From mbdtsnm@hpf.ch.man.ac.uk Fri Oct 10 06:29:43 1997 Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA16611; Fri, 10 Oct 1997 05:46:37 -0400 (EDT) Received: from serenity.mcc.ac.uk by nessie.mcc.ac.uk with SMTP (PP); Fri, 10 Oct 1997 10:46:14 +0100 Received: from hpf.ch.man.ac.uk [130.88.12.28] by serenity.mcc.ac.uk with smtp (Exim 1.651 #21) id 0xJbe7-0000Ku-00; Fri, 10 Oct 1997 10:46:11 +0100 Date: Fri, 10 Oct 1997 10:44:57 +0100 Message-Id: <29864.9710100944@hpf.ch.man.ac.uk> From: "Nathaniel (noj) Malcolm" To: rainer.schork@urz.uni-heidelberg.de Cc: chemistry@www.ccl.net In-Reply-To: (message from Rainer Schork on Thu, 9 Oct 1997 16:19:13 +0200 (METDST)) Subject: Re: CCL:G:G94 problem with CCSD(TQ,FULL) Reply-To: Noj.Malcolm@man.ac.uk X-Beard: Beard v5.3 X-Child: Bethany rainer, try this instead it should work: # CCSD(TQ)(full)/CC-PVTZ SP noj p.s the different formats for specifying the excitation level+excitation window can sometimes lead to routes with funny errors for example using #p bd(t,full) will actually produce a vaild route card its just that it does a ccsd calculation instead of the requested bd(t) -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL e-mail noj.malcolm@man.ac.uk From kantor@usptu.oil.ru Fri Oct 10 09:29:42 1997 Received: from blackoil.oil.ru for kantor@usptu.oil.ru by www.ccl.net (8.8.3/950822.1) id IAA17156; Fri, 10 Oct 1997 08:41:30 -0400 (EDT) Message-Id: <199710101241.IAA17156@www.ccl.net> Received: from [194.84.208.1] by blackoil.oil.ru (SMTPD32-4.0) id A9DD1003012A; Fri, 10 Oct 1997 18:43:57 -0700 From: "Vadim Kantor" To: "CC List" Subject: About MOPAC & AMPAC Date: Fri, 10 Oct 1997 18:41:14 +0500 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 7bit Dear CCLers! I'm a post-graduate student in USPTU (Ufa State Petroleum Technological University). I use MOPAC & AMPAC for the reactions of cyclo-hexane derivatives hydrotation calculations on the IBM PC Pentium under Win95. There is a problem: I can't see the results of calculation straight in the programm. As I heard, the newest versions of MOPAC & AMPAC include graphical user interface. Could you help me to find these programms or demo versions? My e-mail is kantor@usptu.oil.ru. Thank you for the info. With best wishes, Vadim Kantor. From youngd2@mail.auburn.edu Tue Oct 7 04:29:05 1997 Received: from mallard.duc.auburn.edu for youngd2@mail.auburn.edu by www.ccl.net (8.8.3/950822.1) id EAA24322; Tue, 7 Oct 1997 04:20:23 -0400 (EDT) Received: from wood.mail.auburn.edu by mallard.duc.auburn.edu (SMI-8.6/SMI-SVR4) id DAA27747; Tue, 7 Oct 1997 03:20:22 -0500 Received: from localhost by wood.mail.auburn.edu (SMI-8.6/SMI-SVR4) id NAA04956; Mon, 6 Oct 1997 13:40:17 -0500 Date: Mon, 6 Oct 1997 13:40:17 -0500 (CDT) From: David Young X-Sender: youngd2@wood2 To: Chemistry@www.ccl.net Subject: Chem topic: Computational Drug Design Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I have written the following short essay for a computational chemistry class and am posting it here for your enjoyment and comments. Since I have not done drug design in an industrial setting, I would appreciate any comments about which techniques are used most often. My compilation of chemical topics can be accessed via the web at URL http://www.auburn.edu/~youngd2/topics/contents.html --------------------------------------------------------------------------- Computational Drug Design David Young Division of University Computing 144 Parker Hall Auburn University, AL 36849 The purpose of this document is to outline the drug design process and specifically the role of computational modeling techniques. This is not meant to be a comprehensive review. It is meant to list the most important techniques currently in use. The process of designing a new drug and bringing it to market is very complex and can take up to a decade from the start of the process until a new drug is available to physicians. Pieces of this process are often repeated to create successively better drugs for the same condition. In the case of antibiotics, drugs loose effectiveness as an immunity is built up, thus leading to a continuing "arms race". The major steps in the drug design process "from scratch" are. 1. FIND WHAT IS KNOWN Find out all that is known about the disease and existing or traditional remedies. It is also important to look at very similar afflictions and their known treatments. 2. DEVELOP AN ASSAY Develop an assay technique to test drug effectiveness. An ideal assay is one in which a compound can be added to tissue samples or micro-organism colonies and there will be a visible indication of an effective treatment. At worst, there must be a way to test the drug on a laboratory animal that is susceptible to the disease. If the only way to test the effectiveness of a trial compound is to inject an untested compound into a human subject then there is no way to proceed in finding a pharmaceutical treatment. 3. CONSIDER FINANCIAL ISSUES The next step is to make a financial decision about whether to proceed with the development process. The assay technique will determine the cost of testing compounds. If there are existing chemical treatments, it will be a refinement effort which saves the expense of finding lead compounds. All drugs must go through extensive testing so this is a fairly fixed cost. There may be governmental grants or tax incentives associated with certain diseases. The number of patients requiring treatment and merits of existing treatments will determine the long term profitability of producing a drug. Steps 4 and 5 of this procedure are often performed simultaneously. 4. FIND LEAD COMPOUNDS Lead compounds are compounds that have some activity against a disease. These may be only marginally useful and may have severe side effects. However, the lead compounds provide a starting point for refinement of the chemical structures. Lead compounds may come from many sources, including a. The isolation of active compounds from traditional remedies. b. The testing of natural materials followed by an isolation effort. c. Drugs effective against similar diseases. d. Use of combinatorial chemistry techniques which produce large numbers of related chemical compounds. This allows testing a large number of compounds at once. When a mixture that is useful is found, a separation must be done to determine which of the related structures has some drug activity. This has been one of the most promising and rapidly growing techniques in recent years. e. Searching chemical databases to find compounds similar to those found by the above means. This is the only part of the lead finding process that is considered to be a computational technique. There are many different measures of molecular similarity and ways of efficiently handling large databases, so this is not yet a trivial step. 5. ISOLATE THE MOLECULAR BASIS FOR THE DISEASE If it is known that a drug must bind to a particular spot on a particular protein or nucleotide then a drug can be tailor made to bind at that site. This is often modeled computationally using any of several different techniques. Traditionally, the primary way of determining what compounds would be tested computationally was provided by the researchers' understanding of molecular interactions. A second method is the brute force testing of large numbers of compounds from a database of available structures. More recently a set of techniques, called rational drug design techniques or De Novo techniques have been used. These techniques attempt to reproduce the researchers' understanding of how to choose likely compounds built into a software package that is capable of modeling a very large number of compounds in an automated way. Many different algorithms have been used for this type of testing, many of which were adapted from artificial intelligence applications. No clear standard has yet emerged in this area so it is impossible to say what is best the best technique at this time. These techniques have seen quite a bit of active development in recent years. Unfortunately, the complexity of biological systems makes it very difficult to determine the structures of large biomolecules. Ideally a x-ray chrystallography structure is desired, but biomolecules are very difficult to chrystalize. Another very useful technique, called "distance geometry" is to find some of the internuclear distances using NMR Nuclear Overhauser Effect experiments then find molecular geometries that have these distances. If only a protein sequence is known, there are many techniques for predicting how that protein will fold, but none has yet been shown to be 100% reliable. Even once a structure has been determined, identifying the site where a drug must bind is not a trivial task. The difficulty in find geometries makes it possible to bring first generation drugs to market by refinement of lead compounds without ever knowing the target site for the drug in the body. As such, these techniques are being used primarily for designing improved treatments for diseases that have already been characterized extensively. 6. REFINE DRUG ACTIVITY Once a number of lead compounds have been found, computational and laboratory techniques have been very successful in refining the molecular structures to give a greater drug activity and fewer side effects. This is done both in the laboratory and computationally by examining the molecular structures to determine which aspects are responsible for both the drug activity and the side effects. Synthetically, functional groups are removed in order to find out which must be present to give a useful drug and which are not necessary. The back bone of the structure is made more flexible or more rigid. A rigid back bone may hold the functional groups in the exact alignment necessary for the drug to bind. A flexible back bone may be necessary to allow the drug to get into the binding site. Adding bulky groups at other points on the molecule is often done in the hopes that these new groups may hinder the molecule from binding at unwanted sites which are responsible for the side effects. Computationally, the technique used is known as QSAR (Quantitative Structure Activity Relationships). It consists of computing every possible number that can describe a molecule then doing an enormous curve fit to find out which aspects of the molecule correlate well with the drug activity or side effect severity. This information can then be used to suggest new chemical modifications for synthesis and testing. Ideally there is a continual exchange of information between the researchers doing QSAR studies, synthesis and testing. These techniques are frequently used and often very successful since they do not rely on knowning the biological basis of the disease which can be very difficult to determine. 7. DRUG TESTING Once a drug has been shown to be effective by an initial assay technique, much more testing must be done before it can be given to human patients. Animal testing is the primary type of testing at this stage. The scientists doing the testing must be particularly observant of many little details since this is where unexpected side effects can be found. Another question to be answered is whether the drug will work well or poorly with other drugs. This is also where initial data necessary to determine correct dosages is obtained. Eventually, the compounds which are deemed suitable at this stage are sent on to clinical trials. In the clinical trials, additional side effects may be found and human dosages are determined. 8. FORMULATION Before a drug can be produced, there must be a means to administer it. Ideally, a tasteless or bland tablet can be created. Alternatively, an oral liquid, intravenous injection or directly applied cream may be created. Tablets are created by adding other compounds to minimize stomach upset and control timed release of the drug. A tablet may also have a compound which is a matrix that helps it hold it's shape without crumbling into a powder. Oral liquids are often combined with strong flavors and alcohol to mask the taste of the drug and prevent throat irritation. A cream may have to be thickened or have a component that the skin will absorb readily. 9. PRODUCTION The large scale production of complex molecules can be very difficult. Compounds originally isolated from natural products may continue to be harvested. Often natural products are found in nature only in extremely small quantities necessitating a complex synthesis. One route that has been under development more recently is to have compounds produced by genetically engineered micro-organisms or plants. Drugs have a high value per gram. As such production techniques can be viable even though they are far more inefficient than those used by bulk chemical producers. Often all possible production techniques are researched even though only one will be put into practice. This is done so that there are no openings for competing corporations to get around a manufacturers patents by using a different technique. 10. MARKETING If there is only one available treatment for a disease, it is only necessary to see that physicians know about it. If there are several competing treatments, there may be quite a bit of marketing done so that physicians will understand the relative merits of each. 11. NON-PERSCRIPTION SALES After a large amount of experience under a physicians supervision, a drug may be approved for over-the-counter sales. This is often the biggest profit making end of the pharmaceutical industry. 12. GENERIC PRODUCTION Once the chemical patents have expired, a drug can be produced by any manufacturer. Generic drugs are often less expensive for the consumer and yield a low profit margin for the producer. The production of generic drugs favors the most cost effective production process. REFERENCES A good book over all, and chapter 7 in particular, is G. L. Patrick "An Introduction to Medicinal Chemistry" Oxford (1995) An introduction to computational techniques is G. H. Grant, W. G. Richards "Computational Chemistry" Oxford (1995) A more detailed description of computational techniques is A. R. Leach "Molecular Modelling Principles and Applications" Longman (1996) L. Balbes' "Guide to Rational (Computer-aided) Drug Design" is at gopher://www.ccl.net/00/documents/drug.design.guide There are many links on Soaring Bear's web page at http://ellington.pharm.arizona.edu/%7Ebear/ An introduction to structure-based techniques is I. D. Kuntz, E. C. Meng, B. K. Shoichet Acct. Chem. Res. 27 (5), 117 (1994) An introduction to De Novo techniques is S. Borman Chemical and Engineering News 70 (12), 18 (1992) --------------------------------------------------------------------------- From FAU@ps1515.chemie.uni-marburg.de Tue Oct 7 05:29:03 1997 Received: from mail.chemie.uni-marburg.de for FAU@ps1515.chemie.uni-marburg.de by www.ccl.net (8.8.3/950822.1) id FAA24547; Tue, 7 Oct 1997 05:19:24 -0400 (EDT) Received: from ps1515.chemie.uni-marburg.de (ps1515.Chemie.Uni-Marburg.DE [137.248.151.39]) by mail.chemie.uni-marburg.de (8.8.7/8.8.7.ts) with ESMTP id LAA05657 for ; Tue, 7 Oct 1997 11:19:19 +0200 (CEST) Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 7 Oct 97 11:21:14 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 7 Oct 97 11:21:05 GMT+2 From: "Stefan Fau" To: chemistry@www.ccl.net Date: Tue, 7 Oct 1997 11:21:04 MDT MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: G: reasonable geometry Return-receipt-to: "Stefan Fau" Priority: normal X-mailer: Pegasus Mail for Windows (v2.01) Message-ID: <18D4F7516E@ps1515.chemie.uni-marburg.de> Hi, did you use opt=addredundant? Standard optimizations in G94 convert every geometry specification to redundant internal coordinates. the needed keyword is opt = addredundant and, after the molecule specification(s), N1 N2 [N3 [N4]] [value] F with Ni = number of atom in the molecule spec. the value is length, angle or dihedral angle, depending on the number of atoms. F means frozen and the value is reached in the final structure, not necessarily in the intermediate structures. By the way, for questions on Gaussian that are not general TC questions, there is a special list. To subscribe, send the subject "subscribe" to g-request@CCMSD.chem.uga.edu. To subscribe the digested version, send the subject "subscribe" to g-d-request@CCMSD.chem.uga.edu. To post messages to the list, send them to g@CCMSD.chem.uga.edu. Stefan __________________________________________________________ | Stefan Fau fau@mailer.uni-marburg.de | | | | FB Chemie der Philipps-Universitaet Marburg | | Hans-Meerwein-Str. | | D-35032 Marburg | ------------------------------------------------------- From schiffer@h1tw0036.hoechst.com Wed Oct 8 10:38:40 1997 Received: from www.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id JAA03504; Wed, 8 Oct 1997 09:37:08 -0400 (EDT) Received: by www.hoechst.com id PAA26965; Wed, 8 Oct 1997 15:36:56 +0200 Received: from unknown(134.81.76.36) by www id sma026895; Wed Oct 8 15:35:32 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA13180; Wed, 8 Oct 1997 15:33:10 +0200 Message-ID: <343B8B96.FF6@h1tw0036.hoechst.com> Date: Wed, 08 Oct 1997 15:33:10 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Research & Technology To: Computational Chemistry List Subject: [Fwd: Re: CCL:DFT and H2O Dimer] Hi Keith, > Perhaps I am being picky here but BP, BLYP, B3LYP etc are no more or > no less DFT than LDA is. *All* are approximations to the "true" DFT > exchange-correlation functional, which no-one knows -- it's just that > some are better approximations than others. O.k., that is exactly, what I meant. LDA and DFT are not synonyms. > Interesting. But the LDA makes a very good job of graphite, including > the interlayer bonding, which goes to show that not every force that > appears weak is really Van der Waals. What do you mean by van der Waals ? I propose, one should speak about bonding (covalent) and non-bonding forces. The non-bonding forces can be divided into electrostatic, or better call it Coulomb, forces, into (Pauli) repulsion, into dispersion, into polarization, etc. What is weak and what is strong ? It depends: at very short distances the (Pauli) repulsion is very strong, at very long distances the covalent bond forces are very weak, etc. Why LDA is good for graphit, I do not know. One knows, that LDA leads always to a strong overbinding for noble gas dimers. May be the good performance of LDA for graphit is the result of error compensations ( no dispersion, underestimation of the repulsive cores, underestimation of the quadrupole moment ). Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From Steve.Bowlus@sandoz.com Wed Oct 8 13:29:21 1997 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@sandoz.com by www.ccl.net (8.8.3/950822.1) id NAA05572; Wed, 8 Oct 1997 13:06:45 -0400 (EDT) From: Received: by gatekeeper.sandoz.att.nl; id SAA22279; Wed, 8 Oct 1997 18:06:39 +0100 (MET) X400-Originator: Steve.Bowlus@sandoz.com X400-Recipients: CHEMISTRY@www.ccl.net X400-MTS-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700007155973000002] X400-Content-Type: P2-1988 (22) Message-ID: <0034700007155973000002*@MHS> To: Subject: Summary2: Presentation Graphics Date: Wed, 8 Oct 1997 18:08:33 +0100 ---------------------------- Forwarded with Changes --------------------------- From: bear@ellington.Pharmacy.arizona.edu at INTERNET1 Date: 10/2/97 9:50PM To: Steve Bowlus at USPAC01M Subject: convert ------------------------------------------------------------------------------- _______________________________________________________________________________ Subject: convert From: bear@ellington.Pharmacy.arizona.edu at INTERNET1 Date: 10/2/97 9.50 PM I've got a file of prior notes on converting; lacking the time to pick out parts you need, I'm sending the file. -------- http://www.handmadesw.com/hsi/web_alchemy.html converts many image types From: rwcox@post.its.mcw.edu (Robert W. Cox) Subject: Re: rgb format Date: Thu Mar 23 08:13:52 MST 1995 Organization: Medical College of Wisconsin; Milwaukee Wisconsin Tero T Weckroth (tweckrot@cc.Helsinki.FI) wrote: : I have some molecular images in RGB format and I'd like to transform them : into GIF. If this is SGI's RGB format, the "netpbm" package of image conversion utilities (for Unix) can convert it to a myriad of other formats. A quick search with archie shows a number of sites, but I didn't get one in Finland. In Europe: ftp://ftp.cyf-kr.edu.pl/ftp.cyf-kr.edu.pl/netpbm-1mar1994.tar.gz ftp://ftp.ibp.fr//pub/X11/R5contrib/netpbm-1mar1994.tar.gz I believe that it has been compiled for MS-DOS and other platforms as well, but don't know where those might be found. Bob Cox / Biophysics Research Institute / Medical College of Wisconsin voice: 414-456-4038 / FAX: 414-266-8515 / rwcox@mcw.edu From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) For Unix, there is the PBMPlus suite of programs. Each one is a small filter between two formats. By piping them together you can convert almost anything into almost anything else! The package is fairly large, and it *won't* cope with jpeg, but most raster formats (BMP, PCX, XBM, XPM, GIF etc) are catered for. The more common formats are also all readable and writeable by XV, which also has the advantage that you can see the image! Tim. >How do I remove the background color in a GIF image so only the >objects are displayed? If you're using Unix, try "giftrans" - widely available via anon FTP From Steve.Bowlus@sandoz.com Wed Oct 8 13:29:21 1997 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@sandoz.com by www.ccl.net (8.8.3/950822.1) id NAA05572; Wed, 8 Oct 1997 13:06:45 -0400 (EDT) From: Received: by gatekeeper.sandoz.att.nl; id SAA22279; Wed, 8 Oct 1997 18:06:39 +0100 (MET) Message-ID: <0034700007155973000002*@MHS> To: Subject: Summary2: Presentation Graphics Date: Wed, 8 Oct 1997 18:08:33 +0100 *** This message was "doctored by Jan Labanowski, CCL Admin. *** I had to do it, since some lines had unprotected From at *** at the beginning and were splitting message in pieces in UNIX mail >From kfink@u.washington.edu Fri Dec 30 15:07:59 MST 1994 From: Kevin Fink Subject: Re: Interlacing GIFs Organization: University of Washington > In article <3ddjqg$3qd@news-2.csn.net>, tholmes@csn.net says... > > Where can I find a utility to convert a GIF image to an > interlaced GIF image, and vice-versa? For those of us who know and love XV, I have modified the code slightly so that it can write interlaced GIFs (it could already read them) and can set the transparent flag on (although right now the transparent background color has to be the first color in the color map. I haven't had time to add a simple form to ask the user which color map entry to make transparent. Should be really simple, except that this is ski season...) Kevin kfink@u.washington.edu http://alfred1.u.washington.edu:8080/~kfink/homepage.html >From norbert@kassandra.uni-hamburg.de Fri Dec 30 15:12:14 MST 1994 From: norbert@kassandra.uni-hamburg.de () Newsgroups: comp.infosystems.www.misc,alt.hypertext Subject: Re: How do I make GIF background match grey of Web browsers? Organization: University of Hamburg -- Germany : I've set up a descriptive page on creating transparent gifs on : http://www.achilles.net/~kkeogan/homepage.htm Here is an additional SHORT answer: 1) get the program "giftrans" from the net 2) type " giftrans -t '#ffffff' " and RETURN. norbert@philosophie.uni-hamburg.de >From gordo@interlog.com Wed Apr 12 21:46:17 MST 1995 From: Gordon Jessop Subject: Re: Mac and Transparent Backgrounds Organization: Interlog Internet Services -Voice (416) 975-2655 -Data 515-1414 fischer@cs.umn.edu (Tim Fischer) wrote: >> jwyckoff@ux4.cso.uiuc.edu (Jason Wyckoff) wrote: >> > Is there some (shareware possibly) Mac program that can turn regular >> >GIFs to GIFs with the transparent background? I thought Photoshop 3.0 >> >would have it, but I haven't found a way to do it yet. >> >JASON D. WYCKOFF URH 314 Carr >> >Univ. of Illinois at Urbana/Champaign 906 W. College Court >> >jwyckoff@uiuc.edu Urbana, IL 61801-4786 >> >http://ux4.cso.uiuc.edu/~jwyckoff/ (217) 332-3926 > >GraphicConverter is an indispensible utility for WWW design. It does >conversions to/from most formats, does transparent/interlaced GIF's, etc. >The transparency function is a bit hidden, it's controled by a "set >transparent color" entry in a "colors" heirarchical menu, or something >like that. You just set your background color, and you're all set. >GraphicConverter also does neat stuff like clipping sizes, minor editing, >etc, so it's great for those last-minute touch-ups. >Timothy S. Fischer >Teaching Assistant/Comp. Sci. Grad Student >University of Minnesota, Twin Cities >fischer@cs.umn.edu if you're wondering where you can find it, you can pick it up at one of these places ftp://ftp.pht.com/mirrors/info-mac/Graphic/util/graphic-converter-207.hqx ftp://ftp.tidbits.com/pub/tidbits/tisk/Graphic/util/graphic-converter-207.hqx Otis INDEX http://www.interlog.com/~gordo/ gordo@interlog.com rklama@interlog.com >From chemistry-request@www.ccl.net Tue Aug 12 21:15:43 1997 From: "Jeffrey J. Ayres" To: chrirena@techunix.technion.ac.il Subject: CCL:converting cacao output into html PSP, paint shop pro converts .hgl files, resolution is not as good as the orginals. In addition if size of the image is reduced too much the colors are lost and the images must be viewed in black and white. MS Word 97 is the easiest to use, however once the files are converted to .html resolution is poor. To improve the resolution for smaller size images use PSP, first resize, second crop the image using the square selection tool(should save as a .gif image) under the edit menu copy the cropped image using the paste function into a new selection, it should convert the file into a .gif file. Save the file. Gif files are readable with several browsers. The post script files mentioned by John Nash were not verifiable using my system. The post script files were not copied into files on my hard drive. Jeff Ayres MS Biochemistry Cal. State Univ. Hayward You may download paintshop from ftp://ftp.support.lotus.com//pub/utils/pubutils/win32/psp32.zip --- the file of cacao are HPGL files, you produce them for all the picture on the screen and they are colected under /moan with the names cacao1.hgl cacao2.hgl.. and so on togheter with moan1.hgl... you can preview them with view (if you installed printgl) or you can easily import in WORD6.0 (htere is a filter for HPGL file) or in any other graphic program able to read hpgl files, then form there you may be able to convert them in .bmp or jpg Davide Proserpio --- CACAO can output its pictures in PostScript and I think HPGL. (You have to have the PRINTGL package installed as well.) From there, you can use Illustrator, GhostScript, or anything else that will convert PS for the former, and I believe that PC WordPerfect will read in HPGL. On the Mac, Graphic Converter can read HPGL, too. Personally, I've had good luck with the color postscript files. Since they are "true" PostScript files, they are small and easily manipulatable (i.e. vector not bitmap). I've had the best luck using Illustrator to make my figures. -==-John R. Nash-==-nash@chem.wisc.edu-==-UW-Madison Chem. Dept-==- SOARING BEAR bear@pharmacy.arizona.edu O-topoisomerase Computational Medicinal Chemistry 5'*: :*.* Cancer Biochemistry & Drug Design |'*. .*'| | Protein & DNA Structural Biology | | *.,* | | | Pharmacognosy & Natural Dentistry 3'*.DNA helix| * http://ellington.pharm.arizona.edu/~bear '***' '**' >From Steve.Bowlus@sandoz.com Wed Oct 8 14:39:19 1997 From: To: Subject: Summary: Presentation Graphics Date: Wed, 8 Oct 1997 18:08:34 +0100 The original posting: I'm looking for a converter program which will take a screen capture image (e.g. an RGB file from the SGI snapshot utility, or a postscript file generated from it) and generate a high quality postscript file. By high quality, I mean with the jaggies removed from letters and edges of smooth curves, and some color/ pattern dithering for shaded surfaces, etc. I know I can generate high quality images from molscript and/or Raster3D. I wish, however, specifically to process screen images (grabbed at screen resolution) and upgrade them to printer resolution. My thanks to all who responded. >From the responses, there appears to be two problems. _Text_ can be overlaid on a screen image using a layout program such as Photoshop, whence high quality printing is no problem. Improving the image is another kettle of fish, however. Some responders expect some (marginal?) improvement by processing the image through a layout program, while others expect none -- making a silk purse from a sow's ear, as one person put it. I haven't had a chance to check on any of these, but several seem reasonable (and cheap!) to try. There were also a number of responses specifically targeting use of SGI tools, which is the environment of greatest interest to me. Soaring Bear (bear@pharmacy.arizona.edu) provided an extensive summary from a related query. His response will be separately posted with the subject: Summary2: Presentation graphics. ------------------------------------------------------------------------------ Richard G. A. Bone (rgab@proteus.co.uk): I saw a program which did exactly this at an Expo in San Francisco a couple of years ago. So, yes, they do exist, but the price-tag was fairly high (around $600US, as I recall). I'm not sure if it worked on PostScript though: it was more for scanned images. >From my program to the '96 MacExpo up at the Moscone Center, I deduced that the company I saw was "ScanVec" and their product was called "Tracer". They appear to be still in business (from a web-search on 'scanvec' and 'scanvec tracer') and a reasonably useful review is at: http://www4.zdnet.com/macuser/mu_0696/reviews/review08.html The trouble is, I'm not 100% sure that it's exactly what you want but it may sprout a few pointers. ---------- Malcolm A. Cline (mac@tripos.com): What you are asking to do is virtually impossible. Think about it--you go from screen resolution (72dpi) to printer resolution (300dpi or higher). This means you have to invent new pixels. It's trivial to double or quadruple the number of pixels, but to have the image "tailored" to be better is something the algorithms cannot do. There are definitely smoothing algorithms, but even the best of them just muddle the sharp edges instead of preserving the sharp edges in new sets of pixels. In a color image, there is not enough information in the existing pixels to know what's a shadow, a shaded surface, a sharp edge of text overlays or the like. What I do typically, BTW, is to process the image as best as I can with something like Adobe Photoshop WITHOUT the text, and then add text at the final resolution. We encounter this problem repeatedly in trying to "blow up" SYBYL screen images for posters and full size graphics. The only way to have a solution is to start with vectorized images. They scale infinitely, unlike screen images or postscript files. %%%%%%%%%% I replied off-line to this, spelling out my thinking on how this might be accomplished, even if no one has written a program (yet?!). Being neither a mathemetician or a programmer, I don't know whether this is feasible: What I'm really talking about, I think, is image enhancement. I know that we can do edge detection, so what we now need is a program that would do something like this: For each edge/line segment detected: Look at the existing pixels in the segment and decide whether it is a straight line or a curve; If it is a straight line, find the ends and calculate the equation fitting the line; Calculate the color/intensity of the pixels for the line at the new resolution and store the results; For each new line segment at higher resolution: Do some sort of check to insure that line segments are smoothly joined; Look at the old pixel color/intensity on either side of the old line; Compare this with some "bulk" color/intensity n pixels away; Blend the bulk color up to the new line, at the higher resolution, and store the results. For edges/line segments which are not straight lines, one would do the same thing, but do some sort of spline fit to get the equation of the line that you would then pixelate. This would, of course, give _huge_ files. Is what I described above a means of "vectorizing" the image? %%%%%%%%%% ---------- Robert B. Funchess (bobf@msi.com): Most printers will automatically handle dithering for any color they can't reproduce as a pure tone, so you're probably better off leaving that and concentrating on smoothing the edges unless you _really_ dislike the way the printer's doing it. In general, there's no magic way to recover lost detail, though some of the painting/photo-refinishing programs these days are capable of amazing things and would be worth looking into. Normally the feature you need will be called something like "smooth" or "blur", or possibly "convolve" or "filter". If you don't have access to a program like that, you could try rescaling the image to the size (in terms of number of pixels) that you need, and then using a convolution function to blur the jagged edges a bit; SGI has tools for doing this sort of thing in the imgtools subsystem on the IRIX CD-ROMs. There are also some programs available from their website (go to http://www.sgi.com/ and poke around a bit). As for the text, personally I'd suggest removing it from the original bitmapped image whenever possible and adding real postscript text later using showcase or something similar. It may be tricky to do that if the text overlaps something other than the background, though. ---------- Dave Reichert (reichertd@@mirlink.wustl.edu): Here's what I do using Mac systems. I take the SGI snapshot and then bring it to my Mac. A shareware program "GraphicConverter" can read the SGI file and save it in a huge number of different formats. Typically I'll convert it to Photoshop format, then use Adobe Photoshop to tweak the image and add captions. GraphicConverter can also save files directly in eps format. ---------- Joel (joelp@agiss.com): Hmm. Corel's PhotoTRACE, followed by "node reduction" of the curves in their PhotoPaint package, seems to do a decent job of cleaning up jaggies in lines and curves. I haven't worked with it extensively, and I don't know what Corel's software does for dithering, but I'd be a bit surprised if one or the other package didn't handle it. I've generally been pleased with Corel's software, though recent releases have suffered from featuritis and from inadequate debugging. As far as I know, their software is for PCs only; you'd need to port the image over. If you're working from an RGB file, you'd need to translate it to some other format, but even if your SGI doesn't have those translation utilities as part of the OS, you shouldn't have any trouble finding them. ----------- Malcolm (gillies@cmcind.far.ruu.nl): Some good in-depth discussion of this can be found in the Raster3D FAQ at http://www.bmsc.washington.edu/raster3d/r3d_FAQ.html#PostScript as well as a recipe for getting reasonable results using the ImageMagick convert utility. http://www.bmsc.washington.edu/raster3d/html/r3d_hints.html#PostScript Some general comments (apologies if you know all this already): No image conversion program can remove jaggies from a screen image, except by decreasing the resolution. The quality of the output image can never be better than what appears on screen, given that you are operating with a raster image of predetermined resolution. Rendering of continuous tones is highly dependent upon the printing technology you use. Mostly, they are rendered as half-tone process colour. Precisely the type of half-toning, screen frequency, etc. will depend upon the relative resolution of your image and your printer. The Postscript language contains many facilities for manipulating colour information, and for rendering continuous tone images. By default, these are configured to give good results, on average, for the particular printer that is being used. However, getting the best possible image quality will depend upon factors such as matching the image resolution to the printer resolution (and adjusting halftoning parameters accordingly) and making sure the image colours match the output capabilities of the printer. Unfortunately, there are no general recipes for optimising this. Commercial software such as Adobe Photoshop (or alternatively, commercial colour pre-press software) is probably the easiest solution, but you can also achieve good results using freeware image manipulation and conversion tools (like the pbm tools), if you know what you're doing. ----------- Some tips/comments on using the SGI image conversion programs utilities: Paul Veilleux (veilleux@corp.sgi.com): I am a Systems Engineer in Mountain View and received a copy of your question regarding converting a SGI screen image and outputting to Postscript. Have you tried the 'tops' conversion program on the SGI? It takes an image and converts to whichever format you select. However, I am not certain about the resolution that the resultant image is converted to. Below is the syntax for using 'tops': chembio 7% tops usage: tops inimage [-l screendensity] [-p pixelsperinch] [-a screenangle] [-b bitsperpixel] [-B ] [-x xpixelsperinch] [-y ypixelsperinch] [-t scaletrim [-m maxxinches maxyinches] [-h horrizontal line screen] [-o xorg yorg] [-rgb] [-RGB] [-cmyk] [-CMYK] [-eps ] [-I ] The -eps option should be used for your case. ----------- Dorina Kosztin (dorina@ks.uiuc.edu): If you have a Next computer and the TIFFany2.app application, then all you have to do is load the rgb file in it and fix whatever you want to have fixed. If you don't, then you may use Image Magic on the SGI's but I don't think you can change the resolution of the picture without having to shrink it. So you should take a snapshot of the screen as big as you can and then size it down and by doing this you'll increase the resolution of the picture. ---------- David A. Larson (dlarson@tripos.com): I recommend using imgworks which comes with the graphics tools on your SGI. It has the image processing tools you are looking for. The path to imgworks is /usr/sbin/. You can import RGB images into Showcase which comes with the IRIX CD. Once the image is in Showcase you can scale the image on the page as you like and then print to a postscript file if you like. The nice thing is that the full RGB image data is used when doing the postscript conversion. To maintain the image's aspect ratio hold down the SHIFT key while scaling. Another caveat is to select the menu "View >> Full Color" to maximize the image quality. ----------- Gene Fleischmann (gene@q-chem.com): If you have not already tried on SGI systems you might use: /usr/lib/print/sgi2ps -C rgb "filename".rgb "filename".ps to do the conversion and then: /usr/bin/X11/xpsview "filename".ps to view the results immediately and compare with: /usr/sbin/imgworks "filename".rgb ---------- And thanks to responders who made similar suggestions: Joseph I. Landman (landman@firestorm.physics.wayne.edu) Hongyu Zhang (hyzhang@carb.nist.gov) ---------- Michael K. Gilson (gilson@indigo14.carb.nist.gov): Try the program xv. It can read rgb, do a 24-->8bit conversion, and write out color postscripts. ---------- Steve Greatbanks (Steve.Greatbanks@anu.edu.au): There are two slightly different problems here. With molscript, you get vector postscript output which will take maximum advantage of the resolution of whatever postscript output device you use - thus, on a good printer, there will be no jaggies or aliasing, and hence, no problem. I think the problem that you are referring to is a result of the printer `aliasing' the postscript because your postscript file has a resolution (in dpi) different from the printer. To get rid of this, you must ensure you generate postscript files which match the target resolution of the output device. The best way I've found of doing this from your rgb file is to use xv, and when saving as postscript, make sure you resize the picture using the dials until you get the resolution you require in terms of multiples of the printer resolution - for standard laser printers, try 100, 150 (usually fine), 300 (good) and 600 (often overkill) dpi. Obviously, this will change the size of the graphic. In the case of screendumps you are clearly limited in the size of image you can capture, but 150 dpi (especially for colour pictures) is often good enough on a 300 or 600 dpi laser printer. For programs like raster3d, or if you raytrace your own outputs, you can work out the size of the postscript file you want (in inches), the resolution of your output device (in dpi) and then render an appropriately large picture (the resulting postscript may be huge, but will look excellent on your output device). For example - if you have a 600 dpi printer, and you want a 5x3 inch picture, just render the screen image to 3000x1800 pixels and things will look great (provided your printer can cope with the size of the ps file!). Text added in modelling packages often looks rather poor as the fonts are generally not antialiased. To improve the quality of the text on screendumps, it might well be better to add the text in another program. You can add either to the bitmap (e.g. using something like the gimp (http://www.gimp.org) which has flexible text handling and can add antialiased text), and then generate your postscript at the appropriate resolution or generate the unlabelled postscript (ensuring it contains a bitmap preview, using something like ps2epsi) and then read it into a program where you can add postscript text and export the compound object as an encapsulated postscript graphic (which ensures the text will make maximum use of the resolution of the output device). I used to do this in showcase on SGIs, but the newer versions don't show the preview (so you can't see where the labels go) - that's progress for you! I now do it on the mac instead. In general, even though programs like xv will dither colour pictures to black and white for you, you are much better off letting the printer decide. Just pass the printer colour postscript and take advantage of the rasterising of the printer (which is optimised for the particular engine used in the printer). Trust the printer. You need to bear in mind that you are never going to do better than the picture on screen. If there are visible jaggies on screen, the higher resolution of the printer will only exacerbate them. Sometimes you can use a little judicious image manipulation to help things (e.g. using the smooth option in xv prior to generating the postscript can *occasionally* help). From seabra@NPD.UFPE.BR Wed Oct 8 15:29:21 1997 Received: from NPD1.NPD.UFPE.BR for seabra@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id PAA06379; Wed, 8 Oct 1997 15:07:44 -0400 (EDT) Received: from danon (danon.dqf.ufpe.br) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01IOKJ53UJ74000QEH@NPD.UFPE.BR> for chemistry@www.ccl.net; Wed, 8 Oct 1997 16:06:44 GMT-3 Date: Wed, 08 Oct 1997 11:32:18 -0300 From: Gustavo de Miranda Seabra Subject: Sorry: Langmuir films To: Computational Chemistry Letters Message-id: <343B9972.5BFBE2CF@npd.ufpe.br> > Dear CCLers, > > Does anyone have info about calculations on Langmuir films? > > Thanks in advence, What I really want is a way to quantify the interaction of the reagent with water, in Langmuir-Blodget films. Sorry. ---------------------------------------------------------------------------------- Gustavo de Miranda Seabra MSc Student in Chemistry E-Mail: seabra@npd.ufpe.br Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil ----------------------------------------------------------------------------------- From ccl@www.ccl.net Wed Oct 8 19:29:23 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA07527; Wed, 8 Oct 1997 18:45:13 -0400 (EDT) Received: from msuvx1.memphis.edu for tcundari@cc.memphis.edu by bedrock.ccl.net (8.8.6/950822.1) id SAA05274; Wed, 8 Oct 1997 18:45:11 -0400 (EDT) Received: from [141.225.145.9] by MSUVX1.MEMPHIS.EDU (PMDF V5.1-8 #16781) with SMTP id <01IOKMLCCT9C8XSIA8@MSUVX1.MEMPHIS.EDU> for chemistry@ccl.net; Wed, 8 Oct 1997 17:45:20 CST Date: Wed, 08 Oct 1997 17:45:40 -0600 From: tcundari@cc.memphis.edu (Tom Cundari) Subject: ECPs in DFT To: chemistry@ccl.net Message-id: Hi, Has there been any research on the application of effective core potential methods to density functional theory? I am more concerned with applications for discrete chemical systems as opposed to calculations on extended, solid-state systems. I saw a paper by Hay and coworkers a LANL on the use of HF-derived ECPs in DFT calcs, but a literature survey has otherwise come up empty. Any pointers to names or literature references would be most welcome. Thanks in advance. Sincerely, Tom Cundari Associate Professor of Chemistry =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ Tom Cundari Department of Chemistry Associate Professor The University of Memphis e-mail:tcundari@cc.memphis.edu Memphis, TN 38152-6060 phone: 901-678-2629 FAX: 901-678-3447 http://www.chem.memphis.edu/umchem.html **** U of Memphis is searching for an Asst. Prof. of Computational Chemistry, contact me by email for details or see these URLs www.chem.memphis.edu/ccad.html www.chem.memphis.edu/ccletter.html **** =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ From freunsch@pctc.chemie.uni-erlangen.de Thu Oct 9 10:45:34 1997 Received: from faui40.informatik.uni-erlangen.de for freunsch@pctc.chemie.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id JAA11077; Thu, 9 Oct 1997 09:41:48 -0400 (EDT) Received: from pctc.chemie.uni-erlangen.de (pctc.chemie.uni-erlangen.de [131.188.120.2]) by faui40.informatik.uni-erlangen.de (8.8.6/8.0.101-FAU) with SMTP id PAA19696 for ; Thu, 9 Oct 1997 15:41:39 +0200 (MET DST) Received: from gaston.chemie.uni-erlangen.de by pctc.chemie.uni-erlangen.de (AIX 3.2/UCB 5.64/4.03) id AA21870; Thu, 9 Oct 1997 15:40:38 +0200 Received: from localhost by gaston.chemie.uni-erlangen.de (5.65v3.2/1.1.10.5/14Jul97-1224PM) id AA12493; Thu, 9 Oct 1997 15:41:38 +0200 Date: Thu, 9 Oct 1997 15:41:38 +0200 (MET DST) From: Peter Freunscht Reply-To: Peter Freunscht Cc: chemistry@www.ccl.net Subject: Re: CCL:G:frequency output of g94 In-Reply-To: Message-Id: On Thu, 9 Oct 1997, Christian Rummey wrote: > Since I do not have access to commercial programms like gaussview, I'm > looking for a free package that can display vectors from the g94 > frequency-output. > > maybe someone can help... > Try xvibs (version 4) by Bradley A. Smith, available through ftp from ftp://www.ccl.net/pub/chemistry/software/SOURCES/C/xvibs/ Its output can be read eg by xmol. Peter ----------------------------- Dipl. Chem. Peter Freunscht Inst. f. Physikalische Chemie I der Universitaet Erlangen Egerlandstr.3 - 91058 Erlangen - Deutschland/Germany Tel:09131/85-7335 Fax:09131/85-8307 eMail:freunsch@pctc.chemie.uni-erlangen "Chase your dreams - the money will follow." -- Colman McCarthy From mckelvey@kodakr.kodak.com Thu Oct 9 12:35:26 1997 Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by www.ccl.net (8.8.3/950822.1) id LAA12338; Thu, 9 Oct 1997 11:49:00 -0400 (EDT) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA24487 (5.67b/IDA-1.5 for ); Thu, 9 Oct 1997 11:46:23 -0400 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id MAA19133; Thu, 9 Oct 1997 12:00:39 -0400 (EDT) Received: from stomper (stomper.rl.kodak.com [150.220.76.39]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id LAA23950 for ; Thu, 9 Oct 1997 11:49:06 -0400 Message-Id: <343C0D6F.6AB3@kodak.com> Date: Wed, 08 Oct 1997 23:47:11 +0100 From: John McKelvey Reply-To: mckelvey@kodakr.kodak.com Organization: Eastman Kodak Company To: chemistry@www.ccl.net Subject: Call for Posters and General Oral Papers for Dallas... Drawing Near... October 20, 1997 Colleagues: A reminder that the deadline for all abstracts for all papers and posters are due to the respective Chairpersons by October 20,1997. If you need an abstract form, one can be downloaded from http://www.acr.org under MEETINGS. Please send all Poster abstracts and abstracts for the General Oral Presentations session to me. See you in Dallas! John McKelvey Program Chair Computers in Chemistry -- ************************************ * John McKelvey * * Computational Science Laboratory * * Imaging Research and Development * * Building 83 * * Research Laboratories * * Eastman Kodak Company * * Rochester, NY 14650-2216 * * (V)716-477-3335 * * (F)716-722-2327 * * (E)McKelvey@Kodak.COM * ************************************ >From linaras@njmsa.UMDNJ.EDU Thu Oct 9 14:39 EDT 1997 Received: from njmsa.UMDNJ.EDU for linaras@njmsa.UMDNJ.EDU by www.ccl.net (8.8.3/950822.1) id OAA13500; Thu, 9 Oct 1997 14:39:41 -0400 (EDT) Received: (from linaras@localhost) by njmsa.UMDNJ.EDU (8.7.6/8.7.3) id OAA17707 for CHEMISTRY-REQUEST@www.ccl.net; Thu, 9 Oct 1997 14:39:42 -0400 (EDT) From: Charilaos Linaras Message-Id: <199710091839.OAA17707@njmsa.UMDNJ.EDU> Subject: CHEMKIN Code Help To: CHEMISTRY-REQUEST@www.ccl.net Date: Thu, 9 Oct 1997 14:39:42 -0400 (EDT) Dear CCL Members, Does anybody have any experience with Premixed Flame CHEMKIN Code? I would appreciate your contacting me on this matter. I hope this is not totally unrelated to the issues handled by the members of this list. Thanks a lot in advance, Harry Linaras, PhD Candidate Department of Chemical Engineering New Jersey Institute of Technology Newark, NJ >From Christophe.MAROT@univ-orleans.fr Fri Oct 10 03:29 EDT 1997 Received: from centre.univ-orleans.fr for Christophe.MAROT@univ-orleans.fr by www.ccl.net (8.8.3/950822.1) id DAA16258; Fri, 10 Oct 1997 03:29:23 -0400 (EDT) Received: from SOMPORT.univ-orleans.fr (somport.univ-orleans.fr [193.49.95.23]) by mailhost.univ-orleans.fr (8.8.7/jtpda-5.2) with SMTP id JAA28815 ; Fri, 10 Oct 1997 09:28:32 +0100 (MET) Message-ID: <343DD992.59E2@univ-orleans.fr> Date: Fri, 10 Oct 1997 08:30:26 +0100 From: Christophe MAROT Reply-To: Christophe.MAROT@univ-orleans.fr Organization: ICOA-CNRS UPRES-A 6005 To: Balasubramanian SIVKUMAR CC: CHEMISTRY-REQUEST@www.ccl.net Subject: Re: CCL:logP program Dear Balasubramanian SIVKUMAR, There exists a good programs to calculate the LogP. Its name is CLIP. You can contact: http://www.unil.ch/pharm/clip e-mail: support-ict@ict.unil.ch ______________________________________________________ MAROT Christophe e-Mail: marot@univ-orleans.fr http://web.univ-orleans.fr/ICOA http://web.univ-orleans.fr/IUPchimie Institut de Chimie Organique et Analytique ICOA-CNRS UPRES-A 6005 UNIVERSITE d'ORLEANS BP6759, 45067 ORLEANS Cedex2-FRANCE Tél.(33) 02.38.49.45.91/02.38.49.45.77 Fax (33) 02.38.41.72.81 >From howardp@syrres.com Fri Oct 10 09:48 EDT 1997 Received: from apollo.syrres.com for howardp@syrres.com by www.ccl.net (8.8.3/950822.1) id JAA18240; Fri, 10 Oct 1997 09:48:10 -0400 (EDT) Received: from pc-howard.syrres.com ([204.168.121.208]) by apollo.syrres.com (Netscape Mail Server v2.0) with SMTP id AAA169; Fri, 10 Oct 1997 09:47:17 -0400 Message-Id: <3.0.32.19971010094949.0074e1dc@syrres.com> Date: Fri, 10 Oct 1997 09:49:50 -0400 To: "Balasubramanian SIVKUMAR" , CHEMISTRY-REQUEST@www.ccl.net From: howardp@syrres.com (phil howard) Subject: Re: CCL:logP program Take a look at http://esc.syrres.com/~ESC/logkow.htm Philip H. Howard, Ph.D. Phone: 315-452-8417 Environmental Sciences Center Fax: 315-452-8440 Syracuse Research Corporation Email: howardp@syrres.com 6225 Running Ridge Rd. Website http://esc.syrres.com North Syracuse, NY 13212 At 06:55 AM 10/6/97 PDT, Balasubramanian SIVKUMAR wrote: >Dear friends, > I am looking for a program that calculates logP. Is any body provide >me the softwares. Please. >Thanking you, >B.Sivakumar, >SRF. Chemistry, >Bharathidasan University, >Tiruchirappalli-24. >Tamilnadu. India. >e-mail:chem@bdu.ernet.in From guile@cbs.univ-montp1.fr Fri Oct 10 11:29:49 1997 Received: from ecir.cbs.univ-montp1.fr for guile@cbs.univ-montp1.fr by www.ccl.net (8.8.3/950822.1) id KAA19307; Fri, 10 Oct 1997 10:40:38 -0400 (EDT) Received: from ecir ([127.0.0.1]) by ecir.cbs.univ-montp1.fr with SMTP (8.7.1/8.7.1) id QAA06891 for ; Fri, 10 Oct 1997 16:34:17 +0200 (METDST) Sender: guile@ecir.cbs.univ-montp1.fr Message-ID: <343E3CE9.67F6@cbs.univ-montp1.fr> Date: Fri, 10 Oct 1997 16:34:17 +0200 From: Guillaume Campioni X-Mailer: Mozilla 3.01 (X11; I; HP-UX B.10.20 9000/802) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: bilayer coordinate Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody ! I am a graduate student working in an academic laboratory. I am trying to study membranes from a electrostatic point of view. But I don't have any file about COORDINATES of atoms constituting a EQUILIBRATED bilayer. So if someone knows where I could get such a file ( for example "bilayer.pdb" !!!), I will be very happy to know about it. thanks for your help guile -- Guillaume Campioni Centre de Biochimie Structurale faculte de pharmacie, Montpellier, France (http://www.cbs.univ-montp1.fr/ ) From mckelvey@kodakr.kodak.com Fri Oct 10 11:37:21 1997 Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by www.ccl.net (8.8.3/950822.1) id LAA19657; Fri, 10 Oct 1997 11:18:08 -0400 (EDT) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA22213 (5.67b/IDA-1.5 for ); Fri, 10 Oct 1997 11:15:34 -0400 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id LAA21097; Fri, 10 Oct 1997 11:29:52 -0400 (EDT) Received: from stomper (stomper.rl.kodak.com [150.220.76.39]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id LAA27264 for ; Fri, 10 Oct 1997 11:18:19 -0400 Message-Id: <343D57B8.254B@kodak.com> Date: Thu, 09 Oct 1997 23:16:24 +0100 From: John McKelvey Reply-To: mckelvey@kodakr.kodak.com Organization: Eastman Kodak Company X-Mailer: Mozilla 3.0 (WinNT; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: G94W Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Could someone please comment on the relative speeds of G94 under Linux and the 32-bit G94W version, running on a PPRO? Thanks! John -- ************************************ * John McKelvey * * Computational Science Laboratory * * Imaging Research and Development * * Building 83 * * Research Laboratories * * Eastman Kodak Company * * Rochester, NY 14650-2216 * * (V)716-477-3335 * * (F)716-722-2327 * * (E)McKelvey@Kodak.COM * ************************************ From akutatel@du.edu Fri Oct 10 11:40:09 1997 Received: from odin.cair.du.edu for akutatel@du.edu by www.ccl.net (8.8.3/950822.1) id KAA19326; Fri, 10 Oct 1997 10:43:08 -0400 (EDT) Received: by odin.cair.du.edu id AA04609; Fri, 10 Oct 1997 08:42:29 -0600 Received: by kizh.biochem.du.edu with Microsoft Mail id <01BCD557.5D8E2900@kizh.biochem.du.edu>; Fri, 10 Oct 1997 08:34:46 -0600 Message-Id: <01BCD557.5D8E2900@kizh.biochem.du.edu> From: Andrei Kutateladze To: "'wibke@theochem.uni-duesseldorf.de'" , "'CCL'" Subject: RE: G:G:frequency output of g94 Date: Fri, 10 Oct 1997 08:34:45 -0600 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Actually, there is a program for Windows/W95 from Innovative Software, = Inc - AniMol which I believe can fetch the frequency output from g94 and = animate the modes (+ visualize IR/Raman spectra) Regards, Andrei=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Andrei Kutateladze Asst. Professor of Chemistry and Biochemistry University of Denver ---------- From: = wibke@theochem.uni-duesseldorf.de[SMTP:wibke@theochem.uni-duesseldorf.de]= Sent: Thursday, October 09, 1997 12:11 PM To: CHEMISTRY@www.ccl.net Cc: wibke@lithium.theochem.uni-duesseldorf.de Subject: CCL:G:G:frequency output of g94 >=20 >=20 > Hi there, >=20 > Since I do not have access to commercial programms like gaussview, I'm > looking for a free package that can display vectors from the g94 > frequency-output.=20 >=20 > I tried molden, but this one can only display moving atoms and not=20 > vectors, wich does not give really clear results.=20 >=20 > maybe someone can help... >=20 > thanks a lot > CR >=20 >=20 Dear Mr. Rummey, there exists a (little, not very comfortable and pretty, but very = usefull for your demands) program called "Vibration Modes for Windows" which can display movements and vectors of vibrations for - I think - GAUSSIAN 92 and before and in its own (ASCII) format. As far as I know pictures can also be saved or exported. Unfortunately, to my knowledge it is only available for WINDOWS. You can download it at: ftp://ftp.ccl.net/pub/chemistry/software/MS-WIN3/Vibration_modes_for_Wind= ows/ vibratio.zip Hope that helps! With best regards Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf Germany -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: wibke@theochem.uni-duesseldorf.de -- Original Sender From: Address: wibke@theochem.uni-duesseldorf.de CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: = Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: = www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive = search Web: http://www.ccl.net/chemistry.html=20 From schrecke@t12.lanl.gov Fri Oct 10 13:29:53 1997 Received: from mailhost.lanl.gov for schrecke@t12.lanl.gov by www.ccl.net (8.8.3/950822.1) id MAA20440; Fri, 10 Oct 1997 12:55:59 -0400 (EDT) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.8.7/8.8.7) with SMTP id KAA06639 for ; Fri, 10 Oct 1997 10:55:57 -0600 (MDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Fri, 10 Oct 1997 10:59:00 -0700 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: DFT MO energies Dear CCL readers, is anybody aware of papers that study DFT orbital energies? More precisely, I would like to learn how those orbital energies (Kohn-Sham eigenvalues) are different in hybrid methods like B3LYP as compared to GGAs like BP86 or PW91, or also as compared to the LDA. If there are systematic differences (which I am sure is the case) then I would like to know how they can be understood. There was recently some discussion on the list about the possible physical meaning of the Kohn-Sham eigenvalues. While this is an interesting subject in itself, it is, this time, *not* my question. Best regards, Georg P.S. I will summarize to the CCL as usual. -- Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ From schrecke@t12.lanl.gov Fri Oct 10 13:37:56 1997 Received: from mailhost.lanl.gov for schrecke@t12.lanl.gov by www.ccl.net (8.8.3/950822.1) id MAA20419; Fri, 10 Oct 1997 12:49:16 -0400 (EDT) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.8.7/8.8.7) with SMTP id KAA05268 for ; Fri, 10 Oct 1997 10:49:09 -0600 (MDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Fri, 10 Oct 1997 10:52:12 -0700 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: 2nd summary: solid state/band structures Dear CCL readers, a while ago, I posted a summary about solid state / band structure methods. In reaction to this summary (dated Sept. 30, if you wish to look into the CCL archives) I got a few more letters, and I thought I should summarize those as well. Here are the new answers: ----------------------------------------------- 1) Excerpt from Ulrike Salzner (she posted also a new question on the CCL, together with this remark) Concerning the comment on ab initio codes in Georg Schreckenbach's summary: there is also a Hartree-Fock solid state program in Erlangen/Germany. This program seems to be able to do MP2 corrections. Moreover, W. =46oerner (also formerly in Erlangen) et al. published a paper in J. Chem. Phys., 1997, 106, pp. 10249 on coulped cluster theory applied to polymers. Sincerely, Dr. Ulrike Salzner e-mail: salzner@fen.bilkent.edu.tr Tel.: (312) 2664000 ext.2122 Department of Chemistry Bilkent University 06533 Bilkent, Ankara Turkey ----------------------------------------------- 2) Luke A. Burke: There is a program called VEH (Valence Effective Hamiltonian) that I wrote i= n 1979 when I was a member of Jean-Marie Andre''s group in Namur, Belgium. The= re have been various improvements to it since. Jean Luc Bredas used the program with much success to study the band structure of electroactive polymers. It = is presently 1D only, but does account for screw axis symmetry. The VEH method replaces the potential part of the hamiltonian with projection operators tha= t are parameterized to reproduce Fock matrix elements for molecules that resem= ble the unit cell. The method for developing these potentials (and the basis of = the VEH method itself) is due to Phillippe Durand of Toulouse). Look up Bredas' name in early-mid 1980 JChemPhys for the potentials (for H,C,N,O,S atoms). I have those for Al, B, Cl, F (unpublished) in my notes somewhere. The program has been incorporated into MOTECC (Clementi's project) but you c= an also get the fortran code at my site: http://camchem.rutgers.edu/~burke The code is old but still workable Fortran IV. I'm ~willing to work with someone who wants to use the method. (sorry this is getting to you after your CCL summary!) -- Luke Anthony Burke tel:609-225-6158 (-6142) Professor and Chair, fax:609-225-6506 Department of Chemistry e-mail: Rutgers University burke@camden.rutgers.edu Camden, NJ 08102, USA http://camchem.rutgers.edu/~burke ----------------------------------------------- 3) Luke A. Burke, again: Georg, BTW, the VEH program could easily be expanded to the 3D case. I just need th= e funding to put the project on the front burner. I didn't mention this, but the VEH method can predict band gaps to within 0.= 1eV of experiment in electroactive polymers and reproduces LCAO coefficients to within 0.001au for any basis set for which it is parameterized. Luke ----------------------------------------------- 4) Francois Gygi Hi Georg, I read your CCL message and thought you might want to have a look at the JEEP project (http://irrmawww.epfl.ch/fg/jeep/jeep.html). This is a free plane-wave DFT MD program that allows you to study periodic solids. Best regards. =46rancois ---------------------------------------------------------------------- Francois Gygi Tel. +41 21 693 5327 IRRMA-EPFL FAX +41 21 693 6655 CH-1015 Lausanne e-mail: gygi@irrma.epfl.ch Switzerland http://irrmawww.epfl.ch/fg.html ---------------------------------------------------------------------- ----------------------------------------------- (End of summary) Best regards, Georg -- Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ From Steve.Bowlus@sandoz.com Fri Oct 10 14:29:48 1997 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@sandoz.com by www.ccl.net (8.8.3/950822.1) id OAA20836; Fri, 10 Oct 1997 14:03:36 -0400 (EDT) From: Received: by gatekeeper.sandoz.att.nl; id TAA02756; Fri, 10 Oct 1997 19:03:35 +0100 (MET) X400-Originator: Steve.Bowlus@sandoz.com X400-Recipients: CHEMISTRY@www.ccl.net X400-MTS-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700007193617000002] X400-Content-Type: P2-1988 (22) Message-ID: <0034700007193617000002*@MHS> To: Subject: Re: CCL:logP program Date: Fri, 10 Oct 1997 19:05:24 +0100 Try CHEMICALC-2 from QCPE, available for VAX and PC (other ports should be trivial). sb _______________________________________________________________________________ Subject: CCL:logP program From: chemistry-request@www.ccl.net at INTERNET1 Date: 10/10/97 2.16 AM Dear friends, I am looking for a program that calculates logP. Is any body provide me the softwares. Please. Thanking you, B.Sivakumar, SRF. Chemistry, Bharathidasan University, Tiruchirappalli-24. Tamilnadu. India. e-mail:chem@bdu.ernet.in ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --- From elewars@alchemy.chem.utoronto.ca Fri Oct 10 15:29:51 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id OAA21042; Fri, 10 Oct 1997 14:45:15 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id OAA21008 for chemistry@www.ccl.net; Fri, 10 Oct 1997 14:45:07 -0400 (EDT) Date: Fri, 10 Oct 1997 14:45:07 -0400 (EDT) From: "E. Lewars" Message-Id: <199710101845.OAA21008@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: ANIMATING GAUSSIAN FREQS There was a recent request for a program to animate G94W freqs. The program Molwin will animate freqs from G92 or G94 output; it works with Gaussain output from UNIX workstations--I don't know if G Windows output looks different. You should be able to find how to get Molwin >from the CCL archives; the program was written by Dr Pavel Ganelin of the Catholic University of America. Molwin also lets you expot a picture (from a Gaussian freq .out file of a set of Cartesians) into WordPerfect, annotate it, and print it for publication. With G94 you must request the "long form" of the freqs, with HPMode, e.g. # freq=HPMode MP2/6-31G* E. Lewars ========================= From brunob@helix.nih.gov Fri Oct 10 15:33:01 1997 Received: from mgcct6.nci.nih.gov for brunob@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id OAA21015; Fri, 10 Oct 1997 14:39:58 -0400 (EDT) Received: from mgcct6 (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id RAA04780 for ; Fri, 10 Oct 1997 17:04:56 -0400 Sender: brunob@helix.nih.gov Message-ID: <343E9877.4487@helix.nih.gov> Date: Fri, 10 Oct 1997 17:04:55 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: Computer Chemistry List Subject: Summary:Definition of molecular flexibility Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 10 days ago, I posted this question to the CCL: "I am looking for a definition of molecular flexibility. Does anyone know a paper or a book which defines this concept ? Furthermore, are molecular flexibility and conformational flexibility the same concept ?" Here follow the 8 responses I received: ---------------------------------------------- For a quantification of molecular flexibility, see QSAR: Quantitative Structure-Activity Relationships in Druig Design, Alan R. Liss, Inc., 1989, pp. 105-109. S. Shapiro toukie@zui.unizh.ch ---------------------------------------------- A keyword to look for may be: persistence length But I'm not familiar with this, so I can't give you any good reference. But this concept was recently used by Cheatham (J. Mol. Biol. 259, 434-444, 1996) to analyse DNA flexibility in a molecular dynamics run. Peter Slickers slickers@imb-jena.de ---------------------------------------------- Clark, D.E., Willett, P. and Kenny, P.W. Pharmacophoric Pattern Matching in Files of Three-Dimensional Chemical Structures: Implementation of Flexible Searching. Journal of Molecular Graphics 11. 146-156, 1993. We compared 4 different measures of molecular flexibility. Best regards David DAVID-E.CLARK@rhone-poulenc.com ---------------------------------------------- We have tried to do some work in the area. Just a few references of our papers. The key papers are the last two references. Kriz Z, Koca J, Carlsen~P.H.J.: {\it Conformational behavior and flexibility of terminally blocked cysteine and cystine}. J.~Mol.~Mod. {\bf 2}, 51-61 (1996). Koca J., Carlsen P.H.J.: {\it Conformational Behavior and Flexibility of Met-enkephalin}. J.~Mol. Struct. (Theochem) {\bf 337}, 17-24 (1995). Koca J., Perez S., Imberty A.: {\it Conformational Analysis and Flexibility of Carbohydrates using the CICADA approach with MM3.} J. Comput. Chem. {\bf 16}, 296-310 (1995). !!!!!!!!!!!!!!!!!!! !!! Koca J.: {\it Potential Energy Hypersurface and Molecular Flexibility.} J. Mol. Struct.~{\bf 291}, 255-269~(1993). !!!!!! !!!!!!!!!!!!!!!!!!! !!! Koca J., Carlsen P.H.J.: {\it DAISY, A Computational Method. A Novel Tool for a Study of Conformational Behavior of Flexible Molecules}. J.~Mol. Struct.~(Theochem)~{\bf 257}, 105-130 (1992). Jaroslav Koca www: http://web.chemi.muni.cz/~jkoca; e-mail: jkoca@chemi.muni.cz ---------------------------------------------- Polymer science uses several rigidity metrics for linear macromolecules. (e.g. Coon's segment (spelling probably wrong since I only saw it in Russian)). You might want to consult a basic book on polymer science. Regards, Eugene Eugene Leitl ---------------------------------------------- In response to your recent request for a definition of molecular flexibilty we would like to make the following comments. We cannot provide you with a reference to a paper or a book containing a formal definition of "molecular flexibility", but in our own work on the molecular modelling of metal-ligand complex species, we have found it useful to view conformational flexibility as one of the components of molecular flexibility. Viewed in terms of the multi-dimensional potential/steric energy (PE) surface of a molecule involved in molecular mechanics, each minimum in the surface corresponds to a conformation. The conformational flexibility might be quantified as proportional to the number of minima in that surface which are of reasonably low energy. This includes the global minimum and all the other local minima of reasonably low energy. A Boltzman weighting factor could be used to weight the relative contributions of the various minima found. The set of potential energy minima could, in principle, be found by a technique like quenched dynamics. Another contribution to molecular flexibility is the flexibility of a particular conformation of a molecule towards an applied distorting force. An example would be the response of a macrocyclic ligand (or indeed any ligand system) in a metal-ligand complex to change in the size of a metal ion. This can be quantified as the curvature (or second derivative) of the section through the PE surface corresponding to change in the metal ion size, at the PE minimum. This we have termed the "stiffness" of a conformation. We feel therefore that there are at least two contributions to molecular flexibility. One of them is related to the number of accessible minima in the PE surface, and the other to the curvature of the minima in that surface. There may, of course, be yet other contributions to consider. We hope this reply is helpful. We are interested in any debate that may ensue on CCL on this subject, so we would be most obliged if you would kindly post a summary of responses on CCL in due course. Kind regards, GARY PATTRICK, ROBERT D. HANCOCK, & FABRI MARSICANO "Fabri Marsicano" ---------------------------------------------- Thanks to all who replied. Bruno -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://schiele.organik.uni-erlangen.de/Bruno_Bienfait ] From rkrocha@dedalus.lcc.ufmg.br Fri Oct 10 17:29:48 1997 Received: from dedalus.lcc.ufmg.br for rkrocha@dedalus.lcc.ufmg.br by www.ccl.net (8.8.3/950822.1) id QAA21770; Fri, 10 Oct 1997 16:43:01 -0400 (EDT) Received: from localhost by dedalus.lcc.ufmg.br (AIX 3.2/UCB 5.64/4.03) id AA22654; Fri, 10 Oct 1997 18:45:29 -0200 Organization: Universidade Federal de Minas Gerais - LCC - Brasil Date: Fri, 10 Oct 1997 18:45:29 -0200 (BDB) From: ramon kleber da rocha To: Computational Chemistry Mailing List Subject: Binding energy by MM Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I would appreciate any help in getting some references (comments will be very appreciated) on how to calculate the interaction (binding) energy in systems like drug-receptor by using only molecular mechanics (molecular minimization and dynamics). What kind of relationship can be make about the energy calculated by molecular mechanics (energy of forcefield) and energy of Gibbs (delta G), and what background theoretical is necessary to do that. I will sumarize. Best regards. Ramon. ____________________________________________________________________________ Ramon Kleber da Rocha VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de Espectroscopia e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM Departamento de Quimica - Instituto de Ciencias Exatas Universidade Federal de Minas Gerais Av. Presidente Antonio Carlos, 6627 Campus Pampulha CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil ____________________________________________________________________________ From vhelms@chemcca10.ucsd.edu Fri Oct 10 18:29:51 1997 Received: from mailbox1.ucsd.edu for vhelms@chemcca10.ucsd.edu by www.ccl.net (8.8.3/950822.1) id SAA22113; Fri, 10 Oct 1997 18:05:32 -0400 (EDT) Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.68.250]) by mailbox1.ucsd.edu (8.8.5/8.6.9) with SMTP id PAA26363; Fri, 10 Oct 1997 15:05:12 -0700 (PDT) Received: by chemcca10.ucsd.edu (951211.SGI.8.6.12.PATCH1502/931108.SGI.ANONFTP) id PAA13407; Fri, 10 Oct 1997 15:04:55 -0700 From: "Volkhard Helms" Message-Id: <9710101504.ZM13405@chemcca10.ucsd.edu> Date: Fri, 10 Oct 1997 15:04:55 -0700 In-Reply-To: ramon kleber da rocha "CCL:Binding energy by MM" (Oct 10, 6:45pm) References: X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net, rkrocha@dedalus.lcc.ufmg.br, vhelms@chemcca10.ucsd.edu Subject: Re: CCL:Binding energy by MM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Ramon, you might be interested in the following study : HELMS, V., E. DEPREZ, E. GILL, C. BARRET, G. HUI BON HOA, R.C. WADE (1996) Biochemistry, Vol. 35, p.1485-1499. Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket . This paper stresses the importance of properly accounting for all solvent contributions. Binding energies to cytochrome P450cam were calculated from molecular dynamics simulations for a series of camphor derivatives, and agreed very well with experimental binding enthalpies. Yet, the experimental binding free energies follow a completely different trend ... Hope this example gives you some ideas. Volkhard Helms Dept. of Chemistry and Biochemistry UCSD San Diego From rami.reddy@gensia.com Fri Oct 10 20:29:53 1997 Received: from gtc05f for rami.reddy@gensia.com by www.ccl.net (8.8.3/950822.1) id TAA22338; Fri, 10 Oct 1997 19:42:01 -0400 (EDT) From: Received: from smtpgwy.gensia.com (gtc03f.gensia.com) by gtc05f (5.x/SMI-SVR4) id AA13805; Fri, 10 Oct 1997 16:41:25 -0700 Received: from ccMail by smtpgwy.gensia.com (SMTPLINK V2.11 PreRelease 4) id AA876526978; Fri, 10 Oct 97 16:50:42 PST Date: Fri, 10 Oct 97 16:50:42 PST Encoding: 50 Text Message-Id: <9709108765.AA876526978@smtpgwy.gensia.com> To: ramon kleber da rocha , chemistry@www.ccl.net Subject: Re: CCL:Binding energy by MM Dear Ramon Kleber, The following papesr would be helpful for calculating binding energies using molecular mechanics calculations. J. Med. Chem. vol 39, pages 705-712 (1996) J. Med. Chem. vol 38, pages 305-317 (1995) J. Am. Chem. Soc. Vol 118, pages 3959-3969 (1996) Good Luck, M. Rami Reddy Email: reddy@gensia.com Dear CCLers, I would appreciate any help in getting some references (comments will be very appreciated) on how to calculate the interaction (binding) energy in systems like drug-receptor by using only molecular mechanics (molecular minimization and dynamics). What kind of relationship can be make about the energy calculated by molecular mechanics (energy of forcefield) and energy of Gibbs (delta G), and what background theoretical is necessary to do that. I will sumarize. Best regards. Ramon. ____________________________________________________________________________ Ramon Kleber da Rocha VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de Espectroscopia e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM Departamento de Quimica - Instituto de Ciencias Exatas Universidade Federal de Minas Gerais Av. Presidente Antonio Carlos, 6627 Campus Pampulha CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil ____________________________________________________________________________ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: rkrocha@dedalus.lcc.ufmg.br -- Original Sender From: Address: rkrocha@dedalus.lcc.ufmg.br CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From wriggers@ks.uiuc.edu Fri Oct 10 01:29:38 1997 Received: from london.ks.uiuc.edu for wriggers@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id AAA15431; Fri, 10 Oct 1997 00:34:02 -0400 (EDT) Received: from vaticano.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.20/16.2 [TBG Mods]) id AA058658041; Thu, 9 Oct 1997 23:34:02 -0500 Message-Id: <199710100434.AA058658041@london.ks.uiuc.edu> Received: by vaticano.ks.uiuc.edu (NX5.67e/NX3.0X) id AA02089; Thu, 9 Oct 97 23:34:26 -0500 Content-Type: text/plain Mime-Version: 1.0 (NeXT Mail 3.3risc v118.3) In-Reply-To: <199710090751.HAA14439@chemistry.leeds.ac.uk> X-Nextstep-Mailer: Mail 3.3 (Enhance 1.2) Received: by NeXT.Mailer (1.118.3) From: Willy Wriggers Date: Thu, 9 Oct 97 23:34:25 -0500 To: chemistry@www.ccl.net Subject: Re: CCL:isosurfaces in volumetric data References: <199710090751.HAA14439@chemistry.leeds.ac.uk> Thanks for your replies! For the record, here is a compilation of messages I received: The original question was: > I'm looking for a free implementation (preferably in c) of an > algorithm that renders isosurfaces of 3D data on a grid. > > One example would be the Marching Cubes algorithm by Lorensen and > Cline, but any other method that generates triangles and > corresponding surface normals is welcome, too. ------------------------------------------------------------ Richard Gillilan , Michael Potter : VTK will do isosurfaces with Marching cubes etc (see http://www.cs.rpi.edu/~martink/) VTK is a C++ class library that I've used for a variety of visualization tasks in the past. I believe their copyright is fairly flexible. The code is fairly modular so you should be able to take just the pieces you need. At the very least you could look at the source for the method. Matthew Ward : Alternatively, if you buy the book "The Visualization Toolkit" by Schroeder, Martin, and Lorensen you get the software on a CD. It gives you a wide range of rendering options, including Marching Cubes. Andrew Dalke : You might also do a web search for a volume renderer, if you want some pre-built tools. The ones I recall are VolVis (http://miles.cnuce.cnr.it/cg/TAn.html) and the Visualization Tool Kit. [see above] Joel Welling : DrawP3D has an implementation of a Marching Cubes-type algorithm; see http://www.psc.edu/Packages/DrawP3D. There is also one in the vtk toolkit [see above]. I'm not sure what to say about either one being free, however, as GE (I believe) has a patent on the whole idea of isosurfaces from gridded data. (Believe it or not). They are unlikely to pay attention to an academic product, but if you start selling something for money they may want some of it. Stuart Green : To overcome the lack of this type of rendering in Chime and Rasmol, I've coded the marching cubes algorithm to generate coordinates and connections for a surface in PDB format. The surface PDB can then be added to the molecular PDB with selection controlled residue id number. This is all in C and is freely available. Check out the MO and MEP examples at:- http://www.chem.leeds.ac.uk/stuartg/marching/surface.html Joerg-Ruediger Hill : You might want to take a look at my program Viewmol (file://www.ccl.net/pub/chemistry/software/SOURCES/C/viewmol/). It contains a C implementation of the marching cube algorithm in the file marcub.c. Feel free to use it. _______________________________________________ wriggers@uiuc.edu (NeXT-mail OK) Willy R. Wriggers Theoretical Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801, USA Telephone (217) 244-1612 Telefax (217) 244-6078 Web Site: http://www.ks.uiuc.edu/~wriggers/ _______________________________________________ From ccl@www.ccl.net Fri Oct 10 10:30:00 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA18735; Fri, 10 Oct 1997 10:08:59 -0400 (EDT) Received: from XRAY.CHEM.RPI.EDU for breneman@XRAY.CHEM.RPI.EDU by bedrock.ccl.net (8.8.6/950822.1) id KAA21543; Fri, 10 Oct 1997 10:08:53 -0400 (EDT) From: Date: Fri, 10 Oct 1997 10:01:50 EDT To: chemistry@ccl.net Message-ID: <009bb8eb.ff778540.14227@XRAY.CHEM.RPI.EDU> Subject: Reminder: QSAR Symposium Abstracts Due Oct 20 for Dallas ACS Meeing! Dear Chemistry Netters, This is a reminder that abstracts on ACS forms are due on Oct 20 for the Dallas ACS Meeting Symposium on "QSAR and Related Phemonena" Please send completed abstracts to: Prof. Curt M. Breneman Department of Chemistry Rensselaer Polytechnic Institute Troy, NY 12180 From ccl@www.ccl.net Fri Oct 10 10:30:12 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA18225; Fri, 10 Oct 1997 09:47:23 -0400 (EDT) Received: from mailbox.syr.edu for desingh@syr.edu by bedrock.ccl.net (8.8.6/950822.1) id JAA20343; Fri, 10 Oct 1997 09:47:24 -0400 (EDT) Received: from fermi.cat.syr.edu (fermi.cat.syr.edu [128.230.59.16]) by mailbox.syr.edu (8.8.7/8.8.7) with SMTP id JAA00735 for ; Fri, 10 Oct 1997 09:47:23 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <343CEF56.59E2@syr.edu> Date: Thu, 09 Oct 1997 10:51:02 -0400 From: Deepak Singh Organization: Dept. of Chemistry, Syracuse University X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi. I read in the latest issue of C & EN the Cambridge soft has an add-on for Gaussian 94 for ChemOffice Ultra. However I could not find it on their web-site. Does anyone have any information on this? Thanks -- Deepak ---------------------------------------------------------------------- Deepak Singh Graduate Student Department of Chemistry & W. M. Keck Center for Molecular Electronics 1-014 Scitech Syracuse University Syracuse, NY 13244 Voice: (315) 443 1739, 443 5928 email:desingh@syr.edu Fax : (315) 443 4070 URL:http://web.syr.edu/~desingh ......the time is gone the song is over, thought I'd something more to say. Roger Waters in "time" ----------------------------------------------------------------------- From ccl@www.ccl.net Fri Oct 10 11:39:54 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA19548; Fri, 10 Oct 1997 11:17:29 -0400 (EDT) Received: from postoffice.npac.syr.edu for bernhold@tarkovsky.npac.syr.edu by bedrock.ccl.net (8.8.6/950822.1) id LAA24013; Fri, 10 Oct 1997 11:17:27 -0400 (EDT) Received: from tarkovsky.npac.syr.edu (tarkovsky-164.npac.syr.edu [128.230.164.139]) by postoffice.npac.syr.edu (8.7.5/8.7.1) with ESMTP id LAA19774 for ; Fri, 10 Oct 1997 11:17:27 -0400 (EDT) Received: from localhost (bernhold@localhost) by tarkovsky.npac.syr.edu (8.8.5/8.7.1) with SMTP id LAA22614 for ; Fri, 10 Oct 1997 11:17:27 -0400 (EDT) Message-Id: <199710101517.LAA22614@tarkovsky.npac.syr.edu> X-Authentication-Warning: tarkovsky.npac.syr.edu: bernhold@localhost didn't use HELO protocol To: chemistry@ccl.net Subject: Charmm-bbs has a new home! Date: Fri, 10 Oct 1997 11:17:26 -0400 From: "David E. Bernholdt" With Donovan Chin's blessing and help, operation of the charmm-bbs list has been taken over by the Chemistry Software and Information Resources Project (CSIR, pronounced caesar). The list is back in operation and ready for new subscribers. To subscribe, send a message to majordomo@csir.org with 'subscribe charmm-bbs' on a line by itself in the body. Visit CSIR (http://www.csir.org) for archives of this and many other chemistry-related lists, as well as a catalog of chemistry software and other information. Enjoy! -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From wriggers@ks.uiuc.edu Fri Oct 10 19:29:50 1997 Received: from london.ks.uiuc.edu for wriggers@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id SAA22230; Fri, 10 Oct 1997 18:55:13 -0400 (EDT) Received: from vaticano.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.20/16.2 [TBG Mods]) id AA101664115; Fri, 10 Oct 1997 17:55:15 -0500 Message-Id: <199710102255.AA101664115@london.ks.uiuc.edu> Received: by vaticano.ks.uiuc.edu (NX5.67e/NX3.0X) id AA02878; Fri, 10 Oct 97 17:55:38 -0500 Content-Type: text/plain Mime-Version: 1.0 (NeXT Mail 3.3risc v118.3) X-Nextstep-Mailer: Mail 3.3 (Enhance 1.2) Received: by NeXT.Mailer (1.118.3) From: Willy Wriggers Date: Fri, 10 Oct 97 17:55:37 -0500 To: Computer Chemistry List Subject: Summary: isosurfaces in volumetric data Hi, I send this summary again because it looks like it did not get posted last time. Thanks to everyone who replied! For the record, here is a compilation of messages I received: The original question was: > I'm looking for a free implementation (preferably in c) of an > algorithm that renders isosurfaces of 3D data on a grid. > > One example would be the Marching Cubes algorithm by Lorensen and > Cline, but any other method that generates triangles and > corresponding surface normals is welcome, too. ------------------------------------------------------------ Richard Gillilan , Michael Potter : VTK will do isosurfaces with Marching cubes etc (see http://www.cs.rpi.edu/~martink/) VTK is a C++ class library that I've used for a variety of visualization tasks in the past. I believe their copyright is fairly flexible. The code is fairly modular so you should be able to take just the pieces you need. At the very least you could look at the source for the method. Matthew Ward : Alternatively, if you buy the book "The Visualization Toolkit" by Schroeder, Martin, and Lorensen you get the software on a CD. It gives you a wide range of rendering options, including Marching Cubes. Andrew Dalke : You might also do a web search for a volume renderer, if you want some pre-built tools. The ones I recall are VolVis (http://miles.cnuce.cnr.it/cg/TAn.html) and the Visualization Tool Kit. [see above] Joel Welling : DrawP3D has an implementation of a Marching Cubes-type algorithm; see http://www.psc.edu/Packages/DrawP3D. There is also one in the vtk toolkit [see above]. I'm not sure what to say about either one being free, however, as GE (I believe) has a patent on the whole idea of isosurfaces from gridded data. (Believe it or not). They are unlikely to pay attention to an academic product, but if you start selling something for money they may want some of it. Stuart Green : To overcome the lack of this type of rendering in Chime and Rasmol, I've coded the marching cubes algorithm to generate coordinates and connections for a surface in PDB format. The surface PDB can then be added to the molecular PDB with selection controlled residue id number. This is all in C and is freely available. Check out the MO and MEP examples at:- http://www.chem.leeds.ac.uk/stuartg/marching/surface.html Joerg-Ruediger Hill : You might want to take a look at my program Viewmol (file://www.ccl.net/pub/chemistry/software/SOURCES/C/viewmol/). It contains a C implementation of the marching cube algorithm in the file marcub.c. Feel free to use it. _______________________________________________ wriggers@uiuc.edu (NeXT-mail OK) Willy R. Wriggers Theoretical Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801, USA Telephone (217) 244-1612 Telefax (217) 244-6078 Web Site: http://www.ks.uiuc.edu/~wriggers/ _______________________________________________ >From sunger@a.crl.com Fri Oct 10 11:51 EDT 1997 Received: from a.crl.com for sunger@a.crl.com by www.ccl.net (8.8.3/950822.1) id LAA20055; Fri, 10 Oct 1997 11:51:28 -0400 (EDT) Received: from [168.75.103.12] (A103012.sfo3.as.crl.com [168.75.103.12]) by a.crl.com (8.8.6/) via ESMTP id IAA12726 for ; Fri, 10 Oct 1997 08:50:43 -0700 (PDT) env-from (sunger@a.crl.com) Message-Id: In-Reply-To: <19971006135527.1915.qmail@hotmail.com> Mime-Version: 1.0 Date: Fri, 10 Oct 1997 08:52:56 -0700 To: CHEMISTRY-REQUEST@www.ccl.net From: Stefan Unger Subject: Re: CCL:logP program Content-Type: text/plain; charset="us-ascii" Several are listed at the BIO Online Store http://store.bio.com Hope this is helpful to you. >Dear friends, > I am looking for a program that calculates logP. Is any body provide >me the softwares. Please. >Thanking you, >B.Sivakumar, >SRF. Chemistry, >Bharathidasan University, >Tiruchirappalli-24. >Tamilnadu. India. >e-mail:chem@bdu.ernet.in > >______________________________________________________ >Get Your Private, Free Email at http://www.hotmail.com > > >--- >Administrivia: This message is automatically appended by the mail exploder: >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html >--- NEW CONTACT INFO!+*+*+*+*+*+*+*+**+*+*+*+*+*++*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* Stefan Unger, Ph.D. President BioSoftware Marketing 4151 Middlefield Rd, Ste 110 Palo Alto, CA 94303-4743 ph: 650-858-0522 fx: 650-494-6564 email: URL: http://bio.com/home/bsm/bsm.html BioSoftware Marketing specializes in a full range of marketing services (market studies to collateral design) for technical software and hardware companies. Product Manager, Scientific Software, Bio Online Store (http://store.bio.com/) *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* >From eugene@genome.biotech.washington.edu Fri Oct 10 20:21 EDT 1997 Received: from genome.biotech.washington.edu for eugene@genome.biotech.washington.edu by www.ccl.net (8.8.3/950822.1) id UAA22545; Fri, 10 Oct 1997 20:21:12 -0400 (EDT) Received: (from eugene@localhost) by genome.biotech.washington.edu (8.8.5/8.8.5) id RAA18609 for chemistry-request@www.ccl.net; Fri, 10 Oct 1997 17:20:55 -0700 Date: Fri, 10 Oct 1997 17:20:55 -0700 From: Eugene Kolker Message-Id: <199710110020.RAA18609@genome.biotech.washington.edu> To: chemistry-request@www.ccl.net Subject: Recomb98 deadline: Oct 20 Content-Type: text CALL FOR PAPERS SECOND ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 98) March 22 - 25, 1998 New York City Sponsored by Association for Computing Machinery SIGACT with support from SLOAN Foundation US Department of Energy http://www.mssm.edu/biomath/recomb98.html The Second Annual Conference on Research in Computational Molecular Biology (RECOMB 98) will be held in New York City, March 22 - 25, 1998. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics - Molecular sequence analysis - Recognition of genes and regulatory elements - Molecular evolution - Protein structure - Combinatorial libraries and drug design ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Professor Pavel Pevzner RECOMB 98 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 An abstract must be received by October 20 (!), 1997. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. For more information please visit the conference web page: http://www.mssm.edu/biomath/recomb98.html >From arthur@csb0.IPC.PKU.EDU.CN Fri Oct 10 22:03 EDT 1997 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id WAA23117; Fri, 10 Oct 1997 22:03:29 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY-REQUEST@www.ccl.net id AA12895; Sat, 11 Oct 97 10:02:52 -0700 Date: Sat, 11 Oct 1997 10:02:49 -0700 (PDT) From: Wang Arthur To: Balasubramanian SIVKUMAR Cc: CHEMISTRY-REQUEST@www.ccl.net Subject: Re: CCL:logP program In-Reply-To: <19971006135527.1915.qmail@hotmail.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 6 Oct 1997, Balasubramanian SIVKUMAR wrote: > Dear friends, > I am looking for a program that calculates logP. Is any body provide > me the softwares. Please. > Thanking you, > B.Sivakumar, > SRF. Chemistry, > Bharathidasan University, > Tiruchirappalli-24. > Tamilnadu. India. > e-mail:chem@bdu.ernet.in > Dear Netters, Dear, We have developed an atom-addition method to calculate LogP. The original paper is on J.Chem.Inf.Comput.Sci., 1997, 37, 615-621. The program, XLOGP, together with its dataset, is available by anonymous ftp to 162.105.177.12, under 'pub/software/xlogp'. Please read the file 'README' carefully and fill in the license agreement form. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/