From chemistry-request@server.ccl.net Thu Feb 3 17:43:14 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05798 for ; Thu, 3 Feb 2000 17:43:10 -0500 Received: from pssamsg02.providence.org (dyn179.provnw.org [204.182.142.179]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA20492 for ; Thu, 3 Feb 2000 16:37:39 -0500 (EST) Received: by pssamsg02.provnw.org with Internet Mail Service (5.5.2448.0) id ; Thu, 3 Feb 2000 13:38:23 -0800 Message-ID: <1B59B7D10E2BD211AB7600805FBE1FFAD13B84@pssamsg02.provnw.org> From: "Schilling, Richard" To: "'eugene.leitl@lrz.uni-muenchen.de'" , Computational Chemistry List Subject: RE: Advice on computer Date: Thu, 3 Feb 2000 13:38:19 -0800 $30,000 - $40,000 is very reasonable. I've recently priced out a Sun Microsystems workgroup server for my employeer at about $20,000 which should do the trick for starters. Then, you'd have to add any networking, workstations, etc. . . Workstations could be standard PC's or X terminals at about $1,000 a piece. Used Digital Alphas can be bought within your budget as well. Hope that helps. Richard Schilling Providence Everett Medical Center -----Original Message----- From: eugene.leitl@lrz.uni-muenchen.de [mailto:eugene.leitl@lrz.uni-muenchen.de] Sent: Tuesday, February 01, 2000 2:31 PM To: Computational Chemistry List Subject: CCL:Advice on computer (((this is a bounce from the CCL list. please reply to below address))) From: Angelica Garcia-Zacarias Dear CCL's We are looking for a crunching number computer(s), and we wonder which would be the best deal for a budget between 30 to 40K Any advice will be appreciated Thanks in advance Angelica -- ____________________________________________________________ Angelica G. Zacarias Chemistry and Biochemistry E-mail: cagz@psc.sc.edu University of South Carolina Phone: (803) 777 0720 Columbia, SC 29208 Fax: (803) 777 9521 ____________________________________________________________ Happiness is a conscious choice, not an automatic response. -- Mildred Barthel ____________________________________________________________ From chemistry-request@server.ccl.net Thu Feb 3 18:35:19 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA06073 for ; Thu, 3 Feb 2000 18:35:19 -0500 Received: (qmail 7088 invoked from network); 3 Feb 2000 22:29:50 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 3 Feb 2000 22:29:50 -0000 Received: (qmail 9030 invoked from network); 3 Feb 2000 22:26:57 -0000 Received: from egppp1.physics.upatras.gr (HELO stelios) (150.140.159.93) by pythagoras.physics.upatras.gr with SMTP; 3 Feb 2000 22:26:57 -0000 Message-ID: <002e01bf4f1e$6cf0d940$5d9f8c96@stelios> From: "garoufal" To: Subject: HOMO-LUMO gap Date: Sat, 25 Dec 1999 23:24:27 +0200 Hi all does anybody know or have some reference about what method (or what functional for DFT) is more reliable for the calculation of HOMO-LUMO gap? Especially I am interested in semiconductor clusters Thanks in advance ____________________________________ Christos S. Garoufalis Dept. of Physics, University of Patras, Greece ____________________________________ From chemistry-request@server.ccl.net Thu Feb 3 17:52:17 2000 Received: from saratoga.orconet.com (saratoga.orconet.com [206.66.136.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05849 for ; Thu, 3 Feb 2000 17:52:17 -0500 Received: from molecules.com ([216.98.228.87]) by saratoga.orconet.com (Post.Office MTA v3.5.3 release 223 ID# 0-63161U1000L100S0V35) with ESMTP id com for ; Thu, 3 Feb 2000 13:52:24 -0800 Message-ID: <3899F649.C1AEB789@molecules.com> Date: Thu, 03 Feb 2000 13:42:33 -0800 From: James Givens Reply-To: jamesg@molecules.com Organization: Molecular Arts Corp - http://www.molecules.com X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: WebMolecules Update - Feb 2000 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The February update of WebMolecules.com is now online at: http://www.webmolecules.com New Features: -------------------------------------------------------------- - Another 25,000 CAS-indexed molecular models have been added. We now have over 150,000 molecular models on-site. Search for these by CAS number or exact formula. http://www.webmolecules.com/search.shtml - The upgrade of the WebMolecules server/network was completed on January 20th. You should notice a 20% performance boost (avg.) Any access problems that occurred over the December holidays are now behind us. Our apologies for any problems you may have seen. For those of you who are interested, we are currently running on a Dual-550 Mhz Pentium III, Red Hat Linux, and Apache 1.3.4 From there it's 100baseT > Cisco router > DS3 connection. - Search now uses exact formula matching to search the entire database and it also uses partial formula matching to look into the Top 2000. Search coverage/reach of the WebMolecules database: - Formula: 100% - CAS RN: ~99% - Name: ~2% (only used to search the Top 2000) Molecule for February 2000 -------------------------------------------------------------- Diborane http://www.webmolecules.com/cgi-bin/webmolpage.cgi?b2h6.m3d Formula: B2H6 Weight: 27.670(5) g/mol Also known as boroethane and diboron hexahydride. Commonly formed from the reduction of boron halides. Exists as a colorless, flammable gas with a repulsively sweet odor. Each boron has a tetrahedron (approx) of hydrogen atoms about it. The bridging hydrogens are somewhat farther from the boron centers than the terminal hydrogens. Considered the simplest of the boron cage compounds. Used as a reducing agent, rubber vulcanizer, an olefin polymerization catalyst and in rocket propellants. Suggestion Box -------------------------------------------------------------- Have an idea for a new feature you would like to see at WebMolecules? Let us know at: newideas@webmolecules.com Recent Upgrades and New Features -------------------------------------------------------------- - You can search the entire WebMolecules Library by formula. - SEARCH can now accept formula strings in any order. - Email Models to Friends. Use the Email-a-Model link. - 100's of large macro-structures have been added. - New Visitor Uploads are available in Category 28.0 - Support for both Chime and VRML plug-ins - For performance reasons, large molecules (>150 atoms) are available for the Chime viewer only. - Mirror sites for the VRML plug-ins have been added. See: http://www.webmolecules.com/vrmlint.shtml - Mirror sites for the Chime plug-in has been added. See: http://www.webmolecules.com/chimeint.shtml - Resizable viewing window - Support for uploads and model requests - Improved support for bookmarks - 3D coordinate downloads (M3D, MOL, PDB) -------------------------------------------------------------- WebMolecules.com is a FREE, sponsor-supported site. Designed for the 3D visualization of molecules, it contains over 150,000 molecular structures in 3D. Thousands of common molecules are organized into 30+ categories. Our TOP 2000 includes molecules of commercial value, educational importance, and of topical interest. It is indexed by formula and category and is also fully searchable. Our TOP 2000 molecules include: - Top 100 pollutants - Top 100 commercial chemicals - Top 200 pharmaceuticals - Common valence geometries - Common orbital configurations -------------------------------------------------------------- Enjoy, -- James Givens ---------------------------------------------------------------- Molecular Arts Corporation | Hanover Corporate Centre, Suite 1000 | http://www.molecules.com 1532 East Katella Avenue | Main: (714) 634-8100 Anaheim, California 92805-6627 USA | FAX: (714) 634-1999 ---------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Feb 4 04:51:53 2000 Received: from batch16.uni-muenster.de (BATCH16.UNI-MUENSTER.DE [128.176.188.114]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA08436 for ; Fri, 4 Feb 2000 04:51:51 -0500 Received: from mail1.uni-muenster.de (MAIL1.UNI-MUENSTER.DE [128.176.188.91]) by batch16.uni-muenster.de (Postfix) with ESMTP id EDD5A101F; Fri, 4 Feb 2000 09:46:15 +0100 (MEZ) Received: from asterix (ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by mail1.uni-muenster.de (8.9.3/8.9.3) with SMTP id JAA86366; Fri, 4 Feb 2000 09:46:14 +0100 Sender: grimmes@uni-muenster.de Message-ID: <389A91D6.31DF@uni-muenster.de> Date: Fri, 04 Feb 2000 09:46:14 +0100 From: Stefan Grimme Organization: Westfaelische Wilhelms-Universitaet Muenster X-Mailer: Mozilla 2.02 (X11; I; AIX 2) MIME-Version: 1.0 To: garoufal Cc: chemistry@ccl.net Subject: Re: CCL:HOMO-LUMO gap References: <002e01bf4f1e$6cf0d940$5d9f8c96@stelios> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Christos, the orbital energy gap from HF theory is a very crude and unreliable approximation to an excitation energy which is given by Delta ^1E(i->j)=eps_j-eps_i-(ii|jj)+2(ij|ij) for one single excitation between MOs i an j. This is due to the fact that the third term is of similar magnitude than the gap so that HF gaps are typically 2-3 times larger than excitation energies (for molecules). In TD-DFT it is different because the third term is replaced by some kind of response integral of the density which is usually much smaller and tends to cancel with 2(ij|ij). Thus, DFT gaps are quite near to excitation energies at least for valence states. Inclusion of exact exchange worses the agreement and thus, pure functionals like B-P86 or B-LYP do a quite good job. Stefan ___________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet Corrensstrasse 40 D-48149 Muenster Tel (+49)-251-83 36512/33241 Fax (+49)-251-83 36515 Email:grimmes@uni-muenster.de ___________________________________________ From chemistry-request@server.ccl.net Fri Feb 4 06:36:34 2000 Received: from cid.csic.es (cid.cid.csic.es [161.111.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA08867 for ; Fri, 4 Feb 2000 06:36:25 -0500 Received: from iiqab.csic.es (ramon@picasoques.iiqab.csic.es [161.111.222.58]) by cid.csic.es (8.8.8/8.8.8) with ESMTP id LAA08771 for ; Fri, 4 Feb 2000 11:27:32 +0100 (MET) Sender: ramon@cid.csic.es Message-ID: <389AAAC4.71D05EA1@iiqab.csic.es> Date: Fri, 04 Feb 2000 11:32:36 +0100 From: Ramon Crehuet Organization: C.S.I.C. X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Re, References on exact solutions ... References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Lingran Chen writes: > > I'm looking for the references about the mathematically *exact* > > solutions to Schroedinger equations for any chemical systems. > There is system that can be considered somehow chemical: Hooke's atom. It consists of an atom with two Coulomb interacting electrons bounded to a nucleus by an harmonic potential. This is very briefly described by Burke, Perdew and Ernzerhof in J. Chem. Phys, Vol. 109, No. 10, p. 3760 and the mathematical solution can be found in references therein. Ramon From chemistry-request@server.ccl.net Fri Feb 4 07:24:54 2000 Received: from host23.lctn.u-nancy.fr (host23.lctn.u-nancy.fr [192.54.210.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA09960 for ; Fri, 4 Feb 2000 07:24:46 -0500 From: assfeld@host23.lctn.u-nancy.fr Received: (from assfeld@localhost) by host23.lctn.u-nancy.fr (AIX4.3/8.9.3/8.7) id MAA18762; Fri, 4 Feb 2000 12:15:46 +0100 Date: Fri, 4 Feb 2000 12:15:46 +0100 Message-Id: <200002041115.MAA18762@host23.lctn.u-nancy.fr> To: chemistry@ccl.net, rcsqtc@iiqab.csic.es Subject: Re: CCL:Re, References on exact solutions ... > Lingran Chen writes: > > I'm looking for the references about the mathematically *exact* > > solutions to Schroedinger equations for any chemical systems. > Any FULL CI calculations are *exact* solutions, at least for the basis set considered. And there is a lot of litterature about it. Just my 2 cents... ...Xav http://www.lctn.u-nancy.fr/Chercheurs/Xavier.Assfeld From chemistry-request@server.ccl.net Fri Feb 4 08:13:04 2000 Received: from mail.chemie.fu-berlin.de (root@mail.chemie.fu-berlin.de [160.45.24.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA10210 for ; Fri, 4 Feb 2000 08:13:04 -0500 Received: from fu-berlin.de (melchers.dialup.fu-berlin.de[160.45.216.40]) (1353 bytes) by mail.chemie.fu-berlin.de via sendmail with P:esmtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Fri, 4 Feb 2000 13:07:24 +0100 (CET) (Smail-3.2.0.109) Message-ID: <389A0B17.F74F729A@fu-berlin.de> Date: Fri, 04 Feb 2000 00:11:19 +0100 From: Bernd Melchers Organization: Freche =?iso-8859-1?Q?Universit=E4t?= Berlin X-Mailer: Mozilla 4.61 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: Jim Kress CC: chemistry Subject: Re: CCL:postscript to pcx References: <000d01bf6e7a$4d313840$072c2880@ucl.ac.uk> <001201bf6e89$171525a0$a2b5aec7@ameritech.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jim Kress wrote: > > Which programs can you recommend me for converting postscript > > (*.ps) files into *.pcx, *.bmp, *.jpeg or *.gif format. I will summarise > > on request. Thanks a lot. Corel Draw has a usable postscript interpreter: you can import postcript as vector(!) graphics, doing some work on it(!) and export it as raster graphics (bmp, png, gif, ... whatever you need). CorelDraw is a windows program but there is also a Linux-Version in the pipe (last week freely available as a beta-Version from corel.com, but i don't have it). Ciao Bernd Melchers -- melchers@fu-berlin.de Freie Universitaet Berlin From chemistry-request@server.ccl.net Fri Feb 4 10:18:36 2000 Received: from mail1.manquehue.net (mail1.manquehue.net [216.72.16.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA10726 for ; Fri, 4 Feb 2000 10:18:33 -0500 Received: from carlos (tc2-037.manquehue.net [216.72.18.170]) by mail1.manquehue.net (8.9.3/8.9.3) with ESMTP id LAA09848 for ; Fri, 4 Feb 2000 11:10:51 -0300 Message-Id: <200002041410.LAA09848@mail1.manquehue.net> From: "Carlos Robles V. " To: "=?ISO-8859-1?Q?Lista_de_Qu=EDmica?=" Subject: C code for xyz coordinates Date: Fri, 4 Feb 2000 11:09:56 -0600 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all; I'm looking for a C code (under Linux) to draw molecular organic structures in space coordinates. I only have the atom names and the type of bonds between them, and I would like to obtain the xyz coordinates for the atoms cause I will draw through XBS, but that program needs the coordinates, and don't have it. Thank you in advance, Carlos Robles . From chemistry-request@server.ccl.net Fri Feb 4 07:14:06 2000 Received: from angelos.phc.chalmers.se (angelos.phc.chalmers.se [129.16.97.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA09905 for ; Fri, 4 Feb 2000 07:14:03 -0500 Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by angelos.phc.chalmers.se (8.9.3/8.9.3) with ESMTP id MAA21708 for ; Fri, 4 Feb 2000 12:08:25 +0100 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id MAA14307; Fri, 4 Feb 2000 12:08:24 +0100 Date: Fri, 4 Feb 2000 12:08:22 +0100 (MET) From: Harald Svedung To: chemistry@server.ccl.net Subject: summary CO-He scan Omega... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone! The quick fix i asked for yesterday conserning an interrupted pes scan was as many of you pointed out (elaborately or direct) to simply turn off symmetry. Doing this it all works all right with gaussian giving the final words: IF YOU WANT TO LEARN FROM THE THEORETICAL PHYSICISTS ABOUT THE METHODS WHICH THEY USE, I ADVISE YOU TO FOLLOW THIS PRINCIPLE VERY STRICTLY: DON'T LISTEN TO THEIR WORDS; PAY ATTENTION, INSTEAD, TO THEIR ACTIONS. -- A.EINSTEIN, 1934 ;-) again, thanks all of you! /Harald Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Fri Feb 4 07:39:04 2000 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA10055 for ; Fri, 4 Feb 2000 07:39:01 -0500 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id NAA16324; Fri, 4 Feb 2000 13:31:38 +0200 (EET) Date: Fri, 4 Feb 2000 13:31:38 +0200 (EET) From: John Kerkines To: chemistry@ccl.net cc: chminf-l@listserv.indiana.edu Subject: Program Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello! I am looking for a program that will calculate the limiting molar conductance and association constant of electrolytes with the use of Raymond Fuoss' model (J.Phys.Chem. 1978, 82(22), 2427-40). Does anybody know where I can find such a program? With Regards, John Kerkines From chemistry-request@server.ccl.net Fri Feb 4 08:34:55 2000 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA10346 for ; Fri, 4 Feb 2000 08:34:54 -0500 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by mserv.rug.ac.be (8.9.3/8.9.3) with ESMTP id NAA01370 for ; Fri, 4 Feb 2000 13:29:05 +0100 (MET) Received: from houston (houston.rug.ac.be [157.193.89.160]) by allserv.rug.ac.be (8.9.3/8.9.3) with SMTP id NAA13578 for ; Fri, 4 Feb 2000 13:28:35 +0100 (MET) Received: by localhost with Microsoft MAPI; Fri, 4 Feb 2000 13:29:26 +0100 Message-ID: <01BF6F13.DB95C2B0.jeanluc.verschelde@rug.ac.be> From: Verschelde Jean-Luc To: "'CCL'" Subject: Amber + MPI on Dec Alpha linux 5.2 cluster -- help please... Date: Fri, 4 Feb 2000 13:29:21 +0100 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear all, I installed and compiled AMBER5.0 and MPICH on a cluster od DEC alpha's with os Redhat linux 5.2. When I start sander, I receiver following message: # 0 - MPI_COMM_RANK : Null communicator # [0] Aborting program # p0_1331: p4_error : 197 Is there someone who can help me. Attached is the machine file I used for compiling. Greetings, Verschelde Jean-Luc #! /bin/csh -f ######################################################################## # # # Copyright (c) 1986, 1991, 1995 # # Regents of the University of California # # # # All Rights Reserved # # # # Machine Dependency Handling System # # # # Bill Ross ross@cgl.ucsf.edu # # An extension of work of George Seibel # # # # Dependencies written by various authors. # # # # Permission to use, copy, modify, and distribute this software and # # its documentation for any purpose and without fee is hereby # # granted, provided that the above copyright notice appear in all # # copies and that both that copyright notice and this permission # # notice appear in supporting documentation, and that the name of # # the University of California not be used in advertising or # # publicity pertaining to distribution of the software without # # specific, written prior permission. # # # # THE REGENTS OF THE UNIVERSITY OF CALIFORNIA DISCLAIM ALL # # WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED # # WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE # # UNIVERSITY OF CALIFORNIA BE LIABLE FOR ANY SPECIAL, INDIRECT OR # # CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM # # LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, # # NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN # # CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # # ######################################################################## # # Machine dependencies adapted from f2c version of Thomas Huber. # # When using g77 it is important to resize the COMMON blocks # if you are using ld version less than 2.6! The other option # is to download binutils-2.6 from GNU and the default sizes # works fine. I have done both and there is no problem. # # Dr. R.R. Joshi, Bioinformatics Centre, University of Poona, India # # Copy this file to .../src/MACHINE to install. # # These aliases let us use the same command files for compilation # on Unix systems with different names and/or flags for the fortran # compiler. Environment variables set here specify the location # of system-specific source and control the use of Integer*2. # See install.doc: "Setting Up the Configuration File" # # setenv MACHINE "linux/FreeBSD PC" setenv MACH F2C setenv MACHINEFLAGS " -DSHARED_MEMORY_MAX_PROCESSOR=4 -DPROFILE -DREGNML * DEWALD -DHAS_FTN_ERFC -DMPI -I/home/jeanluc/mpich-1.2.0/include " # CPP is the cpp for this machine setenv CPP "/lib/cpp -traditional -DSECOND=secondx -Dsecond=secondx " # SYSDIR is the name of the system-specific source directory relative to src/*/ setenv SYSDIR Machine/alpha # COMPILER ALIASES: # LOADER/LINKER: setenv LOAD "/home/jeanluc/mpich-1.2.0/bin/mpif77 -O6" setenv LOADLIB "-L/home/jeanluc/mpich-1.2.0/lib -lmpich " setenv LOCINCLUDE Machine/mpi setenv G77_COMPAT "-fno-globals -Wno-globals -ff90 -funix-intrinsics-hide " # little or no optimization: setenv L0 "/home/jeanluc/mpich-1.2.0/bin/mpif77 -c -g" # modest optimization (local scalar): setenv L1 "/home/jeanluc/mpich-1.2.0/bin/mpif77 -c -O -ffast-math * fomit-frame-pointer $G77_COMPAT" # high scalar optimization (but not vectorization): setenv L2 "/home/jeanluc/mpich-1.2.0/bin/mpif77 -c -O3 -ffast-math * fomit-frame-pointer $G77_COMPAT" # high optimization (may be vectorization, not parallelization): setenv L3 "/home/jeanluc/mpich-1.2.0/bin/mpif77 -c -O3 -ffast-math * fomit-frame-pointer $G77_COMPAT" # ranlib, if it exists setenv RANLIB ranlib # spasms configuration #SPASMS MACHINE.f2c_spasms_config #SPASMS unix #SPASMS n390 #SPASMS large From chemistry-request@server.ccl.net Fri Feb 4 09:12:44 2000 Received: from wirehead.arqule.com (email.arqule.com [12.27.160.89]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA10487 for ; Fri, 4 Feb 2000 09:12:43 -0500 Received: by WIREHEAD with Internet Mail Service (5.5.2650.21) id ; Fri, 4 Feb 2000 08:03:07 -0500 Message-ID: <6B00FB949906D211A88800104B8AE520F41B61@WIREHEAD> From: "Czerminski, Ryszard" To: "'CCL'" Subject: RE: Re postscript to pcx Date: Fri, 4 Feb 2000 08:03:03 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Artem R. Oganov wrote: >>Which programs can you recommend me for converting postscript >>(*.ps) files into *.pcx, *.bmp, *.jpeg or *.gif format. I will summarise >>on request. Thanks a lot. try GIMP: http://www.gimp.org What is the GIMP ? The GIMP is the GNU Image Manipulation Program. It is a freely distributed piece of software suitable for such tasks as photo retouching, image composition and image authoring. This site contains information about downloading, installing, using, and enhancing GIMP. This site also serves as a distribution point for the latest releases, patches, plugins, and scripts. We also try to provide as much information about the GIMP community and related projects as possible R Ryszard Czerminski phone: (781)994-0479 ArQule, Inc. e-mail: ryszard@arqule.com 19 Presidential Way http://www.arqule.com Woburn, MA 01801 fax: (781)376-6019 From chemistry-request@server.ccl.net Fri Feb 4 11:29:41 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA11369 for ; Fri, 4 Feb 2000 11:29:41 -0500 Received: from aurora.nal.usda.gov (aurora.nal.usda.gov [192.54.138.38]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA04350 for ; Fri, 4 Feb 2000 10:24:00 -0500 (EST) Received: from cliff.nal.usda.gov ([192.54.138.2]) by aurora.nal.usda.gov with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id 1JGRJ7L4; Fri, 4 Feb 2000 10:13:49 -0500 Received: (from srheller@localhost) by cliff.nal.usda.gov (8.8.8+Sun/8.8.8) id KAA17300; Fri, 4 Feb 2000 10:15:00 -0500 (EST) Date: Fri, 4 Feb 2000 10:15:00 -0500 (EST) From: "Stephen R. Heller" To: jcicshelp , chemweb@ic.ac.uk, chminf-l@listserv.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Software/Database for Review Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII February 4, 2000 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have one (1) new software product. I am looking for someone who is willing to review this software product. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past four years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e-mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 8 February 2000 (Tuesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@NAL.USDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The package I now have is: SolEq from Academic Software. SolEq is a software and tutorial package on solution equilibria. SolEq comes on a CD and is written for the Windows operating system. Stephen R. Heller, Ph. D. Guest Researcher NIST/SRD, Mail Stop: 820/113 100 Bureau Drive 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA Phone: 301-975-3338 FAX: 301-926-0416 E-mail: srheller@cliff.nal.usda.gov WWW: www.hellers.com/~steve From chemistry-request@server.ccl.net Fri Feb 4 11:41:38 2000 Received: from rutchem.rutgers.edu (rutchem.rutgers.edu [128.6.1.216]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA11437 for ; Fri, 4 Feb 2000 11:41:37 -0500 Received: from rutchem.rutgers.edu (localhost [127.0.0.1]) by rutchem.rutgers.edu (8.9.3/8.9.3) with ESMTP id KAA393631 for ; Fri, 4 Feb 2000 10:35:59 -0500 (EST) Sender: marczerw@rutchem.rutgers.edu Message-ID: <389AF1DE.2321F012@rutchem.rutgers.edu> Date: Fri, 04 Feb 2000 10:35:58 -0500 From: Margaret Czerw X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP27) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: MM3 Content-Type: multipart/alternative; boundary="------------6E47892CD98864264C05520A" --------------6E47892CD98864264C05520A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Can anybody tell me if there is a version od Allinger's MM3 newer that MM3(92), abnd how can get it Thanks -- Margaret Czerw **** **** Rutgers, The State University of New Jersey ** **** ** Wright-Rieman Laboratories, Chemistry ** ** ** 610 Taylor Road ** ** ** Piscataway, NJ 08854-8087 ******** Phone: 732-445-5164 ** email: marczerw@rutchem.rutgers.edu ** http://members.tripod.com/~mczerw/index.html **** --------------6E47892CD98864264C05520A Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi,
Can anybody tell me if there is a version od Allinger's MM3 newer that MM3(92), abnd how can get it
Thanks 
-- 
                       
Margaret Czerw                                    ****          ****
Rutgers, The State  University of New Jersey       **    ****    **
Wright-Rieman Laboratories, Chemistry               **    **    **
610 Taylor Road                                      **   **   **
Piscataway, NJ 08854-8087                              ********
Phone:  732-445-5164                                      **
email:  marczerw@rutchem.rutgers.edu                      **
http://members.tripod.com/~mczerw/index.html             ****
  --------------6E47892CD98864264C05520A-- From chemistry-request@server.ccl.net Fri Feb 4 12:47:21 2000 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA12011 for ; Fri, 4 Feb 2000 12:47:21 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id LAA00413; Fri, 4 Feb 2000 11:43:50 -0500 (EST) Date: Fri, 4 Feb 2000 11:43:49 -0500 (EST) From: Iraj Daizadeh To: chemistry@ccl.net cc: aas@omega.ucdavis.edu, stuchebr@indigo.ucdavis.edu, daizadeh@fas.harvard.edu, Iraj Daizadeh Subject: SUMMARY: Identifying water in proteins Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id MAA12012 Here's the summary collected from responses to my query concerning the identification of water molecules within a protein from the CCL (chemistry@ccl.net) and the PDB (pdb-l@rcsb.org) mailing lists. Programs listed below: GRID, webmol, DOWSER, CNS Thanks to all participants as well as interested parties. Iraj. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx QUESTION: --- Are there any programs that identify water molecules within a protein (from crystallographic data)? We have a one paper which referenced the GRIN/GRID program from Molecular Discovery Ltd., UK....any information would on this or other programs would be appreciated.... Will summarize as typical....iraj Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX Dear Dr. Daizadeh , **GRID is a powerful tool for research on biological target. I use it in my computational studies also to complement 3D QSAR techniques applied to drug design. It was created from a high merit Scientist , Peter Goodford (Oxford University) who is my my personal friend . He recently spent a week in my department as visiting Professor. GRID is free for the Academy. Contact Peter at: peter@biop.ox.ac.uk Best Regards, Salvatore Guccione Salvatore Guccione, Ph.D. Associate Editor of the European Journal of Medicinal Chemistry University of Catania, -Faculty of Pharmacy- Dipartimento di Scienze Farmaceutiche, viale Andrea Doria, 6, Ed. 12 Cittą Universitaria I-95125 Catania (ITALY) Telephone: +39 095 738-4020 Fax:+39 095 504572 email: guccione@mbox.unict.it XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX From: G M To: daizadeh@nucleus.harvard.edu Subject: Searching for waters To Iraj Daizadeh, We do have a program which will identify water molecules inside of proteins. Our program is called DOWSER and Helmut Grubmuller in Germany has a program called SOLVENT. I have not used his program so I am not aware of its full functionality. However, I am very familiar with Dowser. If you would like, I will send you a .tar file with the full src/executable or you can try and log into a development site at NCSA where I am adding the browser-based version ( it is still in trial mode but should be working ). ( M.L. CONNOLLY, "solvent-accessible surfaces of proteins and nucleic acids", Science, Vol. 221, 709-713 (1983). here is URL for development version of the Biology Workbench. You will have to register to try Dowser. http://glycine.ncsa.uiuc.edu/structure.html Geoff Mann XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX You'll probabvly get this answer more often: checkout dowser from Jan Hermans group at UNC chapel hill. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX Try WebMol at EMBL. I think it shows cavities and water molecules in the protein. Bahram Goliaei XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX Hi, CNS has a routine to automatically pick water molecules in an X-ray map. Another option is the program watpeak in the CCP4 suite. In both cases, it is a good idea to manually check the peaks output by these programs. Hope this helps, regards Luca -------------------------------------------------------------------------------- Luca Jovine Structural Studies Division, MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, ENGLAND. Voice: +44.1223.402443. FAX: +44.1223.213556. Telex: 81532. E-Mail: lj1@mrc-lmb.cam.ac.uk -------------------------------------------------------------------------------- XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX Iraj, You might find further information here: Goodford's grid Henrietta Elton Molecular Discovery Limited West Way House, Elms Parade Oxford OX2 9LL ENGLAND Phone +44-993-830385 Fax +44-993-830966 My understanding is that GRID will give you potential favorable water sites in the absence of xray data. Given xray data it's rather straight forward to look at peaks that have high enough sigma value and are at proper distances and orientations to potential donors or acceptors. A number of software packages can be used in concert to 'pick' electron density peaks and score them as suitable water or possible solvent ions. http://xray.bmc.uu.se/usf/ http://www.dl.ac.uk/CCP/CCP4/ http://xplor.csb.yale.edu/cns_solve/ Hth. Mike Michael Merckel XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX From: Gert.Vriend@embl-heidelberg.de To: pdb-l@rcsb.org There are two different things: 1) Analysing where waters sit in macromolecules, or, if there are no waters in the PDB file, finding the cavities that are large enough to hold a water. Most of the better molecular modelling programs can do those things. Lets call this ANALYSIS in the rest of this discussion. 2) Predicting where waters would be likely to sit, i.e. calculate positions where the potential for water is favourable. Not all programs can do that. GRID, as suggested in the original question that triggered this discussion, is one of the better programs for this type of work. Lets call this PREDICTION in the rest of this discussion. Gert Vriend XXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX From chemistry-request@server.ccl.net Fri Feb 4 16:32:27 2000 Received: from mailsrv.rz.fh-merseburg.de (nowak@mailsrv.rz.fh-merseburg.de [149.205.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13044 for ; Fri, 4 Feb 2000 16:32:27 -0500 Received: from localhost (nowak@localhost) by mailsrv.rz.fh-merseburg.de (8.9.3/8.9.1) with ESMTP id VAA21401 for ; Fri, 4 Feb 2000 21:27:07 +0100 (MET) X-Authentication-Warning: mailsrv.rz.fh-merseburg.de: nowak owned process doing -bs Date: Fri, 4 Feb 2000 21:27:06 +0100 (MET) From: Thomas Nowak X-Sender: nowak@mailserv To: chemistry@ccl.net Subject: Summery: ionicity of a bond In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'er Last week I have posted a messages to the board. Thanks for all which have answer my question! Below is the summury of the posting Regards Thomas Nowak Martin-Luther Universitaet Halle FB Chemie (Merseburg) IPC 06099 Halle email: nowak@chemie.uni-halle.de The orginal message was: On Thu, 20 Jan 2000, Thomas Nowak wrote: > > Dear CCLers, > > I want to study various Nd complexes of the type Nd(L)3-olefin with DFT > calculation. I want to characterize the Nd-olefin bond. The main > contribution of the bond should be an ionic quadropole interaction. But I > am looking for a tool to get a quantity of this ionic part and the > covalent part ( donation from olefin pi-bond to the Nd ). I have tried to > get the ionic part by an interaction of a point charge with the olefin, > but because of the ligands I don't know exactly how big this charge must > be. > > > Thanks in advance, > > Thomas Nowak > Martin-Luther Universitaet Halle > FB Chemie (Merseburg) > IPC > 06099 Halle > > email: nowak@chemie.uni-halle.de > > > > Fred P. Arnold wrote: >It's a cheap-seats way to go, but you may want to look into the current >version of NBO, since the NRT (natural resonance theory) module breaks >the >bonding contributions down into ionic/covalent. It gives chemically >reasonable results for hypervalent main-group complexes, but I don't know >how well it would handle lanthanides. It certainly gave me enough >trouble >with traditional organometallics. > > -fred > >"No science has ever made Frederick P. Arnold, Jr. > more rapid progress in a A&HPRC, U. of Chicago > shorter time than Chemistry." 5640 S. Ellis Ave > -Martin Heinrich Kloproth, 1791 Chicago, IL 60637 > Stefan Fau wrote: >Hi Thomas, > >if you are interested in analysing the energetics of a donor-acceptor >complex, you might want to use some sort of energy decomposition scheme. > >Since both fragments are so close together, approximating the charge >distribution of the NdL3 fragment by a point charge will probably not >produce meaningful results. > >The above mentioned scheme is implemented in ADF. There are other energy >decomposition schemes, too, but as I said, this is my favourite. If you >are interested, contact Dr. Matthias Bickelhaupt (bickel@chem.vu.nl) in >Amsterdam, he knows much more. > >Stefan >______________________________________________________________________ >Dr. Stefan Fau fau@qtp.ufl.edu >Quantum Theory Project >University of Florida >Gainesville FL 32611-8435 and Wannere Chaitanya S. wrote: >Hi Thomas, > >I was also trying to look in to one analogous problem of that kind. Well, >I am not sure about the tool. But may be GAMESS can give the answer to >this question by decomposition of the energy in to various components. I >am still working on this problem. Well, I can tell you 2 papers which >shall more or less answer the problem you have adressed. The following >are >the papers: > >"NATURAL ENERGY DECOMPOSITION ANALYSIS: AN ENERGY PARTITIONING >PROCEDURE FOR MOLECULAR INTERACTIONS WITH APPLICATION TO WEAK HYDROGEN >BONDING, STRONG IONIC, AND MODERATE DONOR-ACCEPTOR INTERACTIONS" by >Glendening and Streitwieser appeared in J. Chem. Phys. in >1994. vol. 100, >pg 2900. > >This is the latest scheme devised and then before this there was >a scheme by Morokuma which was applied quantitatively to metal-ligand >complex, the reference to which is Frey and Davidson, J. Chem. Phys. 90, >5555, (1989). This paper should also have the back references which >would >help you to theoretically understand Morokuma scheme. From chemistry-request@server.ccl.net Fri Feb 4 19:44:20 2000 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA13773 for ; Fri, 4 Feb 2000 19:44:20 -0500 Received: from chagall.scripps.edu (chagall.scripps.edu [137.131.252.60]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id PAA14011 for ; Fri, 4 Feb 2000 15:36:35 -0800 (PST) Received: from localhost (salsb@localhost) by chagall.scripps.edu (8.9.2/TSRI-3.0) with SMTP id PAA59822 for ; Fri, 4 Feb 2000 15:36:34 -0800 (PST) Date: Fri, 4 Feb 2000 15:36:34 -0800 (PST) From: Fred Salsbury X-Sender: salsb@chagall Reply-To: Fred Salsbury To: chemistry@ccl.net Subject: Gaussian 94 cube command question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello -- I am trying to use the g94 cube command to obtain the density and its gradient on a grid of points. I'm having some difficulty. I've checked the archive on ccl out without success. So I'm wondering if anyone can help. 1) I can't change the defaults for example with the following input: #sto-3g cube=(card,density) energy zn plus subsr 0 1 h 0. 0. 0. h 0. 0. 0.74 h.out -1, 0.0, 0.0, 0.0 -10, 1.0, 0.0, 0.0 -10, 0.0, 1.0, 0.0 -10, 0.0, 0.0, 1.0 I end up with : Evaluate density. Using the total density. Map the density over a grid of points, CutOff= 1.00D-06 Writing cube to file h.out. IGUnit= -31 Origin= 0.000000 0.000000 0.000000 N1= -10 XYZInc= 1.000000 0.000000 0.000000 N2= -10 XYZInc= 0.000000 1.000000 0.000000 N3= -10 XYZInc= 0.000000 0.000000 1.000000 s_rsfe: end of file -1 apparent state: unit 5 named /tmp_mnt/cb/munch1/sals/gaussian/g94-7524.inp last format: (A1) Unit 5 is a sequential formatted external file *** Execution Terminated (-1) *** thanks in advance Fred Salsbury salsb@scripps.edu From chemistry-request@server.ccl.net Fri Feb 4 23:03:18 2000 Received: from goshen.rutgers.edu (goshen.rutgers.edu [165.230.180.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA14439 for ; Fri, 4 Feb 2000 23:03:18 -0500 Received: from email.eden.rutgers.edu (arcpc62.rutgers.edu [128.6.83.75]) by goshen.rutgers.edu (8.8.8/8.8.8) with ESMTP id VAA01179; Fri, 4 Feb 2000 21:57:06 -0500 (EST) Message-ID: <389B9146.A9377B6C@email.eden.rutgers.edu> Date: Fri, 04 Feb 2000 21:56:06 -0500 From: jianquan Organization: Rutgers University X-Mailer: Mozilla 4.61 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: Jie Liu CC: chemistry@ccl.net Subject: Re: CCL:About autodock3 References: <3898536F.C2743ADB@bcm.tmc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, you should debug autodock and track into readPDBQ.cc file to see the value of variable nrecord. I think it may be 2*523 although you read only 523 atoms, so nrecord will be above 1000 and give the wrong error message. I think the your ligand file have been transfered between Unix and windows. After being transferred the file will has double lines because the end symbols of a line in the two OS are different. if my answer is true, you should add codes to check that every line read begin with ATOM or HETATM. If my answer works please tell the author of autodock3 for me. I have reported the same question about autogrid to them, but no reply. Jianquan chen Rutgers Univ. please visit www.eden.rutgers.edu/~jianquan/AEDock.html Jie Liu wrote: > Dear CCLers: > I docked a ligand (oligonucleotide with 523 atoms) into the > protein by using Autodock3.0.2.When I executed " autodock3 -p name.dpf > -l name.dlg &", Autodock3 can not complete the task successfully. It > gave me following information: > * autodock3: ERROR: ERROR: 523 records read in, but only dimensioned for > 512. * Change "MAX_RECORDS" in "constants.h". * autodock3: Aborting... * autodock3: Unsuccessful Completion. > I ever tried to incerease the grid map dimensions of the > ligand, but the problem still existed. > Does it mean that this program can not work on ligand with > more than 512 atoms or I should modify some parameters of the > program?How can I modify the parameters?Thanks a lot for any advices. > > Best regards, > > Jie Liu > > -- > > Jie Liu, Ph.D. > Department of Molecular Physiology and Biophysics > Baylor College of Medicine > Houston, TX 77030 > USA > > From chemistry-request@server.ccl.net Fri Feb 4 14:11:42 2000 Received: from mail-a.bcc.ac.uk (mail-a.bcc.ac.uk [144.82.100.21]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA12546 for ; Fri, 4 Feb 2000 14:11:41 -0500 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-a.bcc.ac.uk with SMTP (Mailer); Fri, 4 Feb 2000 18:05:57 +0000 Message-ID: <009601bf6f3b$1a22b8e0$072c2880@ucl.ac.uk> Reply-To: "Artem R. Oganov" From: "Artem R. Oganov" To: chemistry Subject: CCL: Review on Postscript to PCX Date: Fri, 4 Feb 2000 18:10:21 -0000 Dear all, Many thanks for a number of replies with useful suggestions. Below you'll find a review of these suggestions. I have already tried today Ghostscript under Win98, which is a free program, and it works well and is quite transparent. Artem ************************************************** Artem R. Oganov, Crystallography and Mineral Physics, Dept. of Geological Sciences, University College London, Gower Street, London WC1E 6BT, U.K. E-mail : a.oganov@ucl.ac.uk Tel. : +44 (020)-7679-3449 Fax : +44 (020)-7679-1612 http://slamdunk.geol.ucl.ac.uk/~artem ************************************************** No. 1 I have found "xv" to be a very nice software to convert .ps files to .gif, .jpeg etc. I am not sure whether it is freeware. There is also some loss of resolution in converting file formats. Good Luck Venkataraman Pallassana E-mail : venkat@virginia.edu -------------------------------------------------------------------------= ---- No. 2 I use Inso Corporation's ImageStream 97 for Microsoft Office . It is a set of filters for use with WORD, POWERPOINT etc. It will convert *.ps into forms that can be used by other programs. From their literature, here is a sub-set of the filters: AI Adobe Illustrator File Format (version 6.0) CMX Corel ClipArt Format (version 5) DSF Micrografx Designer 6.0 (Win95) DWG AutoCAD Native Drawing Format (versions 12 & 13) EPS Encapsulated Postscript File GDF IBM Graphics Data Format (GDDM) IGES Initial Graphics Exchange Specification MET OS/2 PM Metafile PDF Portable Document Format (Acrobat version 2.0) PIC Lotus 123 Picture File Format PNG Portable Network Graphics/Internet Format PS* ImageStream PS (Level 2 PostScript Interpretation) RAS Sun Raster File Format XBM X-Windows Bitmap XPM X-Windows Pixelmap XWD X-Windows Dump Jimmy Stewart E-mail: jstewart@fujitsu.com -------------------------------------------------------------------------= ------ No. 3 Though not straightforward and not for free - I use Coreldraw for that kind of things. Peter Burger E-mail : chburger@aci.unizh.ch -------------------------------------------------------------------------= ----- No. 4 I think Ghostscript/GSview will probably do this. Certainly it can get you to bmp and pcx if I remember correctly. See www.cs.wisc.edu/~ghost Rob Bell E-mail: rob@ri.ac.uk -------------------------------------------------------------------------= ----- No. 5 A **high-end** solution is PhotoShop. It will interpret and rasterize postscript files beautifully. And it will manipulate and output raster formats to your heart's content. Another approach is to use a PS drawing program such as CorelDraw, Illustrator, Freehand, etc. These will allow you to display and edit the postscript contents and export to all popular raster image formats. However palette and image manipulation tools are not nearly as advanced as PhotoShop. The latest versions of these programs can be quite expensive, however, older versions (which are quite capable) are generally available and much cheaper. A potentially free method is to use a PS interpreter utility such as GhostScript/GhostView/GSView (available on the Web). Just read the PS file and display it on your screen. It supports standard Copy and Paste operations by placing a bmp file in the Clipboard. James Givens jamesg@molecules.com ---------------------------------------------------------------- No. 6 Use ghostscript, a.k.a. gs; on my Linux system, gs --help shows: Rick Venable E-mail : rvenable@deimos.cber.nih.gov --------------------------------------------------------------- No. 7 The program GhostScript will do this by "printing" to a "pcx", "bmp" or "jpeg" device. GhostScript and GhostView are available for a number of platforms. Information is available at: http://www.cs.wisc.edu/~ghost/aladdin/ Steve Andruski E-mail: stephena@albmolecular.com ----------------------------------------------------------------- No. 8 gs (aka ghostscript) ! The Gimp, xv, ..., any good graphics program :-) Jochen Kipper jochen@uni-duesseldorf.de ---------------------------------------------------------------- No. 9 Photoshop. Marcel Swart E-mail : m.swart@chem.rug.nl ---------------------------------------------------------------- No. 10 Corel Draw has a usable postscript interpreter: you can import postcript as vector(!) graphics, doing some work on it(!) and export it as raster graphics (bmp, png, gif, ... whatever you need). CorelDraw is a windows program but there is also a Linux-Version in the pipe (last week freely available as a beta-Version from corel.com, but i don't have it). Bernd Melchers E-mail : melchers@fu-berlin.de ---------------------------------------------------------------- No. 11 Corel Draw 8 does it all... Igor Shamovsky E-mail : harry@chem.queensu.ca ---------------------------------------------------------------- No. 12 If you use Linux try the GIMP (Gnu Image manipulation Program). It can do what you want and much more. it is free. You can find detailed information about it at http://www.gimp.org Ivan Rossi E-mail : ivan@biocomp.unibo.it --------------------------------------------------------------- No. 13 try GIMP: http://www.gimp.org Ryszard Czerminski E-mail : ryszard@arqule.com --------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Feb 4 16:45:07 2000 Received: from mailsrv.rz.fh-merseburg.de (nowak@mailsrv.rz.fh-merseburg.de [149.205.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13138 for ; Fri, 4 Feb 2000 16:45:06 -0500 Received: from localhost (nowak@localhost) by mailsrv.rz.fh-merseburg.de (8.9.3/8.9.1) with ESMTP id VAA21561 for ; Fri, 4 Feb 2000 21:39:46 +0100 (MET) X-Authentication-Warning: mailsrv.rz.fh-merseburg.de: nowak owned process doing -bs Date: Fri, 4 Feb 2000 21:39:46 +0100 (MET) From: Thomas Nowak X-Sender: nowak@mailserv To: chemistry@ccl.net Subject: Profiling of G98 In-Reply-To: Message-ID: Dear CCLers, We want to profile Gaussian98 on an SGI workstion running on IRIX 6.5 or a HP X-Class workstaion running under HP-UX spp2000 B.10.01. On the SGI the profiling switch is no longer supported, and whit speedshop I see only the g98 executibale, so I think I must use pixie on the intresting executibales, but if I try I get an error messages: Could not map rld from file rld.pixn32 On our HP we have compiled the whole program with the -p switch and set the enviroment variable PROFDIR=. , so that each executable should write its own profile-file. Here G98 writes an core file very soon in g98 after start. So I dont know whats go wrong on it! Thanks Thomas Nowak Martin-Luther Universitaet Halle FB Chemie (Merseburg) IPC 06099 Halle email: nowak@chemie.uni-halle.de