From chemistry-request@server.ccl.net Mon Jan 15 04:51:57 2001 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0F9prd13288 for ; Mon, 15 Jan 2001 04:51:54 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for CHEMISTRY@ccl.net id 14I6IW-0003Aq-00; Mon, 15 Jan 2001 11:51:32 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id LAA07335 for ; Mon, 15 Jan 2001 11:51:33 +0200 (GMT) Message-ID: <3A622D00.5196E108@vaidila.vdu.lt> Date: Sun, 14 Jan 2001 23:49:36 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 CC: CHEMISTRY@ccl.net Subject: CCL: SUMMURY - NBO documentation/overview References: Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hi CCL'ers, SUMMURY of about NBO documentation/overview. The initial question was : >I am searching for documentation/overview or some other detailed >information about NBO on on-line resources. Have you something about >that ? Answers: ******************************************************** The NBO documentation is available at http://www.ccl.net/cca/software/MS-WIN95-NT/mopac6/nbo/NBO.HTM Good luck, Matthias ---------------------------------------------------------------------------- Dr. Matthias Hofmann Anorganisch-Chemisches Institut Ruprecht-Karls Universitaet Heidelberg Tel.: (INT+) 6221 54-8451 In Neuenheimer Feld 270 Fax.: (INT+) 6221 54-8439 D-69120 Heidelberg e-mail: matthias.hofmann@urz.uni-heidelberg.de Germany http://www.uni-heidelberg.de/institute/fak12/AC/hofmann ---------------------------------------------------------------------------- ********************************************************** Hello please contact the author, prof. Weinhold, at Pedro ********************************************************** From chemistry-request@server.ccl.net Mon Jan 15 10:15:03 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FFF2d14466 for ; Mon, 15 Jan 2001 10:15:02 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA16368 for ; Mon, 15 Jan 2001 10:15:03 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A63130D.DD7335CB@cornell.edu> Date: Mon, 15 Jan 2001 10:11:09 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:babel development? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit David van der Spoel wrote: > Hi, > > Is anybody still actively developing/maintaining babel? The latest version > (1.6) seems to be from 1996. > > Groeten, David. > ________________________________________________________________________ > Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel > phone: 46 18 471 4205 fax: 46 18 511 755 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ This is an interesting question, because Babel is SUPPOSED to be able to read CHARMM files as input, yet it doesn't. And since there is no program other than Quanta that will allow one to easily view CHARMM crd files, it would be nice to be able to convert them to some other format, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Mon Jan 15 11:21:27 2001 Received: from fulcrum.physbio.mssm.edu ([146.203.4.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FGLRd14687 for ; Mon, 15 Jan 2001 11:21:27 -0500 Received: from mezei (helo=localhost) by fulcrum.physbio.mssm.edu with local-esmtp (Exim 3.11 #1) id 14ICNr-0046gA-00; Mon, 15 Jan 2001 11:21:27 -0500 Date: Mon, 15 Jan 2001 11:21:27 -0500 From: Mihaly Mezei X-Sender: mezei@fulcrum.physbio.mssm.edu To: "Dr. Richard Wood" cc: chemistry@ccl.net Subject: Re: CCL:convert from Charmm format In-Reply-To: <3A63130D.DD7335CB@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Mihaly Mezei > input, yet it doesn't. And since there is no program other than Quanta that > will allow one to easily > view CHARMM crd files, it would be nice to be able to convert them to some > other format, Among the several options of my program Simulad is conversion from (among others) Charmm CRD to PDB, Macromodel and some other formats. It also does trajectory conversions and there is a (rudimentary) display option for the SGI. It can be downloaded from http://inka.mssm.edu/~mezei/simulaid . Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of Medicine Voice: (212) 241-2186 Fax: (212) 860-3369| WWW: http:// adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 From chemistry-request@server.ccl.net Mon Jan 15 11:37:11 2001 Received: from mercury.chem.nwu.edu (hutchisn@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FGbBd14729 for ; Mon, 15 Jan 2001 11:37:11 -0500 Received: from localhost by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id KAA13579; Mon, 15 Jan 2001 10:39:22 -0600 (CST) Date: Mon, 15 Jan 2001 10:39:22 -0600 (CST) From: Geoff Hutchison Reply-To: Geoff Hutchison To: "Dr. Richard Wood" cc: chemistry@ccl.net Subject: Re: CCL:babel development? In-Reply-To: <3A63130D.DD7335CB@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 15 Jan 2001, Dr. Richard Wood wrote: > David van der Spoel wrote: >> Is anybody still actively developing/maintaining babel? The latest version >> (1.6) seems to be from 1996. Yes and no. I asked a very similar question a few months ago. Both Matt Stahl and Pat Walters are assisting on a GPL'ed library called OELib, that is essentially based on Babel. Matt said that at some point OELib should probably be released as "Babel 2.0." At one point, there was a webpage at I use OELib in some of my work and it's pretty good and evolving relatively quickly. Hopefully it will soon have all the Babel translators and then some. > This is an interesting question, because Babel is SUPPOSED to be able to read > CHARMM files as input, yet it doesn't. As someone who's written some file translators, it's hard to know what the problem might be without example files. Cheers, -- -Geoff Hutchison Northwestern Chemistry From chemistry-request@server.ccl.net Mon Jan 15 12:30:18 2001 Received: from smtp.biosci.ki.se (smtp.biosci.ki.se [130.237.109.196]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FHUId14831 for ; Mon, 15 Jan 2001 12:30:18 -0500 Received: from whale.csb.ki.se (whale.csb.ki.se [130.237.109.8]) by smtp.biosci.ki.se (8.9.3+Sun/8.9.3) with SMTP id SAA11839 for ; Mon, 15 Jan 2001 18:30:19 +0100 (MET) Received: from bio246.csb.ki.se by whale.csb.ki.se (5.65v4.0/1.1.10.5/03Feb98-0237PM) id AA31293; Mon, 15 Jan 2001 18:30:17 +0100 Message-Id: <3.0.6.32.20010115182521.00a0dd60@whale.csb.ki.se> X-Sender: nicolas@whale.csb.ki.se X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 15 Jan 2001 18:25:21 +0100 To: chemistry@ccl.net From: Nicolas Foloppe Subject: CCL: babel development / visualizing CHARMM CRD files In-Reply-To: <3A63130D.DD7335CB@cornell.edu> References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" >> Is anybody still actively developing/maintaining babel? The latest version >> (1.6) seems to be from 1996. >> >> Groeten, David. >> ________________________________________________________________________ >> Dr. David van der Spoel Biomedical center, Dept. of Biochemistry >> s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden >> e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel >> phone: 46 18 471 4205 fax: 46 18 511 755 >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >This is an interesting question, because Babel is SUPPOSED to be able to read >CHARMM files as >input, yet it doesn't. And since there is no program other than Quanta that >will allow one to easily >view CHARMM crd files, it would be nice to be able to convert them to some >other format, I would also very much like to know something about the status of babel development. In passing, RasMol allows to visualize charmm coordinate files. Nicolas Foloppe ========================================= = Nicolas Foloppe = = Center for Structural Biochemistry = = Department of Bioscience = = Karolinska Institutet = = S-141 57 Huddinge, SWEDEN = = = = email: nicolas.foloppe@csb.ki.se = = Phone: International + 46-8-6089193 = = Fax : International + 46-8-6089290 = ========================================= From chemistry-request@server.ccl.net Mon Jan 15 12:39:22 2001 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FHdLd14875 for ; Mon, 15 Jan 2001 12:39:21 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA42717; Mon, 15 Jan 2001 12:33:49 -0500 (EST) Date: Mon, 15 Jan 2001 12:33:49 -0500 From: Rick Venable To: "Dr. Richard Wood" cc: chemistry@ccl.net Subject: Re: CCL:babel development? In-Reply-To: <3A63130D.DD7335CB@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > David van der Spoel wrote: > > Is anybody still actively developing/maintaining babel? The latest version > > (1.6) seems to be from 1996. > > ________________________________________________________________________ > > Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > > s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > > e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel > > phone: 46 18 471 4205 fax: 46 18 511 755 > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ On Mon, 15 Jan 2001, Dr. Richard Wood wrote: > This is an interesting question, because Babel is SUPPOSED to be > able to read CHARMM files as input, yet it doesn't. And since there > is no program other than Quanta that will allow one to easily view > CHARMM crd files, it would be nice to be able to convert them to > some other format, > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Cornell University, Ithaca, NY 14853 Actually, I believe that both Rasmol and VMD can read and display CHARMM .crd files, and write them back out in PDB format. For Rasmol, the process requires using the command line, and can't be automated easily; something like load charmm file.crd save pdb file.pdb should handle the file format conversion. Note, however, that there are a few naming conflicts for amino acids between CHARMM and PDB, for both residue names (HIS) and heavy atom names (ILE, C-terminal O). For molecules besides the standard 20 amino acids, e.g. cofactors and AA analogs, there is considerably more divergence in naming. My experiences with automated coordinate file conversion have, in general, not been very good, esp. with Babel. Conversions from Cambridge FDAT to PDB are particularly bad; all the numeric atom labels are discarded, and all carbons become simply 'C' instead of 'C1', 'C2', etc. I realize that these are arbitrary numeric labels assigned by the crystallographer and don't necessarily correspond to IUPAC numbering, but they would be useful if retained. (I developed my own procedure, using Cambridge 'quest' prog directly, and a little file editing.) =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Mon Jan 15 12:57:12 2001 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FHvCd14931 for ; Mon, 15 Jan 2001 12:57:12 -0500 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id TAA40530 for ; Mon, 15 Jan 2001 19:50:22 +0100 (CET) Date: Mon, 15 Jan 2001 19:50:22 +0100 From: Christian Pilger To: chemistry@ccl.net Subject: PS to EPS or TIFF In-Reply-To: <3A63130D.DD7335CB@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I know, this is another off-topic question, but maybe somebody can help me. I have onlty little experience with postscript files. Can someboy point a way to me how I can directly convert postscript to EPS or TIFF ? Are there non-commercial programs available that run on SGI ? Regards, Christian ----------------------------------------------------------------- Dr. Christian Pilger Istituto di Strutturistica Chimica "Giordano Giacomello" C.N.R. - Sezione di Trieste Area Science Park - Basovizza Strada Statale 14 - Km. 163.5 I-34012 Trieste/Italy Tel.: +39+040+226881 Fax : +39+040+9221126 e-mail: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Jan 15 13:00:33 2001 Received: from server3.safepages.com ([216.127.146.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FI0Xd14972 for ; Mon, 15 Jan 2001 13:00:33 -0500 Received: from kressj (5131-196-251.008.popsite.net [209.69.196.251]) by server3.safepages.com (Postfix) with SMTP id 62F6722FAF; Mon, 15 Jan 2001 17:58:40 +0000 (GMT) Message-ID: <001801c07f1c$cb2e60c0$0100a8c0@webrise.net> From: "Jim Kress" To: "Geoff Hutchison" , "Dr. Richard Wood" Cc: References: Subject: Re: CCL:babel development? Date: Mon, 15 Jan 2001 12:58:38 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Try: http://www.eyesopen.com/oelib.html Jim ----- Original Message ----- From: "Geoff Hutchison" To: "Dr. Richard Wood" Cc: Sent: Monday, January 15, 2001 11:39 AM Subject: CCL:babel development? > > On Mon, 15 Jan 2001, Dr. Richard Wood wrote: > > David van der Spoel wrote: > >> Is anybody still actively developing/maintaining babel? The latest version > >> (1.6) seems to be from 1996. > > Yes and no. I asked a very similar question a few months ago. Both Matt > Stahl and Pat Walters are assisting on a GPL'ed library called OELib, that > is essentially based on Babel. Matt said that at some point OELib should > probably be released as "Babel 2.0." At one point, there was a webpage at > > > I use OELib in some of my work and it's pretty good and evolving > relatively quickly. Hopefully it will soon have all the Babel translators > and then some. > > > This is an interesting question, because Babel is SUPPOSED to be able to read > > CHARMM files as input, yet it doesn't. > > As someone who's written some file translators, it's hard to know what the > problem might be without example files. > > Cheers, > -- > -Geoff Hutchison > Northwestern Chemistry > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Mon Jan 15 14:51:58 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FJpwd15173 for ; Mon, 15 Jan 2001 14:51:58 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA24654 for ; Mon, 15 Jan 2001 14:51:59 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A6353F4.1402D9C8@cornell.edu> Date: Mon, 15 Jan 2001 14:48:05 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CHARMM Conversion Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all- I know all about Ras,ol, VMD etc. reading CHARMM crd files. I've tried them all, don't like them very much. My comment regarding Babel was more along the lines of Babel being able to convert CHARMM files to a more usable format (for me), such as xyz or HyperChem hin file format. Since I prefer Windows to UNIX, I would like to be able to open a CHARMM converted file in a program that I know really well, such as HyperChem. So, thanks eeryone that suggested Rasmol and VMD etc. I've alrady tried those. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Mon Jan 15 11:04:42 2001 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FG4fd14656 for ; Mon, 15 Jan 2001 11:04:41 -0500 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id RAA04239; Mon, 15 Jan 2001 17:03:20 +0100 (MET) Message-ID: <005401c07f0c$b6e267c0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "David van der Spoel" , References: Subject: Re: CCL:babel development? Date: Mon, 15 Jan 2001 17:03:27 +0100 Organization: Ist. Chimica Farmaceutica MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear CCLers, if you are interested in software able to manage several file formats (included CHARMM CRD and Quanta MSF), I would like to suggest our VEGA package that is downloadable at: http://users.unimi.it/~ddl Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Mon Jan 15 11:49:19 2001 Received: from bellatrix.pcl.ox.ac.uk (IDENT:root@bellatrix.pcl.ox.ac.uk [163.1.35.134]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FGnId14790 for ; Mon, 15 Jan 2001 11:49:18 -0500 Received: from localhost (ben@localhost) by bellatrix.pcl.ox.ac.uk (8.9.3/8.8.7) with ESMTP id QAA11406; Mon, 15 Jan 2001 16:49:11 GMT Date: Mon, 15 Jan 2001 16:49:11 +0000 (GMT) From: Ben Webb To: "Dr. Richard Wood" cc: chemistry@ccl.net Subject: Re: CCL:babel development? In-Reply-To: <3A63130D.DD7335CB@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 15 Jan 2001, Dr. Richard Wood wrote: > Babel is SUPPOSED to be able to read CHARMM files as input, yet it > doesn't. And since there is no program other than Quanta that will > allow one to easily view CHARMM crd files, it would be nice to be able > to convert them to some other format This is a fairly simple bug to fix. Just apply the following patch (to rdcharmm.c) and recompile. Ben --- babel-1.6/rdcharmm.c Tue Jan 21 15:52:39 1997 +++ babel1.6-2/rdcharmm.c Fri Feb 12 14:51:16 1999 @@ -51,9 +56,9 @@ Type(i)[1] = the_line[16]; Type(i)[2] = '\0'; } - sscanf(&the_line[22],"%lf",&X(i)); - sscanf(&the_line[32],"%lf",&Y(i)); - sscanf(&the_line[42],"%lf",&Z(i)); + sscanf(&the_line[21],"%lf",&X(i)); + sscanf(&the_line[31],"%lf",&Y(i)); + sscanf(&the_line[41],"%lf",&Z(i)); } result = assign_radii(mol); result = assign_bonds(mol); From chemistry-request@server.ccl.net Mon Jan 15 13:32:33 2001 Received: from blackadder.cis.McMaster.CA (blackadder.CIS.McMaster.CA [130.113.128.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FIWXd15041 for ; Mon, 15 Jan 2001 13:32:33 -0500 Received: from mcmaster.ca (opus.Chemistry.McMaster.CA [130.113.108.24]) by blackadder.cis.McMaster.CA with ESMTP id NAA29430; Mon, 15 Jan 2001 13:32:13 -0500 (EST) Sender: jenkins@blackadder.cis.McMaster.CA Message-ID: <3A63422D.F9554ED9@mcmaster.ca> Date: Mon, 15 Jan 2001 13:32:13 -0500 From: Samantha Jenkins Organization: McMaster University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Yoshiyuki Hase , chemistry@ccl.net Subject: Re: CCL:basis set optimiser in solid X-Priority: 1 (Highest) References: <5.0.2.1.1.20010112104052.009eb070@eros.iqm.unicamp.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Yoshiyuki, Thankyou for your attachments, however, I have now got a patch for LOPTCG maybe this is of interest to you. Please see message below too: ************************************************************************************ Concerning your problem with the optimizer: attached I send you a patch that will correct (I hope!) this bug. In principle it is enough to include the whole file within the optimizer input deck. Alternatively you can place the file containing the new function in the appropriate directory, for instance: ~/LoptFnc, and then source it into the procedure by adding in any part of your input file a line like this: . ~/LoptFnc/UpdateProfile.fnc Any of these two posibilities would redefine the function UpdateProfile that likely causes the error you found. This function is active when the FIXINDEX keyword is used in the profile, and it doesn't work in the case of basis set optimization. function UpdateProfile { /bin/ksh -p $inp $* | awk ' BEGIN { str["GEOM"]="ENDG" ; str["BASE"]="ENDBS" str["GEBA"]="ENDBS" } /GEOM/ || /BASE/ || /GEBA/ \ { end=str[$1] getline y x = y while ( getline == 1 ) if ( $1 != "STOP" ) x=x"\n"$0 } END { z = "" w = "" getline < fn while ( $0 !~ y ) { z = z""w""$0 getline < fn w = "\n" } while ( $0 !~ end ) getline < fn getline w < fn while ( getline < fn == 1 ) w = w"\n"$0 print z"\n"x"\n"w > fn } ' fn=$inp istart="" return $? } From chemistry-request@server.ccl.net Mon Jan 15 14:02:55 2001 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FJ2td15074 for ; Mon, 15 Jan 2001 14:02:55 -0500 Received: from CONVERSION-DAEMON by Post-Office.UH.EDU (PMDF V5.2-32 #40812) id <0G7700401WWUVM@Post-Office.UH.EDU> for CHEMISTRY@ccl.net; Mon, 15 Jan 2001 13:02:54 -0600 (CST) Received: from uh.edu (Kroll.BCHS.UH.EDU [129.7.2.217]) by Post-Office.UH.EDU (PMDF V5.2-32 #40812) with ESMTP id <0G7700434WWUQ8@Post-Office.UH.EDU>; Mon, 15 Jan 2001 13:02:54 -0600 (CST) Date: Mon, 15 Jan 2001 13:01:18 -0600 From: Hung-Chung Huang Subject: Re: CCL:stereo view of molecules with ELSA support To: "art'" Cc: CHEMISTRY@ccl.net Message-id: <3A6348FE.4040306@uh.edu> MIME-version: 1.0 Content-type: text/plain; charset=KOI8-R; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; m18) Gecko/20001108 Netscape6/6.0 X-Accept-Language: en,pdf References: <3A5C2E20.24E1DAD7@univ-reims.fr> <3A5F99EB.FE303B05@vaidila.vdu.lt> Hi Art, I have tried the video card (RIVA TNT2 chip; 32 MB) and stereo glasses (3D Revelator; wireless Infra Red version or wired version) successfully to view 3D stereo images in OpenGL modeling programs (e.g., WebLabViewer Lite, and SWISSpdbViewer) in Windows 98 OS. This means "stereo glasses from ELSA can view 3D stereo images in D3D or OpenGL programs"! The only thing you need is installing the GLDirect program from SciTech software (http://www.scitechsoft.com); the demo version I used would be expired, but the real version should cost $19.95 US dollars. I may be the first one to know this kind of cheap solution for 3D stereo viewing in the PC platform! Try it and good luck! Joe -- http://adrik.bchs.uh.edu/~jhuang art' wrote: > Hi CCL'ers, > > Have you know any commercial and free software to view molecules in > stereo with ELSA technology ? > I will summuries the replies. > > Thank you all > Arturas Z. > From chemistry-request@server.ccl.net Mon Jan 15 14:37:03 2001 Received: from rubidium.med.cornell.edu (IDENT:root@rubidium.med.cornell.edu [140.251.122.39]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0FJb3d15149 for ; Mon, 15 Jan 2001 14:37:03 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by rubidium.med.cornell.edu (8.9.3/8.9.3) id OAA31084 for chemistry@ccl.net; Mon, 15 Jan 2001 14:30:55 -0500 From: Simon BERNECHE Reply-To: Simon.Berneche@cornell.edu Organization: Université de Montréal / Weill Cornell Medical College To: chemistry@ccl.net Subject: Re: CCL:babel development / visualizing CHARMM CRD files Date: Mon, 15 Jan 2001 14:15:03 -0500 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <3.0.6.32.20010115182521.00a0dd60@whale.csb.ki.se> In-Reply-To: <3.0.6.32.20010115182521.00a0dd60@whale.csb.ki.se> MIME-Version: 1.0 Message-Id: <0101151430540P.22606@rubidium.med.cornell.edu> Content-Transfer-Encoding: 8bit > >This is an interesting question, because Babel is SUPPOSED to be able to read > >CHARMM files as > >input, yet it doesn't. And since there is no program other than Quanta that > >will allow one to easily > >view CHARMM crd files, it would be nice to be able to convert them to some > >other format, > > In passing, RasMol allows to visualize charmm coordinate files. > There's also DINO ( http://www.bioz.unibas.ch/~xray/dino ) that will read CHARMM coordinate (.crd) and trajectory (.dcd) files. DINO gives high resolution output in TIFF, PNG and PostScript formats or it may also write input files for Raster3D and Povray. Simon ********************************************************************************** Simon BERNECHE -------------- Département de physique - Université de Montréal Biochemistry Department - Weill Medical College of Cornell University eMail: Simon.Berneche@cornell.edu Tel: (212) 746-4237 **********************************************************************************