From CLETNER@DESIRE.WRIGHT.EDU Tue Jul 20 18:28:21 1993 Date: Tue, 20 Jul 1993 23:28:21 -0500 (EST) From: CLETNER@DESIRE.WRIGHT.EDU Subject: Brookhaven data To: chemistry@ccl.net Message-Id: <01H0S7CJYQ7S0029XB@DESIRE.WRIGHT.EDU> Hello Everyone, I am wondering if there is a ftp site to obtain the latest crystal structure in the Brookhaven data base. I have an older copy (2-3 yrs) of the database but would like to obtain some of the newer structures? Thanks Chuck From JKONG@ac.dal.ca Wed Jul 21 07:15:32 1993 Date: Wed, 21 Jul 1993 10:15:32 -0300 From: JKONG@ac.dal.ca Subject: Question about IBM RISC qdaemon To: chemistry@ccl.net Message-Id: <01H0SU0JF0PU0068UH@AC.DAL.CA> Dear netters, We got two IBM RISC recently. They run very fast but we've got a problem with qdaemon. The queue we use is actually the printer queue (qprt -Pbsh) and the qdaemon seemingly comsumes more CPU time than running programs. We did not buy NQS program because it is two expansive ($2000 for each machine). Can anyone give us some hints to get around of this problem? Thank you in advance. Jing Kong From raman@bioc01.uthscsa.edu Wed Jul 21 03:36:13 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9307211336.AA03783@bioc01.uthscsa.edu> Subject: Re: Brookhaven data To: CLETNER@DESIRE.WRIGHT.EDU Date: Wed, 21 Jul 1993 08:36:13 -0500 (CDT) Chuck: There are many ways by which you can access the PDB and obtain coordinates of your choice; I shall mention 3 of them: 1. The best method is for you to get a GOPHER client and connect to one of the servers that specializes in Databases like "merlot.welch.jhu.edu". From there you can easily access the PDB and view the files before you email it to 'yourself'! 2. There is a email server at the PDB; Do the following: send an email to "fileserv@pb1.pdb.pdb.bnl.gov" with null subject field and the body of the subject: send info 3. The FTP site at PDB is: pdb.pdb.bnl.gov (IP: 130.199.144.1) Hope this helps! -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From bbesler@ouchem.chem.oakland.edu Wed Jul 21 05:58:55 1993 Date: Wed, 21 Jul 93 09:58:55 -0400 From: bbesler@ouchem.chem.oakland.edu (Brent H. Besler) Message-Id: <9307211358.AA10750@ouchem.chem.oakland.edu> To: chemistry@ccl.net Subject: Getting around G92 I/O bottleneck on RS/6000 I am configuring an RS/6000 cluster for an application(Gaussian 92) which requires 2 Gigabyte scratch files(2 of them most of the time meaning 4 Gigabytes total) to be read in and out multiple times. I/O speed is the concern, data reliability not at all. It seems that a level 0 RAID might solve the problem. In some benchmarks which IBM did for us they used a Zitel "cached" disk. I am not sure if this is a RAID or not? Has anyone encountered this device before. Also RAID's for the IBM RS/6000 are mostly SCSI-2 interface. There is a company which produces RAID's for the RS/6000 called the MC Series which have a proprietary Microchannel bus controller which is faster than SCSI-2 they claim. Has anyone ever used one before on an RS/6000? I believe the comany which manufactures them is Maximum Strategy Incorporated. Also does anyone know of a way around the 2.1 Gigabyte filesize limit of AIX? Finally has anyone used Gaussian 92 with the scratch files going to NFS mounted disks over an FDDI network? From bruce@dggpi2.chem.purdue.edu Wed Jul 21 03:50:30 1993 Date: Wed, 21 Jul 93 08:50:30 -0500 From: bruce@dggpi2.chem.purdue.edu (Bruce Luxon) Message-Id: <9307211350.AA23131@dggpi2.chem.purdue.edu> To: chemistry@ccl.net Subject: SGI compiler options Howdy Netters, Dan Severance recently wrote regarding SGI machines - >If you have an R4000 or R4400 machine, you need to add the "-mips2" >option, since "-mips1" is the default (compatibility mode, will run on >both R3000 and R4000 machines). (The fast square-root is incorporated >when you specify -mips2) ... > > Another compiler option (fairly new) to try is the -sopt, and is >documented in the f77 man page, and under the "fopt" manpage (-sopt >runs the program fopt). One user got a 40% speedup, we don't; it >depends on your code. I and several other users attempted this and were not able to get either of these options to work. I have an Indigo XS24 R4000 with the F77 compiler 3.4.1, Development option 4.0.1, and Irix 4.0.5 so I believe I have most (but apparently not all) the goodies. When trying to make using the -mips2 option I received the following note - f77: Error: malformed or unknown option -mips2 *** Error code 2 I checked my cdroms to see if I had all the options installed and it 'appears' I do. What am I doing wrong or what isn't installed? Regarding -sopt, when this option was included in the makefile the compiler seemed to go into hibernation after it encountered the first routine to compile. After awhile (ca. 10 minutes) I lost patience and aborted the make. Again, any suggestions what went wrong or I didn't do correctly? Thanks in advance to Dan and any others with responses, Bruce ____________________________________________________________________________ | | | |"You can't always get what you want, | Dr. Bruce A. Luxon | | But if you try sometimes, | Chemistry Department | | You'll get what you need ..." | Purdue University | | | W. Lafayette, IN 47907 | | Mick Jagger | (317)494-5289; Fax (317)494-0239 | | | bruce@dggpi2.chem.purdue.edu | |______________________________________|___________________________________| From TSHEHLA@che.und.ac.za Sun Jul 21 19:11:47 1993 Message-Id: To: Chemistry@ccl.net From: TSHEHLA@che.und.ac.za Date: 21 Jul 93 17:11:47 +0200 (SAST) Subject: G92 "alpha density matrix deviates from symmetry by 1.214D-07" Hi netters; I have this problem on optimisation of NO2 by ROMP2 level, "Alpha density matrix deviates from symmetry by 1.214D -07". I tried forced convergence; nothing works. Any one with a suggestion? Thanks very much in advance. T M Tshehla From roberto@demilo.boston.sgi.com Wed Jul 21 10:52:39 1993 Message-Id: <9307211852.AA25464@demilo.boston.sgi.com> To: bruce@dggpi2.chem.purdue.edu (Bruce Luxon) Subject: Re: SGI compiler options Date: Wed, 21 Jul 93 14:52:39 EDT From: Roberto Gomperts Hi Bruce, Your message dated: Wed, 21 Jul 93 08:50:30 EDT |> Howdy Netters, |> |> Dan Severance recently wrote regarding SGI machines - |> |> >If you have an R4000 or R4400 machine, you need to add the "-mips2" |> >option, since "-mips1" is the default (compatibility mode, will run on |> >both R3000 and R4000 machines). (The fast square-root is incorporated |> >when you specify -mips2) ... |> > |> > Another compiler option (fairly new) to try is the -sopt, and is |> >documented in the f77 man page, and under the "fopt" manpage (-sopt |> >runs the program fopt). One user got a 40% speedup, we don't; it |> >depends on your code. |> |> I and several other users attempted this and were not able to get either |> of these options to work. I have an Indigo XS24 R4000 with the F77 compiler |> 3.4.1, Development option 4.0.1, and Irix 4.0.5 so I believe I have most |> (but apparently not all) the goodies. |> |> When trying to make using the -mips2 option I received the following note - |> |> f77: Error: malformed or unknown option -mips2 |> *** Error code 2 I am afraid you are not up to date with the system software for your machine. The "latest-and-greatest" for your equipment is Development Option (IDO) 4.1.1 and Compilers (Fortran) 3.5.1 (aka 3.10.1 compilers) To expand a little on Dan's notes concerning the benefits of the -mips2 flag: On the average I have seen +/- 20% improvement when used on a large variaty of chemistry codes. Also, to have the benefit of the "fast sqrt" you ought to link with -mips2 (as well as compile). |> |> I checked my cdroms to see if I had all the options installed and it 'appears' |> I do. What am I doing wrong or what isn't installed? |> |> Regarding -sopt, when this option was included in the makefile the compiler |> seemed to go into hibernation after it encountered the first routine to |> compile. After awhile (ca. 10 minutes) I lost patience and aborted the make. |> Again, any suggestions what went wrong or I didn't do correctly? |> |> Thanks in advance to Dan and any others with responses, |> |> Bruce |> ____________________________________________________________________________ |> | | | |> |"You can't always get what you want, | Dr. Bruce A. Luxon | |> | But if you try sometimes, | Chemistry Department | |> | You'll get what you need ..." | Purdue University | |> | | W. Lafayette, IN 47907 | |> | Mick Jagger | (317)494-5289; Fax (317)494-0239 | |> | | bruce@dggpi2.chem.purdue.edu | |> |______________________________________|___________________________________| |> |> |> |> |> --- |> Administrivia: This message is automatically appended by the mail exploder: |> CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator |> OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net |> CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first |> --- |> |> -- Roberto Roberto Gomperts roberto@sgi.com phone: (508) 562 4800 Fax: (508) 562 4755 "Gracias a la vida, que me ha dado tanto ..." Violeta Parra From matt@mercury.aichem.arizona.edu Wed Jul 21 04:13:10 1993 Date: Wed, 21 Jul 1993 11:13:10 -0700 (MST) From: Matthew Stahl Subject: animation To: chemistry@ccl.net Message-Id: Sorry for the delay, but here is the summary of responses to my post requesting information about animation. Thanks to everyone who responded! --------------------------------------------------------------------------- Post: Hello Netters, I am wondering how many of you have used animation as a teaching or research tool. What platforms and software are available to do this sort of thing besides Cache? If you had the ability to make an animation on a PC by stringing together coordinate files (like Macromodel or Xmol) what would you want to display? Dynamics simulations? Gaussian vibrational modes? Reaction Mechanisms? Would the ability to do this on a PC be useful? Thanks in advance. Responses will be summarized and posted if this request generates sufficient interest. --------------------------------------------------------------------------- Responses: --------------------------------------------------------------------------- From: Joe M Leonard AVS has the components needed to animate various chemical things, and several demonstration modules showing structural animation were developed 1-2 years ago. Contact Doug Smith at UToledo for additional information, although there are others that worked in this area. The version of SPARTAN currently scheduled for Xmas or so will have the ability to animate structures and mo's and the like. The prototype has been demonstrated for several months, but we were unable to get into the Version 3 release currently being beta tested. I imagine that animation can be done in Explorer as well - contact Henry Rzepa, who has done a bunch of work in this area as I recall (net traffic). Joe Leonard jle@world.std.com ------------------------------------------------------------------------- From: Dongchul Lim What I would animate is trajectories from molecular dynamics calculations, intrinsic recation coordinates and vibratinal modes from gaussian or mopac calculations, motion of solutes and solvents in statistical thermodynamics simulations, etc. I guess HyperChem for MS-Windows is capable of some of these animations (on PC). -DCL Department of Chemistry, Yale University ------------------------------------------------------------------------- From: Norbert Mueller The new version (3.5) of Ball & Stick, the molecular graphics package for Macintosh I have been developing, can create QuickTime movies from static moving structures or from a series coordinate files resulting from an MD run. Ball & Stick is availble from Cherwell Scientific Publishing 15 Auburn Place Brookline MA 02146 Tel: (617) 277 4200 Fax: (617) 739 4836 or Cherwell Scientific Publishing The Magdalen Centre Oxford Science Park Oxford OX4 4GA, UK Phone +44 (865) 784 800 Fax +44 (865) 784 801 or Cherwell Scientific Publishing c/o CHEM Research GmbH BeethovenstraBe 7b D-60325 Frankfurt 1 Tel: +49 (069) 4711114 Fax: +49 (069) 740496 A free demo should appear on info-mac and the michigan archives any tome now. Hope this helps Norbert Mueller Institut fuer Chemie Johannes Kepler Universitaet A-4040 Linz Austria e-mail: NMUELLER@edvz.uni-linz.ac.at (preferred) norbert@soft.uni-linz.ac.at NorbertM (AMDA-Link Linz) ->FirstClass K360171@alijku11.earn \ K360171@alijku11.bitnet > will expire in 1994 K360171@alijku11.edvz.uni-linz.ac.at / ------------------------------------------------------------------------- From: SBPM Marc GINGOLD We use for research the animation in QUANTA on RS/6000. ------------------------------------------------------------------------- From: Henry Rzepa We are using animation modules developed using Explorer 2.0 to display vibrational modes, orbital transformations etc. This is done on SGI. We then convert to Quicktime format, which can be played on Mac or PC. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869. ------------------------------------------------------------------------- From: Phil Bays I use an SGI Indigo with Spartan from WaveFunction, Inc. or LabVision from Tripos. With LabVision, I can do dynamics and "illustrate" the rotational barrier in Butane in a dynamic way (or any other molecule, for that matter). With Spartan, I can do normal mode calculations and display vibrational frequencies. I can also show HOMO's and LUMO's and therby illustrate reactivity, though that is not yer available in a dynamic way. I Understand that the new version of Spartan, due out the end of the month, will allow that. I also use a product put out by Falcon Software in Vt. called Organic Reaction Mechanisms and running on a Mac. It illustrates dynamically most of the standard reactions you want to look at in an organic course. This was put together using MacroMind Director, I thnink. Obviously, I am an organic chemist and teach in an undergraduate college situation. I sue all of these in my sophomore organic course. By the end of the year, thanks to an NSF ILI grant, we will have sufficient workstations that I can give students assignments on the computers, not just use them for classroom demos. Phil Bays Saint Mary's College Notre Dame, IN 46556 (219) 284-4663 pbays@saintmarys.edu bays@indigo.saintmarys.edu ------------------------------------------------------------------------- From: Barry Rowe Matt, We here at the NCSA ChemViz group use animations extensively. We use either NCSA Collage or NCSA Image to animate calculated images to show changes in molecular shape as atoms approach or move apart. We are developing curricular materials for high school Chemistry teaching. Our most useful animations are slices through the centers of (some) of the atoms in a molecule as bonds are formed. We also use graphs of the lowest energy of the total system to determine bond length (and sometimes bond angle). Our images are calculated with NCSA DISCO on a Cray. If you have any questions, please contact me. barry [] [] [] [] [] [] [] [] [] Barry E. Rowe browe@ncsa.uiuc.edu NCSA ChemViz group 240 CAB, 152 E. Springfield Ave. Champaign, IL 61820 ANY PRACTICAL APPLICATION OF PHYSICS OBVIOUSLY INVOLVES MATTER, AND IS THEREFORE CHEMISTRY. [] [] [] [] [] [] [] [] [] ------------------------------------------------------------------------- From: Richard Gillilan > > > Hello Netters, > I am wondering how many of you have used animation as a teaching > or research tool. What platforms and software are available to do this > sort of thing besides Cache? I use IBM Data Explorer. I'm about to release a suite of chemistry modules designed for molecular modeling with emphasis on animation production. I'll announce to the list when available (next couple of weeks). In practice we find that DX is quite a good tool for education (about the use of graphics). When it comes to actual simulation, something like Hyperchem or macromodel may be better. >If you had the ability to make an animation > on a PC by stringing together coordinate files (like Macromodel or Xmol) > what would you want to display? Dynamics simulations? Gaussian > vibrational modes? Reaction Mechanisms? Would the ability to do this on > a PC be useful? Most requests I get are for videos used in conference presentations, although recently one of my clients had a request for a tape to be used in a biophysics class. The subject is normal-mode vibrations of proteins (G-Actin in this case). I'd like to see more of this, but some argue, and justifyably so I think, that video is not a very good medium for education. Students have no chance for interaction or to ask questions and get more detailed explanations or to get the information at a slower pace. Interactive multimedia might be better, but then why not just let them play with the actual data using a modeling program? ------------------------------------------------------------------- stereo pair stereo pair Richard E. Gillilan H H H H Visualization Specialist \ | | \ Cornell Theory Center H--C---C--H H---C---C---H richard@tc.cornell.edu / | | / (607) 254-8757 H H H H ------------------------------------------------------------------- ------------------------------------------------------------------------- From: Williams Brian W Dear Mr. Stahl: You might want to consider contacting John Ranck at Elizabethtown College (ranck@vax.etown.edu) for possible uses of animation in teaching applications. John is heading up a group of several small college professors called the "Molecvue Corsortium" which is trying to use the advances in computational chemistry to develop and improve teaching tools. Although I have just inititated active contact with this group, they appear to be focussing on using programs such as Hyperchem , Gaussian and some commercially available animation products to further teaching goals. Perhaps you could get some ideas/insight from him, or other members of this group. Best, Brian Williams ------------------------------------------------------------------------- From: WILLSD@conrad.appstate.edu Matt: I have recently used animations in a way similar to you interests. I had a student in need of a programming problem and suggested that he write a filter program that reads a g92 freq output file and generates from it sequence of .xyz images that can be animated in xmol. I used this in my physical chemistry class to show the students what normal modes look like, and why they have the symmetry designations that they do. It was effective, but rather cosy: we do not have facilities for this in classrooms, so I had all of the students crowd in my office to look at my screen. Luckily there were only 9 students. I would be interested in hearing what sorts of responses you get, especially if those responses describe the hardware used to display animations in the classroom. Thanks, Steve Williams ----------------------------------------------------------------------- From: CHAMH@INDSVAX1.INDSTATE.EDU Matt: I am familiar with a very nice utility, KGNGRAF, which operates on the RS/6000 platform. It accepts files from GAUSSIAN, MOPAC, and HONDO and can perform animations of the normal modes, as well as provide a schematic IR (RAMAN) spectrum. MO diagrams and van der Waals surfaces (among other nice features) are also represented. KGNGRAF is written by Steve Chin (IBM/Kingston). Arthur M. Halpern Department of Chemistry Indiana State University Terre Haute, IN 47809 ------------------------------------------------------------------------- From: uchjs%earth.dnet@terra.oscs.montana.edu Sounds like a great idea. I have written an MD program that runs on a PC and displays a 3D picture in "real time". It only handles spherical force-field atoms, however. I have used it nonetheless to illustrate collision dynamics, vibrations, rotations, unimolecular dissociation and surface (and cluster) impact processes (sputtering). It should be easy to adopt to simple reaction dynamics, A + BC = AB + C. I strongly believe that simulation/animation will be a great teaching tool. For one thing, it allows for active input from the students as they can easily change parameters and see the effects. The main problem is practical - most lecture rooms do not have the equipment at hand. If market issues are your concern, you may want to take a look at a recent article (May??) on trends in the textbook market in the Wall Street Journal. Give me a message and I'll find you the date of the article. By the way, what is Cache?? Jan Sunner Chemistry Montana State University UCHJS@MTSUNIX1 ------------------------------------------------------------------------- From: Leland Wilson My guess is that PC's are more accessible to more people than are the Mac's for which Cache is designed. Now that prices are more reasonable 486's are going to be more plentiful. Any animation would be useful especially in teaching. lee wilson, Chem. Dept., La Sierra U. ------------------------------------------------------------------------- From: Louis.Grace@um.cc.umich.edu Dear Matthew, A former graduate student in my group and I (currently a graduate student) have performed quite a few GaussianTM frequency calculations. To aid in ascertaining which mode is which, we have been visualizing the molecules as they are displaced for each mode. We have been using a program called Molecular Editor to do this. The version of Molecular Editor which we have runs on a Macintosh. I do not know if there is a PC version available. (I believe it's freeware, but I'm not sure. It was written at Drexel University.) Molecular editor does perform animation by switching back and forth between two files (which contain the coordinates of the atoms at the positive and negative displacements >from equilibrium). I have had to go outside our lab to do this, as our lab has only PC's! It might be desirable to have a program for the PC to do this. I thought this might interest you. Louis Grace Department of Chemistry The University of Michigan Ann Arbor, Michigan 48109 From trevor@grserv.wustl.edu Wed Jul 21 09:46:36 1993 Date: Wed, 21 Jul 93 15:46:36 -0600 From: trevor@grserv.wustl.edu (Trevor Creamer) Message-Id: <9307212146.AA22282@giovanni> To: chemistry@ccl.net Subject: SGI compiler options Bruce Luxon wrote : > >Dan Severance recently wrote regarding SGI machines - > >>If you have an R4000 or R4400 machine, you need to add the "-mips2" >>option, since "-mips1" is the default (compatibility mode, will run on >>both R3000 and R4000 machines). (The fast square-root is incorporated >>when you specify -mips2) ... >> >> Another compiler option (fairly new) to try is the -sopt, and is >>documented in the f77 man page, and under the "fopt" manpage (-sopt >>runs the program fopt). One user got a 40% speedup, we don't; it >>depends on your code. > >I and several other users attempted this and were not able to get either >of these options to work. I have an Indigo XS24 R4000 with the F77 compiler >3.4.1, Development option 4.0.1, and Irix 4.0.5 so I believe I have most >(but apparently not all) the goodies. > >When trying to make using the -mips2 option I received the following note - > > f77: Error: malformed or unknown option -mips2 > *** Error code 2 This worked fine for me with the same set-up. Are you using IRIX 4.0.5F ? Or just plain old 4.0.5 ? > >I checked my cdroms to see if I had all the options installed and it 'appears' >I do. What am I doing wrong or what isn't installed? > >Regarding -sopt, when this option was included in the makefile the compiler >seemed to go into hibernation after it encountered the first routine to >compile. After awhile (ca. 10 minutes) I lost patience and aborted the make. >Again, any suggestions what went wrong or I didn't do correctly? The -sopt option seems to require LOTS of memory - when I did this my machine seemed to spend a lot of time swapping stuff in and out of the swap space. Try watching gr_osview while compiling - it can be educational. > >Thanks in advance to Dan and any others with responses, > >Bruce I tried these options on my Monte Carlo program. Normally I use the -O4 optimization flag with f77. When I added -mips2 I got a 1.15x speed-up. With -sopt as well I got no appreciable difference (other than a much longer compilation time; ~15min.s with -sopt vs. ~1.5 min.s without). Cheers, Trevor Trevor P. Creamer Dept. of Biochemistry Email - trevor@grserv.wustl.edu ,-_|\ & Molecular Biophysics Phone - (314) 362 4123 / \ Washington University Fax - (314) 362 4115 *_,-._/ St. Louis, Missouri 63110 v U.S.A. From dan@omega.chem.yale.edu Wed Jul 21 12:48:35 1993 From: Dan Severance Message-Id: <9307212048.AA26267@omega.chem.yale.edu> Subject: Re: SGI compiler options To: bruce@dggpi2.chem.purdue.edu (Bruce Luxon) Date: Wed, 21 Jul 93 16:48:35 EDT Organization: Laboratory for Computational Chemistry Hi, Once again this may be something that others have run into so I'm also sending it to the net... > > I and several other users attempted this and were not able to get either > of these options to work. I have an Indigo XS24 R4000 with the F77 compiler > 3.4.1, Development option 4.0.1, and Irix 4.0.5 so I believe I have most > (but apparently not all) the goodies. > Did you install the 4.0.5 maintenence updates when you set up your machine? To find out, type the command "versions maint_dev". The first (real) line should read: I maint_dev 12/09/92 Development System Maint, 4.0.5 If you don't see the maint_dev lines then you are not running the 4.0.5 compiler. That would explain the behavior, since 4.0.1 was an OS prior to the R4000 machines existence and of course, would not have the -mips2 option. (I checked against a machine running 4.0.1, it's not there) Your OS is 4.0.5, but your options are 4.0.1. You should have the 4.0.5 maintence tape/CD that came with the computer; just boot the machine and tell it you want to install software. When you get to the options menu, just type go (it will figure out which subsystems need updating). The maintenence CD patches the 4.0.1 optional software to bring them up to 4.0.5, so presumably more than your compiler is non-optimal until you install it. Dan From feng@lisboa.ks.uiuc.edu Wed Jul 21 12:45:10 1993 From: Zhou Feng Message-Id: <9307212245.AA15094@lisboa.ks.uiuc.edu> Date: Wed, 21 Jul 93 17:45:10 -0500 To: chemistry@ccl.net Subject: Re:Brookhaven data To get a most recent version of Brookhaven databank pdb files, you can ftp directly to the ftp site as follows: ftp pdb.pdb.bnl.gov Connected to pdb.pdb.bnl.gov. 220- PDB Network Login to 220 pdb.pdb.bnl.gov FTP server ready. Remote system type is UNIX. Using binary mode to transfer files. Name (pdb.pdb.bnl.gov:u28759): anonymous 331 Guest login ok, type your name as password. Password: 230- --------------------------------------------------------------------- --------- Welcome to the PROTEIN DATA BANK at Brookhaven National Laboratory! UNAUTHORIZED ACCESS TO THIS COMPUTER SYSTEM IS PROHIBITED. --------------------------------------------------------------------- --------- ADVISORY.NOTICE offical notice - REQUIRED READING README this file asn_1 ASN.1 files crystallographer_info crystallographer info and addresses fullrelease all PDB full release files ls-lR directory listing new_uploads deposit your files here newsletter newsletter text and tables prerelease all PDB pre-release files program_tape all files from PDB program tape pub miscellaneous files structure_factors all PDB structure factor files --------------------------------------------------------------------- --------- Please limit the number of files you download each day. If abused, access to this service will be restricted as needed. Each directory contains a ls-lR file containing a listing of that directory and subdirectories. If you have never done so, please complete and return the advisory notice when you download files. File uploads are accepted in the write-only subdirectory "new_uploads". You cannot do a listing of the files in this subdirectory. Send mail to skora@bnl.gov if you have any questions or problems. --------------------------------------------------------------------- --------- This is the README file. Retrieve it using "get README". --------------------------------------------------------------------- --------- 230 Guest login ok, access restrictions apply. ftp> cd fullrelease 250 CWD command successful. etc........ Feng From bruce@dggpi2.chem.purdue.edu Wed Jul 21 15:59:16 1993 Date: Wed, 21 Jul 93 20:59:16 -0500 From: bruce@dggpi2.chem.purdue.edu (Bruce Luxon) Message-Id: <9307220159.AA28029@dggpi2.chem.purdue.edu> To: chemistry@ccl.net Subject: SGI Compile HOWDY NETTERS - Original question was why my SGI Indigo R4000 didn't recognize the -mips2 compiler flag and why the -sopt option is such a slug at compile time. Resolution was that the OS hadn't been updated from 4.0.3 to 4.0.5 using the 'maint_dev' cdrom disc as suggested by Dan Severance. The -mips2 flag works fine now. Note that the -sopt flag takes a whole lot of compile time so patience is the key here. Thanks to all for your suggestions including Dan, Trevor Creamer and Roberto Gomperts. Bruce ____________________________________________________________________________ | | | |"You can't always get what you want, | Dr. Bruce A. Luxon | | But if you try sometimes, | Chemistry Department | | You'll get what you need ..." | Purdue University | | | W. Lafayette, IN 47907 | | Mick Jagger | (317)494-5289; Fax (317)494-0239 | | | bruce@dggpi2.chem.purdue.edu | |______________________________________|___________________________________|