From jaouad@csc.fi Thu Apr 2 01:21:52 1998 Received: from pobox.csc.fi for jaouad@csc.fi by www.ccl.net (8.8.3/950822.1) id AAA00188; Thu, 2 Apr 1998 00:42:03 -0500 (EST) Received: from cypress.csc.fi (cypress-e.csc.fi [128.214.46.7]) by pobox.csc.fi (8.8.8/8.8.8/CSC/Rtrs-1.13) with SMTP id IAA26361 for ; Thu, 2 Apr 1998 08:42:03 +0300 (EET DST) Date: Thu, 2 Apr 1998 08:42:03 +0300 (EET DST) From: Jaouad El-Bahraoui To: CHEMISTRY@www.ccl.net Subject: Inorganic and organometalic chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi!!! my particular interest is the prediction of the electronic coupling between the cluster ligand and the resulting redox properties. I have no experience in this field of research, so any hints or comments would be appreciated. Many thanks in advance, \^ ^/ )@ @( +-----------------------oOO--(_)----------------------------------+ | Jaouad El-Bahraoui , Ph.D | +-----------------------------------------------------------------+ | Inorganic Chemistry Laboratory | Tel: +358-9-19140199 | | department of Chemistry, P.O. BOX 55 | Fax: +358-9-19140198 | | University of Helsinki,FIN-00040 | jaouad@ccsc.fi | | Helsinki, Finland |http://w3.ugr.es/~jaouad/| +----------------------Oooo--oOO----------------------------------+ oooO ( ) ( ) ) / \ ( (_/ \_) -------------------------------------------------------------------- I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. -------------------------------------------------------------------- From tamasgunda@tigris.klte.hu Thu Apr 2 04:21:58 1998 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id DAA01039; Thu, 2 Apr 1998 03:38:39 -0500 (EST) Message-Id: <199804020838.DAA01039@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Thu, 02 Apr 1998 10:32:43 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: CHEMISTRY@www.ccl.net Date: Thu, 2 Apr 1998 10:32:41 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:descriptors for the 'shape' and 'size' of molecules Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Norman Goldberg wrote: > Hello, > > I am looking for a simple (!?) method to describe the 'size' and > topology of a molecule. > The aim is to establish a correlation between experimentally observed > retention times (by liquid cromatography) and the 'shape' of several > pure hydrocarbons > (bigger species including 'disk' and umbrella-shaped molecules). > > I have no experience in this field of research, whatsoever, so any hints > or comments > would be appreciated. > > Many thanks in advance, > > Norman > This problem is similar to those in drug research: how to describe the shape of a molekule or substituent. One of the early approaches (I mean before CoMFA and 3DQSAR era) to this was the use of Verloop's sterimol parameters: these characterize the shape of the molecule. My program Mol2mol can calculate it. To know more about sterimol, contact www.compuchem.com/m2m1.htm, at the end of that page there is summary in nutshell about sterimol. best wishes Tamas Gunda of the molecule. > -- > _____________________________________ > > Dr. Norman Goldberg (N.Goldberg@tu-bs.de) > Technische Universitaet Braunschweig > Institut fuer Organische Chemie > Hagenring 30 > D-38106 Braunschweig (FRG) > > Tel.: +(0)531-391-5312 > Fax : +(0)531-391-5388 > > http://www.tu-bs.de/institute/org-chem/goldberg/WELCOME.htm > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: N.Goldberg@tu-bs.de > -- Original Sender From: Address: N.Goldberg@tu-bs.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 > > > ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 www.klte.hu/~gundat/gunda.htm H-4010 Debrecen Hungary ************************************************************************ From davel@chmqst.demon.co.uk Thu Apr 2 13:21:52 1998 Received: from post.mail.demon.net for davel@chmqst.demon.co.uk by www.ccl.net (8.8.3/950822.1) id MAA04009; Thu, 2 Apr 1998 12:37:01 -0500 (EST) Received: from chmqst.demon.co.uk ([158.152.83.101]) by post.mail.demon.net id aa1017044; 2 Apr 98 17:34 GMT From: David Livingstone Organization: ChemQuest To: Norman Goldberg Date: Thu, 2 Apr 1998 11:12:59 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:descriptors for the 'shape' and 'size' of molecules Reply-to: davel@chmqst.demon.co.uk CC: CHEMISTRY@www.ccl.net Priority: normal In-reply-to: <3521FC2C.2754649C@tu-bs.de> X-mailer: Pegasus Mail for Win32 (v2.54) Message-ID: <891538485.1017044.0@chmqst.demon.co.uk> Norman, you wrote: > I am looking for a simple (!?) method to describe the 'size' and > topology of a molecule. > The aim is to establish a correlation between experimentally observed > retention times (by liquid cromatography) and the 'shape' of several > pure hydrocarbons > (bigger species including 'disk' and umbrella-shaped molecules). > > I have no experience in this field of research, whatsoever, so any hints > or comments > would be appreciated. I think you will find that quite a lot has already been done by others in modelling retention times (of all sorts) often using hydrophobicity descriptors of one form or another (retention times are frequently used as hydrophobicity descriptors themselves). I guess you need to do a search. As for shape descriptors (and others) I suggest you have a look at some QSAR reviews and/or books. I wrote one in 1991: D.J. Livingstone, "Quantitative Structure-Activity Relationships" in: Similarity Models in Organic Chemistry, Biochemistry and Related Fields (Eds, R.I. Zalewski, T.M. Krygowski & J. Shorter), Elsevier, 1991, pp 557-627). You could also try: The book by Hansch & Leo (Exploring QSAR Fundamentals and Applications in Chemistry and Biology, ACS, 1995, ISBN 0-8412-2987-2). Chapter 3 (Parameters) of Hugo Kubinyi's book (QSAR: Hansch Analysis and related Approaches, VCH, Weinheim, 1993, ISBN 3-527-30035-X) and it might pay to take a look at "Partition Coefficient Determination and Estimation", (Eds W. Dunn, J. Block & R. Pearlman), Pergamon, 1986, ISBN ???? - although this is perhaps a little dated now. Hope this helps, Dave. ------------------------------------------------------------------ D.J. Livingstone ChemQuest Cheyney House, 19-21 Cheyney St., Steeple Morden. Herts UK SG8 0LP Phone & Fax: +44 (0)1763 852569 e-mail davel@chmqst.demon.co.uk ------------------------------------------------------------------ From eyoung@biosci.cbs.umn.edu Thu Apr 2 15:21:54 1998 Received: from biosci.cbs.umn.edu for eyoung@biosci.cbs.umn.edu by www.ccl.net (8.8.3/950822.1) id PAA05317; Thu, 2 Apr 1998 15:14:45 -0500 (EST) Received: from localhost (eyoung@localhost) by biosci.cbs.umn.edu (8.8.8/8.6.9) with SMTP id OAA24815 for ; Thu, 2 Apr 1998 14:10:33 -0600 (CST) Date: Thu, 2 Apr 1998 14:10:33 -0600 (CST) From: Eva Young To: chemistry@www.ccl.net Subject: pdb to VRML converters: summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks: Here's the summary of replies to my question about a conversion tool for pdb to VRML. Is there an authoring tool available that will convert pdb files to VRML? Thanks to all of you who responded. The web sites you have referred me to are very helpful. Eva Eva Young University of Minnesota eyoung@biosci.umn.edu ----------------------------------------------- There is a pdb to vrml converter available at the following address http://ws05.pc.chemie.th-darmstadt.de/vrml/ Also, InsightII 95 from MSI will output vrml after it has been patched with updaters from the msi www page. I assume InisghtII 97 will also do the same, but without the patches. Bye Jeff. -------------------------------------------------------------------------- Jeff Dyason e-mail: j.dyason@mailbox.uq.edu.au Drug Design & Development Centre Phone: 61 7 336 52481 University of Queensland Fax: 61 7 336 51990 Brisbane Queensland Australia 4072 -------------------------------------------------------------------------- > Is there an authoring tool available that will convert pdb files to VRML? MSI has a utility called "pdb2vrml" installed in the Visualization/ Workstation Lab. It might also be available at the Basic Sciences Lab or the West bank Lab. Just type pdb2vrml and it will give you the various options you can do. For more information, see: http://www.pc.chemie.th-darmstadt.de/vrml/pdb2vrml.html _____________________________________________________________________ /| | /| Kenneth E. Lind, Graduate Student | /| Department of Medicinal Chemistry, University of Minnesota | /| | /| phone: (612) 626-3551 fax: (612) 626-4429 | /| e-mail: lind@vwl.medc.umn.edu url: http://chet.medc.umn.edu/~lind | /|_____________________________________________________________________| / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / _O YOU WILL NEVER "FIND" TIME FOR ANYTHING. //\ IF YOU WANT TIME, YOU MUST MAKE IT. _/\ oo / -- CHARLES BIXTON ooo I have written a program not only to display a pdb file in vrml, but also to animate long dynamics trajectories of large proteins in vrml. But I am afraid that won't be of much help to you, since my employer will only make it available as part of a large package to our paying clients. Instead, you can check out the following web pages. http://trex.musc.edu/manuals/pdb2vrml.html http://ws05.pc.chemie.th-darmstadt.de/vrmlG/pdbvis.html -- J.Kottalam, Ph.D. | Structural Bioinformatics, Inc. Principal Scientist | 10929 Technology Pl. Computational Sciences | San Diego, CA 92127. email: kottalam@strubix.com | http://www.strubix.com See a list of crystallography-related VRML softwares, including the PDB2VRML translator at : http://fluo.univ-lemans.fr:8001/vrml/intvrml.html Best wishes, Armel Le Bail - Universite du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans cedex 9, France http://fluo.univ-lemans.fr:8001/ http://www.cybercable.tm.fr/~cristal/welcome.html there is a simple command-line tool at the group of Prof. Brickmann in Darmstadt, Germany. You ca find it at http://www.pc.chemie.tu-darmstadt.de/vrml/pdb2vrml.html there is also a lot of VRML-related staff ... :-) Daniel Vitt ---------------------------------------------------------------- | 4sc | Technology Center Wuerzburg | | 4sc | Sedanstr. 27 | | 4sc 4sc 4sc | D-97082 Wuerzburg | | 4sc 4sc 4sc | tel: +49 (0)931 88023-23 | | 4sc 4sc 4sc | fax: +49 (0)931 88023-25 | | 4sc4sc4sc |--------------------------------| | 4sc | Dipl.-Chem. Daniel Vitt | | 4sc 4 Scientific | Geschaeftsfuehrer | | 4sc Computing | | | 4sc GmbH | e-mail: vitt@4sc.com | ---------------------------------------------------------------- you can find our pdb2vrml converter under the following URL: http://www.pc.chemie.tu-darmstadt.de/vrml/pdb2vrml.html Richard -- Dipl.-Ing. Richard J. Marhoefer Technische Universitaet Darmstadt Physikalische Chemie I, Petersenstr. 20, 64287 Darmstadt fon: (+int49) 6151/16-3746 fax: (+int49) 6151/16-4298 mail: ric@pc.chemie.tu-darmstadt.de net: http://www.pc.chemie.tu-darmstadt.de/authors/ric/ please have a look at Konrad Hinsen's MolecularModellingToolkit (MMTK) at http://starship.skyport.net/crew/hinsen/mmtk.html You can read in molecules as PDB and dump them as VRML then. Hope this helps. Lutz Ehrlich --------------------- Lutz Ehrlich Structural Biology EMBL Meyerhofstr. 1 D-69012 Heidelberg Germany email: lutz.ehrlich@embl-heidelberg.de or lutz@metaversum.de web : http://www.embl-heidelberg.de/~ehrlich phone: +49-6221-387-140 fax : +49-6221-387-517 Dear Eva, have a look at: http://ws05.pc.chemie.th-darmstadt.de/vrml/pdb2vrml.html regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it A couple of tools that I use may be helpful. 1) Try the free Weblab viewer for Windows 95 from MSI which can be downloaded at http://www.msi.com/ this can load PDB or many other formats, generate CPK images, protein ribbons etc and save in VRML format. 2) on an SGI you can do the same thing with insightII (which is not free). 3) I have a simple PERL script (pdb2vrml.pl) that converts a PDB file to a set of VRML spheres with anchors that highlight the atom name, residue name and residue number. I will send this is a separate mail message. For a PC VRML plug-in for Netscape I suggest the zeus plug-in which seems much faster than some other VRML rendering tools. This can be obtained from the VRML repository http://www.sdsc.edu/vrml/ Hope this helps. Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk -------- #!/usr/local/bin/perl # read PDB file # for each ATOM line output the following data # read atom name, residue type, residue number, chain ID, x,y,z # create VRML file if ($#ARGV != 0) { die "usage: pdb2vrml.pl file.pdb\n"; } # -------------------------------------------------------- # # read PDB file # $filename1=shift(@ARGV); open(FILE1,$filename1) || die "cant open $filename1: $! \n"; # read only ATOM records not HETATM records $ATOMcount=0; while ($_ = ) { $str1=substr($_,0,6); # # read ATOM records - store for later analysis # if ($str1 eq 'ATOM ') { # print $_; $ATOMcount++; $atomname{$ATOMcount}=substr($_,13,4); $resname3{$ATOMcount}=substr($_,17,3); $chain{$ATOMcount}=substr($_,21,1); if ($chain{$ATOMcount} eq " ") { $chain{$ATOMcount}="-"; } $resnumber{$ATOMcount}=substr($_,23,4); $x{$ATOMcount}=substr($_,30,8); $y{$ATOMcount}=substr($_,38,8); $z{$ATOMcount}=substr($_,46,8); # print "$atomname{$ATOMcount} $resname3{$ATOMcount} $resnumber{$ATOMcount} $chain{$ATOMcount} $x{$ATOMcount} $y{$ATOMcount} $z{$ATOMcount} \n"; } } close(FILE1); # # output VRML # # exit; # print out VRML code in ASCII print "#VRML V1.0 ascii\n"; foreach $i (1..$ATOMcount) { $xx=$x{$i}; $yy=$y{$i}; $zz=$z{$i}; $fullname=$atomname{$i}." ".$resname3{$i}." ".$resnumber{$i}; print " \n"; print "WWWAnchor { \n"; print " name \"\" \n"; print " description \" $fullname \" \n"; print " map NONE \n"; print "\n"; print "Translation { \n"; print "translation $xx $yy $zz \n"; print "} \n"; # end translation print " \n"; print "Material { \n"; # now echo appropriate color $aname=$atomname{$i}; # print "aname= $aname \n"; $c=substr($aname,0,1); # default is carbon gray radius=1.0 $rds=1.0; $col=" 0.5 0.5 0.5 "; if ($c eq H) { $col=" 1.0 1.0 1.0 "; $rds=0.7; } if ($c eq O) { $col=" 1.0 0.0 0.0 "; $rds=1.0; } if ($c eq N) { $col =" 0.0 0.0 1.0 "; $rds=1.0; } if ($c eq S) { $col =" 1.0 1.0 0.0 "; $rds=1.3; } if ($c eq P) { $col= " 1.0 0.0 1.0 "; $rds=1.2; } # print "$aname $c \n"; print " diffuseColor $col \n"; print "}\n"; # end material print "\n"; print "Sphere {\n"; print "radius $rds \n"; print "} \n"; # end sphere $xx=(-1.0*$xx); $yy=(-1.0*$yy); $zz=(-1.0*$zz); print "\n"; print "Translation { \n"; print "translation $xx $yy $zz \n"; print "} \n"; # end translation print " } \n"; # end WWWAnchor } Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk For a heavyweight way to do it, you might want to look at VMD from http://www.ks.uiuc.edu/Research/vmd/ . It can export its display to a variety of 3D formats, including VRML. Andrew Dear Eva, have a look at: http://ws05.pc.chemie.th-darmstadt.de/vrml/pdb2vrml.html regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it Hi, you can find our pdb2vrml converter under the following URL: http://www.pc.chemie.tu-darmstadt.de/vrml/pdb2vrml.html Richard -- Dipl.-Ing. Richard J. Marhoefer Technische Universitaet Darmstadt Physikalische Chemie I, Petersenstr. 20, 64287 Darmstadt fon: (+int49) 6151/16-3746 fax: (+int49) 6151/16-4298 mail: ric@pc.chemie.tu-darmstadt.de net: http://www.pc.chemie.tu-darmstadt.de/authors/ric/ -------Please note our new e-mail / s-mail address------- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: ric@ws0e.pc.chemie.tu-darmstadt.de -- Original Sender From: Address: ric@ws0e.pc.chemie.tu-darmstadt.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 There is a small tool doing exactly that: http://ws05.pc.chemie.th-darmstadt.de/vrml/pdb2vrml.html If you need more influence on the VRML generation, you might try my Molecular Modelling Toolkit at http://starship.skyport.net/crew/hinsen/mmtk.html which can generate various VRML representations for molecular systems and lets you add any graphics objects of your own (e.g. for indicating motion etc.). Also check http://web.inc.bme.hu/~csonka/vrmlchem.html for more links to VRML applications in chemistry. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- I have written a program not only to display a pdb file in vrml, but also to animate long dynamics trajectories of large proteins in vrml. But I am afraid that won't be of much help to you, since my employer will only make it available as part of a large package to our paying clients. Instead, you can check out the following web pages. http://trex.musc.edu/manuals/pdb2vrml.html http://ws05.pc.chemie.th-darmstadt.de/vrmlG/pdbvis.html -- J.Kottalam, Ph.D. | Structural Bioinformatics, Inc. Principal Scientist | 10929 Technology Pl. Computational Sciences | San Diego, CA 92127. email: kottalam@strubix.com | http://www.strubix.com