, the menus are self-explanatory and you should be able to visualize a molecule in under 15 seconds. There are also options for mutating side chains. One can also visualize trajectories generated by CHARMM or other MD programs. There are man pages that come with the program. Source is not available and the program is distributed as object code. GEMM runs on the SGI. Contact: bkl@helix.nih.gov OR jjc@helix.nih.gov ^^^^^^^ 3. XTALVIEW by Duncan McRee, Scripps Research Institute, La Jolla If you are looking for ease of use combined with many different options for inspecting and dissecting macromolecular structure, this is it. It will not produce fancy ribbon or raster renderings, but, can aid in studying the molecule of choice in great detail. This program is my personal favourite because it runs under X and provided you have an X-emulator for the PC or Macintosh, the results can be easily viewed from a remote site. Contact: Author: dem@scripps.edu ^^^^^^^ Distribution: ccms-help@sdsc.edu A recent monograph by Duncan McRee, Practical Protein Crystallography (1994) outlines some of the program feataures in detail. A workshop on this program was conducted at the Protein Society Meeting. 4. PREPI by Suhail Islam, ICRF, London An excellent package for overall structure visualization and manipulation that runs on SGI platforms. It is currently being beta tested and will be released in the next couple of months. I shall provide details on obtaining this program at a later date. 5. MOLSCRIPT & RASTER3D by Per Kraulis and Ethan Merrit respectively. Molscript is absolutely essential if you are interested in producing b/w publication quality ribbon structures. The plot files are in postscript form and can be visualized easily with a postscript viewer. I have permission to distribute the program (to users in the U.S. who have an immediate need) as long as you complete a license agreement and mail it to Dr. Kraulis in Sweden. RASTER3D produces outstanding raster images of molecules. When interfaced with MOLSCRIPT, one can produce spectacular images with shadowing, colours etc. RASTER3D is available via anonymous FTP from: stanzi.bchem.washington.edu Look for it in the directory /pub. A detailed compilation of the various programs available to visualize and manipulate structures will be put on our NMR gopher very soon. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From owner-structural-nmr@net.bio.net Sun Jun 26 23:00:00 1994 Path: biosci!CADMIUM.CSB.YALE.EDU!gardner From: gardner@CADMIUM.CSB.YALE.EDU (Kevin Gardner) Newsgroups: bionet.structural-nmr Subject: Re:PDB Viewers.... Date: 27 Jun 1994 08:33:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406271534.AA21450@cadmium.csb.yale.edu> NNTP-Posting-Host: net.bio.net > Elya: > > >> > >> Are there any PDB viewers that can be compiled on a sparc10 (4.1.3C, > >> OW, no Motif/X11R5) and can all quick viewing of PDB files? > > > >and... > (...thanks to raman for a _great_ compilation of various programs that I've chopped out here...) I realize that everyone's got their favorite program for doing things along this line, and it's in the name of completeness of this list that I'd like to submit the following as an addendum: 6. RASMOL & TKRASMOL by Roger Sayle and Ken Shirriff respectively RasMol is a good program for visualizing protein and nucleic acid structures with particular strengths of: 1). portability (UNIX, VMS, and Windows systems currently supported, Mac on the way), 2). flexibility in the input and output file formats, as well as in the different graphics modes for displaying the molecule (eg. strands, CPK dot surfaces, etc). and 3). _excellent_ support and development by the author, Roger Sayle. Molscript fans should note that this program generates Molscript input files automatically, facilitating generation of graphics with that program. More information can be obtained by email (rasmol@dcs.ed.ac.uk) and the program can be obtained by anonymous ftp from ftp.dcs.ed.ac.uk. TkRasMol incorporates a tk-based frontend onto the RasMol program, making it somewhat easier to use for those who prefer using GUIs over command-line interfaces. Contact Ken Shirriff (shirriff@sprite.berkeley.edu) for more information. That's my $0.02, Kevin -- ************************************************************************* Kevin Gardner Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.csb.yale.edu Bitnet: gardner@yalemed From owner-structural-nmr@net.bio.net Mon Jun 27 23:00:00 1994 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: NMR: Subject Header? Date: 28 Jun 1994 07:42:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406281441.AA05316@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Barry: > How about using 'NMR:' as the first 4 letters of the subject lines > of out NMR group posts? This could either be automated at the server or > a voluntary good habit of members! I suggested the same to David Kristofferson even before the newsgroup was established and was told that it cannot be done. Sorry... Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From owner-structural-nmr@net.bio.net Mon Jun 27 23:00:00 1994 Path: biosci!HELIX.NIH.GOV!bhardy From: bhardy@HELIX.NIH.GOV (Barry J. Hardy) Newsgroups: bionet.structural-nmr Subject: NMR: Subject Header? Date: 27 Jun 1994 20:25:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406280326.AA14358@helix.nih.gov> NNTP-Posting-Host: net.bio.net NMRers, How about using 'NMR:' as the first 4 letters of the subject lines of out NMR group posts? This could either be automated at the server or a voluntary good habit of members! $0.0001 for today, Barry J. Hardy From owner-structural-nmr@net.bio.net Wed Jun 29 23:00:00 1994 Path: biosci!REMCURE.BMB.WRIGHT.EDU!cletner From: cletner@REMCURE.BMB.WRIGHT.EDU (Charles Letner) Newsgroups: bionet.structural-nmr Subject: Imaging program Date: 30 Jun 1994 12:23:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello all, I have an 2D array of numbers between 0 and 255 that has been produced from a NMR data set. I would like to put these into a grey scale image with 256 shades of grey and then output to any common graphics format, ie/ tiff, bmp, etc... Does anyone know of a program/utility that can accomplish this? The array has been created with a C program so it would be fairly easy to change the array so that it is compatable with the image creation program/utility. Any leads will be greatly appreciated. Best regards, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From owner-structural-nmr@net.bio.net Wed Jun 29 23:00:00 1994 Path: biosci!NODDY.CM.UTEXAS.EDU!dave From: dave@NODDY.CM.UTEXAS.EDU (david w. hoffman) Newsgroups: bionet.structural-nmr Subject: (none) Date: 30 Jun 1994 10:17:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406301718.AA20760@noddy.cm.utexas.edu> NNTP-Posting-Host: net.bio.net Dear NMR-netters, I am looking for a program to convert FELIX format data files to VNMR (Varian software) format FID files. I have a program called VNMR2FELIX that format converts in one direction, but I want to go the other way. Has anyone solved this problem? P.S. - I am doing this on an SGI Indigo. Thanks. Dave Hoffman Dept of Chemistry and Biochemistry Univ. of Texas at Austin dave@noddy.cm.utexas.edu