From wdi@ccl.net Mon Mar 20 04:14:00 1995 Received: from schiele for wdi@ccl.net by www.ccl.net (8.6.10/930601.1506) id EAA15557; Mon, 20 Mar 1995 04:02:27 -0500 Received: by schiele (950215.SGI.8.6.10/940406.SGI.AUTO) for chemistry@ccl.net id JAA29731; Mon, 20 Mar 1995 09:58:34 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9503200958.ZM29729@schiele> Date: Mon, 20 Mar 1995 09:58:31 +0100 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Re: malloc() etc. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I don't think this product has already been mentioned: I recommend 'purify' from Pure Soft as the ultimate program checking tool. It will not only detect all kinds of malloc-related problems but also overwrites, overruns, uninitialized reads etc. in normal variables. It is really extremely thorough. For example, problems in the standard system Motif libraries are detected but suppressed by default because they are such are piece of crap and literally contain hundreds of problems. Purify really does amazing things with limited loss of performance (factor 3 is typical - so your program can still do real work, in contrast to competing products from Sun etc). Purify works directly on the object files and libraries and is therefore compiler-independent. You don't even need source code, but information will be reduced without. Unfortunately, purify is available only for a limited number of systems (Sun, HP ... but I don't think DEC). I have no connection with Pure Soft, but I am a satisfied customer. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 From DAFNAN@vms.huji.ac.il Mon Mar 20 05:13:54 1995 Received: from VMS.HUJI.AC.IL for DAFNAN@vms.huji.ac.il by www.ccl.net (8.6.10/930601.1506) id EAA15677; Mon, 20 Mar 1995 04:33:15 -0500 Received: by HUJIVMS (HUyMail-V7b); Mon, 20 Mar 95 11:33:01 +0200 Received: by HUJIVMS (HUyMail-V7b); Mon, 20 Mar 95 11:18:13 +0200 Date: Mon, 20 Mar 95 11:11 +0200 Message-id: <20030095111122@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Conformation Analysis Dear CCL'ers; I'm looking for a Fortran program that compares the similarity of two different conformations and gives their RMS deviation. Does anybody out there know if there's a public domain program of this kind, and what is its method for comparing the conformations? Any help would be greatly appreciated. Sincerely, Daffy Nathan Hebrew University of Jerusalem, Israel From clkao@iris.bc.ntu.edu.tw Mon Mar 20 06:14:07 1995 Received: from iris.bc.ntu.edu.tw for clkao@iris.bc.ntu.edu.tw by www.ccl.net (8.6.10/930601.1506) id FAA16419; Mon, 20 Mar 1995 05:55:00 -0500 Received: by iris.bc.ntu.edu.tw (920330.SGI/920502.SGI) for chemistry@ccl.net id AA11846; Mon, 20 Mar 95 18:57:05 -0800 Date: Mon, 20 Mar 95 18:57:05 -0800 From: clkao@iris.bc.ntu.edu.tw (Chai-Lin Kao) Message-Id: <9503210257.AA11846@iris.bc.ntu.edu.tw> To: chemistry@ccl.net Subject: pesudo-receptor Dear everyone Recently, I am working to generate a pseudo-receptor for drug development. I got some problem and need help. I have used the "Catalyst" to generate a Adenosine A1 pseudo-receptor. The result is not very good. I could get a right answer from docking a known ligand with this p-receptor. Someone tell me that need more substrates to generatreceptor. But, how much? How many compounds what I have to give, at least? Furthermore, every time, I reproduced a pseudo-receptor. I have to work from the beginning. I couldn't start from the last results. It's take a long time to work. What I could to do to reduce my working time. Thank you. Chai-Lin Kao School of Pharmacy College of Medicine National Taiwan University Taipei, Taiwan e-mail clkao@iris.bc.ntu.edu.tw From KUCHARSKI@itots3.ch.pwr.wroc.pl Mon Mar 20 07:13:56 1995 Received: from sun1000.ci.pwr.wroc.pl for KUCHARSKI@itots3.ch.pwr.wroc.pl by www.ccl.net (8.6.10/930601.1506) id GAA16915; Mon, 20 Mar 1995 06:37:27 -0500 Received: from indigo.ch.pwr.wroc.pl (indigo.ch.pwr.wroc.pl [156.17.2.36]) by sun1000.ci.pwr.wroc.pl (8.6.10/8.6.10) with SMTP id MAA13453 for <@SUN1000.CI.PWR.WROC.PL:chemistry@ccl.net>; Mon, 20 Mar 1995 12:37:01 +0100 Received: from itots3.ch.pwr.wroc.pl by indigo.ch.pwr.wroc.pl via SMTP (931110.SGI/930416.SGI) for @SUN1000.CI.PWR.WROC.PL:chemistry@ccl.net id AA08464; Mon, 20 Mar 95 12:38:32 -0100 Received: from ITOTS/MAILQUEUE by itots3.ch.pwr.wroc.pl (Mercury 1.11); Mon, 20 Mar 95 12:22:37 GMT+1 Received: from MAILQUEUE by ITOTS (Mercury 1.11); Mon, 20 Mar 95 12:22:05 GMT+1 From: "Stanislaw Kucharski" To: chemistry@ccl.net Date: Mon, 20 Mar 1995 12:21:56 MET1MDT Subject: MOPAC7 Priority: normal X-Mailer: PMail v3.0 (R1a) Message-Id: <3F214396627@itots3.ch.pwr.wroc.pl> Hi, I have some problems with POLAR option in MOPAC7 DOS version. The test_pol.dat file being a part of Mopac7.tar.Z is looking exactly like this: '==================================================== polar symmetry Formaldehyde, for Demonstration Purposes O C 1.2 1 H 1.1 1 120 1 H 1.1 0 120 0 180 0 2 1 3 3 1 4 3 2 4 0 1 1 0.001 500 150 0.001 ' ===================================================== and when run with (go32 mopac7.sml) gives the for006 file which ends with: ENERGY OF "REORIENTED" SYSTEM WITHOUT FIELD: -32.8817631755 NFREQ= 3 IWFLB= 0 IBET= 1 IGAM= 1 ATOL= .10000E-02 BTOL= .10000E-02 MAXITU= 500 MAXITA= 150 '====================================================== an the program stops with screen info: open: file not found apparent state: unit 17 named .PO lately writing sequential formatted external IO Abort! I tried different combinations of data in the last line of the file always with the same result. Should I in such a case try SETUP option with test_pol.dat? And the format of the SETUP file should be like test_ pol.dat (with no symmetry data) or different ? Could anybody send me a simple data file workable with POLAR option in MOPAC7 DOS program ? Virtually, Stanislaw Kucharski From heelisp@delta.newi.ac.uk Mon Mar 20 08:13:58 1995 Received: from delta for heelisp@delta.newi.ac.uk by www.ccl.net (8.6.10/930601.1506) id HAA17084; Mon, 20 Mar 1995 07:16:20 -0500 From: Date: Mon, 20 Mar 1995 12:03:15 +0100 Message-Id: <95032012031523@delta.newi.ac.uk> To: chemistry@ccl.net Subject: spectra X-VMS-To: SMTP%"chemistry@ccl.net" Dear Netters, I am trying to use the Zindo/s module of Hyperchem 4 to calculate UV/Vis of aromatics and heteroaromatics. However the answers I am getting do not agree with experiment. e.g. benzene has lmax at 191nm. I am minimising the structures with AM1 then doing a single point with Zindo/s with C.I=3 or more. Anyone who has experience of using Zindo (based on CINDO) and can give examples of their calculations or an idea of what sort of agreement with experiment I can expect? Of course I am not expecting a spot on answer, but I did expect a value to be vaguely similar to the experimetal. Thanks in advance for any help Paul Heelis Heelisp@newi.ac.uk From jkong@is.dal.ca Mon Mar 20 09:14:03 1995 Received: from is.dal.ca for jkong@is.dal.ca by www.ccl.net (8.6.10/930601.1506) id IAA17552; Mon, 20 Mar 1995 08:16:55 -0500 Received: by is.dal.ca (AIX 3.2/UCB 5.64/4.03) id AA161226; Mon, 20 Mar 1995 09:14:58 -0400 Date: Mon, 20 Mar 1995 09:14:58 -0400 (AST) From: Jing Kong Subject: Re: CCL:malloc etc. on DEC Alpha To: Simon Kilvington Cc: chemistry@ccl.net In-Reply-To: <199503161813.SAA27313@vision.soton.ac.uk> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 16 Mar 1995, Simon Kilvington wrote: > Konrad Hinsen wrote: > > > > However, in all cases of malloc()-related crashes I have experienced > > so far (and that is a large number), the code calling malloc() was at > > fault. The most typical bug is memory access beyond the allocated space. > > Some versions of malloc() are quite forgiving if only a few more > > bytes are used, which is often the case, and this explains why such > > programs work on some machines but not on others. Another common > > way to ruin malloc's data space is to work with undefined addresses > > (bad pointers in C, or wrong number of subroutine parameters in Fortran). > > > > a (fairly) easy way to check for writing passed the end of malloc > blocks is to replace calls to malloc with calls to a routine which claims > slightly more space than is needed, puts some id characters at the start > and end of the block eg "MALLOC_BLOCK" or something, and returns a ptr to > the first byte after the id. Then replace calls to "free" with a routine > that first checks whether the id characters are still intact. If they have > changed something has writen before/after the start/end of the block. > You can also check if the array index is out of boundary every time you access your array by calling a subroutine instead of going directly x[i]. This is essentially objective-oriented programming. In C++, it can be done invisibly by operator-overloading. Jing From hinsenk@ERE.UMontreal.CA Mon Mar 20 13:15:18 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id MAA23287; Mon, 20 Mar 1995 12:15:12 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA03408 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Mon, 20 Mar 1995 12:12:51 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA12299; Mon, 20 Mar 95 12:12:50 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA28587; Mon, 20 Mar 95 12:12:49 -0500 Date: Mon, 20 Mar 95 12:12:49 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9503201712.AA28587@cyclone.ERE.UMontreal.CA> To: chemistry@ccl.net Subject: How to get FTNCHEK Since many people have asked me where ftnchek can be found, I thought it might be helpul to tell everyone: You can get ftnchek by ftp from netlib.att.com, directory /netlib/fortran, file ftnchek.tar.gz. It comes complete with a manual and test cases. Installation is straightforward and using it is even easier. There is really *no* excuse for not using it. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From hcj@mazda.wavefun.com Mon Mar 20 16:14:07 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id PAA27586; Mon, 20 Mar 1995 15:52:20 -0500 Received: from mazda.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA13229; Mon, 20 Mar 95 12:52:27 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA04097; Mon, 20 Mar 95 12:52:21 -0800 Date: Mon, 20 Mar 95 12:52:21 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9503202052.AA04097@mazda.wavefun.com> To: mcblab43@leonis.nus.sg Cc: chemistry@ccl.net In-Reply-To: (message from Loh Chang Shiung on Sun, 19 Mar 1995 13:31:50 +0800 (SST)) Subject: Re: CCL:mailing ccl (fwd) Reply-To: hcj@wavefun.com >>>>> "Loh" == Loh Chang Shiung writes: Loh> Hello, Anyone knows if there are good packages that use Loh> genetic algorithms or simulated annealing to determine Loh> minimum structures of small molecules (ex: short peptide Loh> chains)? I will post a summary of relevant replies. Spartan 4.0 from Wavefunction Inc. has four new conformational analysis methods, including a genetic algorithm and a Monte Carlo approach. For more information about Spartan, check out our web page at http://wavefun.com. -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From tripos!nova!vandyke@uustar.starnet.net Mon Mar 20 17:14:09 1995 Received: from uustar.starnet.net for tripos!nova!vandyke@uustar.starnet.net by www.ccl.net (8.6.10/930601.1506) id QAA28301; Mon, 20 Mar 1995 16:43:35 -0500 Received: from tripos.UUCP by uustar.starnet.net with UUCP id AA29662 (5.67b/IDA-1.5 for ccl.net!CHEMISTRY); Mon, 20 Mar 1995 15:16:03 -0600 Received: from nova.tripos by tripos (4.1/SMI-4.0) id AA08099; Mon, 20 Mar 95 13:23:29 CST Received: by nova.tripos (920330.SGI/5.6) id AA24128; Mon, 20 Mar 95 13:23:28 -0600 Date: Mon, 20 Mar 95 13:23:28 -0600 From: tripos!nova!vandyke@uustar.starnet.net (Chris Van Dyke) Message-Id: <9503201923.AA24128@nova.tripos> To: CHEMISTRY@ccl.net Subject: 1995 course schedule Tripos, Inc., announces its course schedule for the remainder of 1995. These courses are application-based and are designed to achieve specific research results through use of Tripos software. For more information, please contact Tripos at (800) 323-2960 or send E-mail to chris@tripos.com. Training Sites ============== CA: Mountain View MO: St. Louis NC: Research Triangle Park NJ: Parsippany Course schedule =============== Introductory Molecular Modeling CA July 25-26 NC April 25-26 NJ August 8-9 Biopolymer Modeling Techniques CA July 27-28 NC April 27-28 NJ August 10-11 NMR Data Processing and Analysis MO May 9-11 MO September 26-28 Innovative Solutions for Compound Discovery CA December 5-6 MO May 22-23 NC November 7-8 Molecular Diversity Manager CA December 7-8 MO May 22-23 NC November 9-10 Course Descriptions =================== Introductory Molecular Modeling (2 days) -- This course covers molecular visualization techniques and conformational analysis. Users will gain hands-on experience building molecules, determining realistic molecular geometry, comparing molecular structures, calculating atomic charges, and displaying molecular surfaces and properties. Molecular flexibility will be explored using systematic and stochastic search methods, as well as molecular dynamics. An introduction will be given to various modeling methods and their applicability to different situations. -- Participants in this course need no prior experience with Sybyl. Biopolymer Modeling Techniques (2 days) -- This course covers biopolymer visualization techniques as well as energy-based and knowledge-based methods of biopolymer modeling. Users will learn to construct biological macromolecules and enhance their graphical depiction. Techniques will be explored to study ligand-receptor and protein-solvent interactions, as well as protein conformations and motion. Effects of site-point mutations will be studied. Finally, participants will gain experience in deriving the tertiary structure of proteins from their primary structures. -- Participants in this course need no prior experience with Sybyl. NMR Data Processing and Analysis (3 days) -- This course covers processing and analysis of NMR Spectra, and structural refinement from NMR data. Users will learn to transform FID to spectra and identify informational peaks. Users will also gain experience in assigning atoms to peaks in NMR spectra. Finally, users will learn to determine interatomic distance constraints from volumes of peaks in NMR spectra and generate molecular conformations based on these distance constraints. -- Participants in this course need no prior experience with Sybyl. Innovative Solutions for Compound Design (2 days) -- This course covers pharmacophore model development and lead compound generation. Users will gain hands-on experience in determining a pharmacophore, in the absence of detailed information about essential binding groups. In addition, regions surrounding a series of biologically active molecules where steric or electrostatic interactions play a significant role in activity will be elucidated. Database searching strategies and de novo compound design tools will be used to generate lead compounds. -- Participants in this course should have experience in the topics covered in the Introductory Molecular Modeling course. Molecular Diversity Manager (2 days) -- This course covers the analysis of mass screening data and structures, and statistical analysis. Course participants will learn methods of accessing and analyzing structural data in chemical information systems. Users will gain experience in building and managing combinatorial libraries, through reactant- or product-based entries. Users will also learn to select sets of compounds >from these libraries based on molecular diversity or similarity. Rational selection criteria will be explored, as well as tools for making selections based on these criteria. -- Participants in this course should have experience in the topics covered in the Introductory Molecular Modeling course. From rvgloss@criba.edu.ar Mon Mar 20 20:14:04 1995 Received: from sic4.cnea.edu.ar for rvgloss@criba.edu.ar by www.ccl.net (8.6.10/930601.1506) id TAA01158; Mon, 20 Mar 1995 19:47:39 -0500 Received: from criba.edu.ar by sic4.cnea.edu.ar with smtp (Smail3.1.28.1 #1) id m0rqs5t-00040WC; Mon, 20 Mar 95 21:46 GMT-3:00 Received: by criba.edu.ar (4.1/SMI-4.1) id AA15533; Mon, 20 Mar 95 21:50:27 WST Date: Mon, 20 Mar 95 21:50:27 WST From: rvgloss@criba.edu.ar (Daniel Glossman) Message-Id: <9503210150.AA15533@criba.edu.ar> To: chemistry@ccl.net Subject: gaussian z-matrix for pyrrole Dear netters: Thanks to all who answered my recent query about the gaussian z-matrix for pyrrole. Unfortunately, due to a failure in my system, I lost your messages. I will be grateful if you can send the messages again. Thanks in advance Daniel Glossman rvgloss@arcriba.edu.ar From jkl@ccl.net Mon Mar 20 23:14:10 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id XAA03218; Mon, 20 Mar 1995 23:04:36 -0500 Date: Mon, 20 Mar 1995 23:04:36 -0500 From: Jan Labanowski Message-Id: <199503210404.XAA03218@www.ccl.net> To: chemistry@ccl.net Subject: Support letters deadline passed Cc: jkl@ccl.net Dear CCL subscribers, I hope that it is my last message on support letters for CCL. The deadline passed yesterday, and I concluded letter collection. Of course, it is never too late to send me a support letter, but at some point, it may not be here in time to make its way into a proposal. The figures will probably change slightly, since I got several assurances that "the letter is in the mail". There are also some inconsistencies. E.g., a few of .com or .net addresses do not reside in the US, and some of them were assigned to the respective country domain, but not all. Also, some people are subscribed under addresses in another country, than the one in which they actually physically reside. However, these changes do not really influence the bottom line. I also did not include the support e-mail messages in this statistics, but there are not that many of these. I want to thank you all, who found time to write the letter in support of CCL. At the same time, I understand that some of you were too busy, and some did not want to commit their support for various reasons. I try to cheer myself that my return rate was not that bad compared with other support requests which I witnessed on various other occassions. Now, I will have to read, organize, index, and sort these letters, so they can be easily used by the reviewers. My first impression is that many people included very strong support, and this of course is a great motivation for myself. Thank you again. Domain Subscribers Letters Percent on CCL Received Responded ar 4 0 0.00 at 21 6 28.57 au 52 15 28.85 be 34 8 23.53 br 15 4 26.67 ca 77 17 22.08 ch 26 5 19.23 cl 5 0 0.00 cn 5 5 100.00 co 2 0 0.00 cz 3 1 33.33 de 148 23 15.54 dk 16 7 43.75 ee 4 2 50.00 eg 3 1 33.33 es 49 26 53.06 fi 13 3 23.08 fr 45 14 31.11 gr 5 5 100.00 hk 3 1 33.33 hr 7 1 14.29 hu 13 13 100.00 ie 2 0 0.00 il 25 11 44.00 in 9 0 0.00 ir 2 0 0.00 it 33 8 24.24 jp 34 3 8.82 kr 11 2 18.18 lv 1 0 0.00 mx 11 6 54.55 my 1 0 0.00 nl 43 14 32.56 no 6 1 16.67 nz 2 0 0.00 pl 35 8 22.86 pt 1 1 100.00 ru 4 0 0.00 se 19 13 68.42 sg 5 1 20.00 sk 5 0 0.00 su 5 4 80.00 th 2 0 0.00 tr 3 0 0.00 tw 9 1 11.11 uk 124 33 26.61 us 6 0 0.00 ve 1 0 0.00 za 10 3 30.00 com 345 89 25.80 edu 737 133 18.05 gov 82 15 18.29 mil 15 4 26.67 net 14 1 7.14 org 24 4 16.67 ---------------------------------------- Total: 2176 512 23.53 (Mon Mar 20) For comparison: Total: 2166 432 19.94 (Wed Mar 15) Total: 2157 322 14.93 (Fri Mar 10) Total: 2137 125 5.85 (Thu Mar 2) You can also see that the number of addresses on CCL grows, and it is far >from the saturation. Yours, Jan jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From aiba@ir.phys.chem.ethz.ch Sun Mar 19 12:56:04 1995 Received: from bernina.ethz.ch for aiba@ir.phys.chem.ethz.ch by www.ccl.net (8.6.10/930601.1506) id MAA09439; Sun, 19 Mar 1995 12:56:01 -0500 Received: from volta (actually volta.ethz.ch) by bernina.ethz.ch with SMTP inbound; Sun, 19 Mar 1995 18:55:51 +0100 Date: Sun, 19 Mar 1995 18:55:51 +0200 Message-Id: <95031918555104@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: chemistry@ccl.net Subject: SUMMARY - MOLECULAR GRAPHICS X-VMS-To: smtp%"chemistry@ccl.net" X-VMS-Cc: AIBA Dear Netters, on March 14, 1995, I posted a question about molecular graphics packages. The number of specific responses I have received is just 6. However, one can go ahead with it, it seems. I thank all who responded with advices very very much! It's good that good people are reachable through CCL - so CCL must be supported! Some people (seems very young people) wrote to me strange things and I am not posting them. HOW TO READ SUMMARY: - the string of ambersands '&&&&&&&&&&&&&' serves as a delimiter between two separate messages; therefore search please for this string (one of messages is very long&useful). Sincerely, Ayaz Bakasov. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& The original posting is this: > Dear Netters, > >could someone advise me please on >a molecular graphics software which: > >a) is ftp-able or commercial, > for a workstation like IBM/RS or Alpha DEC; >b) is for not too large molecules (atoms < 20-30); >c) draws bonds and can mark them (length); >d) draws bond angles and dihedral angles > and can mark them; >c) draws selected planes for pairs of bonds; >e) puts (desirable) different colours > on atoms and marks atoms (for slides); >e) any other useful features on top > of above-specified ones will be welcome > (e.g. animation). > > >Tried RASMOL and found that it is for >VERY large molecules, while I need >to draw molecules ranging from hydrogen peroxide >to some first aminoacids. Also, RASMOL doesn't >take care of small details I am interested in >(like specification of bond angles and > dihedral angles on the graph, or drawing > planes of pairs of bonds) > >Perhaps, Mathematica or Maple >have already some supplementary >packages ?! > >Thank you. >It will be my pleasure to summarize >on the net the suggestions. > >Ayaz Bakasov. > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& The responses follow below in chronological ordering: &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 15-MAR-1995 01:19:29.35 From: SMTP%"DOUGH@mdli.com" Subj: ISIS Draw can draw 3D features on structures To: aiba@ir.phys.chem.ethz.ch It doesnt have any rendering capability, but it is designed for generating queries for 3D pharmacophore searching, so distances, angles, dihedrals, lines, planes, centroids, etc can all be drawn, assigned colors, and output to postscript. It is sold thru MDL and thru ACS software (very low price for academics - I think $49). &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 15-MAR-1995 09:28:20.39 From: SMTP%"davide@stinch0.csmtbo.mi.cnr.it" Subj: Re: CCL:QUERY - MOLECULAR GRAPHICS To: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) Dear Ayaz Bakasov I use SCHAKAL, but I do not think that can write the bond lenghts and angles on the picture. You may contact the author and ask him more information here are some general information and please let me know if you find something. Davide ******************************************************** ************ thank you for your email. Please find attached to this messge some information on the SCHAKAL 92 program. Sincerely -- Egbert Keller | Mail: kell@sun1.ruf.uni-freiburg.de Kristallographisches Institut | University Hebelstrasse 25 | Phone: +49 761 203 6438 D-79104 Freiburg i.Br / Germany | FAX: +49 761 203 6434 -------------------------------------------------------- ------------------- ****************************** Some information on SCHAKAL 92 ****************************** SCHAKAL 92 is a computer program for the graphic representation of molecular and crystallographic models. The most important features of this program are specified in the following. Model types: simple on-screen rotatable wire model, ball-and-stick model with optionally broken, optionally exaggeratedly tapered sticks, space filling model, intersection trace between space filling model and plane. Automatic generation of bonds and specific drawing parameters for the individual types of atoms. Facility to generate packing diagrams and (hkl) surface models. Display styles: outlines; hatching by parallels, meridians, or grids; shading by randomly or regularly dithered dots; "realistic" multi-colour shading. Optional addition of shadows and highlights according to a positionable light source. Optional perspective projections; optional stereo drawings with stereo shading or labelling. Optionally depth-dependent line thickness, darkness, or pseudo-transparency. Rotations: on-screen rotations of wire-models. Several possibilities to align the model, e.g. alignment of a least-squares plane or a crystallo- graphic lattice vector. Optional rotations (or translations) of parts of the model, e.g., rotation of substituents about single bonds. Labelling: facility to label atom circles automatically with atom "names", chemical element symbols, or coordinates, in a manner suitable for publica- tion or documentation (label positions are optimized for minimal overlap. Facility to modify label positions via a graphics cursor. Information: facility to get information on atoms, bonds, model statistics, steric trouble, current switch and parameter settings, view direction, distances, angles, and dihedral angles. Miscellaneous: facility to add cursor-defined lines and cursor-positioned text (e.g. chemical formulas) to the drawing (see figure captions); facility to transform crystallographic coordinates; facility to generate broken-off bond sticks in the boundary region of a model. Various predefined 3D and 2D shading patterns. Data Input: atom names and coordinates; optional: space group symbol or single symmetry operations; input defining a parallelepipedal or polyhedral section of a crystal structure or a (hkl) "surface model". Program control: simple unformatted command code, which allows to vary all important drawing variables and to select individual (or groups of) atoms/ bonds; facility to pick atoms or bonds via a graphics cursor; various "distri- buted command files" for routine tasks; detailed on-line help functions; printed tutorial manual including 24 figures. Output devices: screen; paper plotter (HP-GL file); HP LaserJet III (or fully compatible), screen image save file (non-standard format, described in the manual [except V16version]); .PCX file (V256 version only). Speed: On a 33 MHz 80486 DOS-PC with extended VGA card (1024 x 768), the following times were required to draw a molecule of 100 atoms and 100 bonds on the whole screen (BS = ball+stick model; SP = space-filling model): BS: outlines: 4 sec; fully shaded model incl. shadows and highlights: 22 sec SP: outlines: 4 sec; fully shaded model incl. shadows and highlights: 64 sec Examples: see J. Appl. Crystallography 22, 19-22 (1989) (note: high quality LaserJetIII drawings are not included there) DOS-PC versions *************** There are several DOS-PC versions of SCHAKAL 92 available (none of them is WINDOWS- or network compatible) having a capacity of 1200 atoms and 1200 bonds: a) SCHAKAL 92/V16 for DOS-PC with standard VGA card b) SCHAKAL 92/V256 for DOS-PC with extended VGA card (VESA) c) SCHAKAL 92/FGA4 for DOS-PC with Spea FGA-4 card d) SCHAKAL 92/XXHR for DOS-PC with Elsa XHR Omega/Gemini card Requirements: (1) MS-DOS 5.0 or later; 80386/80387 or 80486 processor (the faster the better) (2) either: a powerful Cache driver (for example MS SMARTDRV.EXE) or: a RAM-disk of at least 1 MB (2 or - better - 4 are recommended). (3) at least 560 kB (573000 Byte) free space within the 640 kB RAM (memory); at least 3 MB free space on your hard disk (much more, if you want to store various plotter or image files). (4) a suitable graphics card. For the different versions, "suitable" means: a) SCHAKAL 92/V16: a standard or extended VGA card; the card will be used with a resolution of 640 x 480 and 16 concurrently displayable colours. b) SCHAKAL 92/V256: an extended VGA card with corresponding colour graphics monitor. The VGA card must correspond to the VESA standard (or run with a VESA driver). SCHAKAL 92/V256 uses VESA modes with 256 concurrently displayable colours and one of the following resolutions: 640 x 480; 800 x 600; 1024 x 768; 1280 x 1024 . A number of VESA drivers for most extended VGA cards will be distributed on the SCHAKAL diskette, packed in a .ZIP file. You will have to "unzip" them with your own PKUNZIP.EXE program. c) SCHAKAL 92/FGA4: A Spea FGA-4 graphics controller or a fully compatible with a resolution of 1280 x 1024 and 256 concurrently displayable colours. d) SCHAKAL 92/XXHR: An Elsa XXHR 110 or XHR Omega or XHR Gemini controller with a resolution of 1280 x 1024 and 256 concurrently displayable colours from a palette of 16 millions. (5) not essential: a plotter which understands HP-GL language or stand-alone software which is able to translate an HP-GL file for your plotter/printer (e.g. PRINTGL from Ravitz Software [shareware]). (6) not essential: an HP LaserJet III or fully compatible printer. The printer must have at least 2 MB memory. (7) not essential, and for SCHAKAL 92/V256 only: a software which is able to copy a .PCX file onto a (colour) printer (e.g. Corel Photopaint by Corel Corporation or Graphics Workshop for WINDOWS by Alchemy Mindworks Inc. [shareware]). Other versions: *************** These consist of the "general FORTRAN code" plus (optionally) an adaption of this code to a certain system (performed by a user of the program). All versions require compilation with a FORTRAN compiler and (possibly) a C compiler. X-Windows versions are comparatively slow; they are, like all other versions, command driven (not menu driven): e) SCHAKAL 92 general FORTRAN code with graphic interface to be adapted to any graphics system f) SCHAKAL 92/AIX-GL GL-version for IBM-RS/6000; requires 3D Adapter SCHAKAL 92/AIX-XW X-Windows version for IBM-RS/6000 g) SCHAKAL 92/IRIS-4D GL-version for Silicon Graphics IRIS-4D h) SCHAKAL 92/SUN X-Windows version for SUN workstations i) SCHAKAL 92/VAX X-Windows version for VAXstations (limited functionality) Note: The author (E.K.) is not able to give any direct support with respect to machine-specific problems for versions f) to i). Some Examples for Commands: *************************** All of SCHAKAL's switches and all parameter settings are controlled by commands, which may be given in arbitrary order. The effect of any command may be altered or cancelled by a command of the same type later on (e.g. after generation of a drawing). Any command begins with two label words which may be followed by parameters, atom codes, and/or bond codes. Note: label words may in any case be abbreviated to one letter. A few examples follow: Genr Unitcell [g u] (add unit cell edges to drawing) Genr Shading [g s] (switch for shaded drawing) Use Commandfile [u c] (execute commands stored on a file) Help U C [h u c] (give information on the 'U C' command) Rot X -12 [etc.] (rotate -12 deg. about X-axis) Rot Bond 80 C2=C7 (rotate substituent 80 degrees about the bond between C2 and C7) Kill Bonds <3.2 Ba=nn (Ba=I (delete bonds between all Ba atoms and other atoms, if dist. <3.2A, but not between Ba and I ) Change Radii *1.15 S1 P (P'2 (increase radii by 1.15 for S1 and P atoms, but not for P atoms belonging to numerical group 2) Xqt Xqt C1-O12 C1-O12=nn (draw all atoms >from C1 to O12 and all the bonds in which they are parti- cipating) Various routine tasks may be accomplished by means of "distributed command files" which contain procedures consisting of large numbers of such commands. An example input to execute such a command file follows (generates a shaded drawing of ball-and-stick plus space-filling model including shadows, highlights, and labelling of non-Hydrogen atoms (see. fig.1)): U C ca w Extent of supply: ***************** A SCHAKAL 92 supply consists of the following items [items a) to i) are distributed on one or two 3.5" DOS diskette(s)]: a) the executable program (DOS versions only) b) the FORTRAN source code of about 35000 lines (all versions except SCHAKAL 92/V16 and SCHAKAL 92/V256) c) an interactive hierarchical on-line manual in English (about 300 pages, if printed) d) a program to make a printout of this manual e) a space group database f) some data set examples g) a number of "distributed command files" for routine tasks h) installation hints and installation program or makefile for the distributed version i) a number of VESA drivers packed into a .ZIP file (SCHAKAL 92/V256 only) j) a printed tutorial manual in English (76 pages, 24 figures) k) printed installation hints for the general version (all versions except DOS versions) Licencing agreement and licence fees: ************************************* SCHAKAL 92 is exclusive property of the University of Freiburg (represented by Kristallographisches Institut der Universitaet). Legal use of the program requires undersigning a licencing agreement and the following licence fees to be paid [in Deutschmarks] (PRI = public research institute): version student school univers. PRI commercial -------------------------------------------------------- --------------------- SCH 92/V16 200.- A) 300.- B) 600.- B) 800.- B) 1200.- A) -------------------------------------------------------- --------------------- SCH 92/V256 250.- A) 375.- B) 750.- B) 1000.- B) 1500.- A) -------------------------------------------------------- --------------------- All other versions 1200.- C) 1600.- C) 2400.- A) -------------------------------------------------------- --------------------- A) valid for installation on one computer. B) valid for installation on a group of PCs to which one "responsible user" has legal and practical access (i.e., all PCs of a work group. If the program is installed on a large network, each workgroup has to pay the licence fee). C) valid for installation on one computer within one unit, where unit is, for example, a department of inorganic chemistry, a dept. of experimental physics, etc. (maximally 2 "Lehrstuehle" = full professorships); a corre- sponding department within a public research institute. A discount of 75 % is offered for installation on a second, third, etc. computer within the same unit. A discount of 60% is offered for a SCHAKAL 92/V16 or SCHAKAL 92/V256 licence within the same unit. For any registered SCHAKAL 86 / SCHAKAL 88 licence, there is an update discount of 75 % on the corresponding licence fee given in the table above (72% for update from SCHAKAL 88B/V16 to SCHAKAL 92/V256). Additional multi-installation discounts are offered for "All other versions" only (87 % discount for 2nd, 3rd, etc. installation). The rules given above are applied to decide whether an installation is a 1st, 2nd, or 3rd (etc.) one and whether a certain (group of) computer(s) is covered by an existing SCHAKAL 88 licence. There is an additional shipment fee of DM 15.- for non-European countries. A 50% discount is offered on all licence fees for East-European and for developing countries. Printing or other kind of multiplication of SCHAKAL drawings ... ... in scientific journals, congress invitations, letters, internally used documents or educational scripts: is generally permitted (except for a student's licence). ... in a scientific textbook: requires payment of an additional licence fee of usually DM 50.- to 500.-, depending on the number of drawings and the scope and purpose of the book. ... in other printed or non-printed matter (especially advertising material): requires payment of an additional licence fee of DM 200.- to 4000.-, the latter amount corresponding to an unlimited printing licence. For commerical users of SCHAKAL 88, the difference between the licence fee for SCHAKAL 88 and for SCHAKAL 92 is accounted for, here. -------------------------------------------------------- ----------- Davide M. Proserpio Dipartimento di Chimica Strutturale e Stereochimica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@stinch.csmtbo.mi.cnr.it -------------------------------------------------------- ----------- &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 15-MAR-1995 17:19:01.12 From: SMTP%"lipkowitz@chem.iupui.edu" Subj: RE: CCL:QUERY - MOLECULAR GRAPHICS To: "Ayaz Bakasov, Phys. Chem., ETH Zurich" Don Boyd has been publishing an updated appendix in every volume of Reviews in Computational Chemistry, published by VCH Publishers. It contains information about many kinds of programs that you might find useful. Good luck, Kenny &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 16-MAR-1995 19:26:20.03 From: SMTP%"heuer@chemie.uni-hamburg.de" Subj: Re: CCL:QUERY - MOLECULAR GRAPHICS To: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) Dear Ayaz Bakasov Do you have tried xmol for RS6000 it print angles etc if you want it. Ask archie for the location. Yours sincerely Joerg Heuer Ask archie for the location. Joerg Heuer e-mail: Heuer@chemie.uni-hamburg.de Institut fuer Pharmazie, Universitaet Hamburg, Bundesstraae 45, 20146 Hamburg, Germany. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 16-MAR-1995 20:06:10.80 From: SMTP%"dianat@softshell.com" Subj: Re: CCL:QUERY - MOLECULAR GR To: "Ayaz Bakasov, Phys. Chem., ETH" Dear Mr. Bakasov, I am with SoftShell International, we have a program called ChemWindow for the IBM PC or ChemIntosh for the Mac. This is a chemistry drawing program. I will gladly send you a free demo of the program if you are interested, as well as a catalog of our other products. Please let me know, my address is dianat@softshell.com Thank you. ------------------------------ Date: 3/15/95 6:34 AM To: Diana Tarasiewicz From: Ayaz Bakasov, Phys. Chem., ETH &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 17-MAR-1995 17:33:19.03 From: SMTP%"M.J.C.Crabbe@reading.ac.uk" Subj: Re: CCL:QUERY - MOLECULAR GRAPHICS To: aiba@ir.phys.chem.ethz.ch DeskTop Molecular Modeller sounds to be most appropriate. It runs on any PC, uses Windows, and is available from Oxford University Press for about 250 pounds stirling. It is part of a suite of programs and libraries. Contact Mrs Janet Caldwell, Oxford University Press, Walton Street, Oxford, OX2 6DP (tel: +44 (0)1865 56767 for details. Yours, James Crabbe. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From rlm1003@cus.cam.ac.uk Mon Mar 20 05:38:53 1995 Received: from bootes.cus.cam.ac.uk for rlm1003@cus.cam.ac.uk by www.ccl.net (8.6.10/930601.1506) id FAA16345; Mon, 20 Mar 1995 05:36:46 -0500 Received: from apus.cus.cam.ac.uk [131.111.8.2] (ident = root) by bootes.cus.cam.ac.uk with smtp (Smail-3.1.29.0 #30) id m0rqep8-000BzUC; Mon, 20 Mar 95 10:36 GMT Received: by apus.cus.cam.ac.uk (Smail-3.1.29.0 #27) id m0rqep7-00034TC; Mon, 20 Mar 95 10:36 GMT Message-Id: Date: Mon, 20 Mar 95 10:36 GMT From: rlm1003@cus.cam.ac.uk (Ricardo) To: CHEMISTRY@ccl.net Subject: CCL: Heavy water (D2O) parameters Dear Netters, I would like to know if any people out there have any information regarding optimized parameters for MD/MC simulation of heavy water (D2O), obviously beyond the point of using standard water (H2O) potentials and changing the hydrogens' masses. Thanks in advance. R. L. Mancera Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW, UK