From chemistry-request@server.ccl.net Mon May 17 06:32:38 1999 Received: from originqf.uib.es (originqf.uib.es [130.206.133.180]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA32599 for ; Mon, 17 May 1999 06:27:31 -0400 Received: from originqf.uib.es (localhost [127.0.0.1]) by originqf.uib.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id DAA07682 for ; Mon, 17 May 1999 03:25:38 -0700 (PDT) Sender: juan@originqf.uib.es Message-ID: <373FEEA1.2D85@originqf.uib.es> Date: Mon, 17 May 1999 03:25:37 -0700 From: Juan Frau Munar X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP27) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: SUMMARY: Animations in Power Point Content-Type: multipart/mixed; boundary="------------19A169D8353C" This is a multi-part message in MIME format. --------------19A169D8353C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -- Juan Frau Munar Universitat Illes Balears Departament de Quimica Palma de Mallorca - 07071 Baleares. Spain email: juan@originqf.uib.es fax: 971 - 173426 telf: 971 - 173254 --------------19A169D8353C Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-ID: <373FEB87.31D2@originqf.uib.es> Date: Mon, 17 May 1999 03:12:23 -0700 From: Juan Frau Munar X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP27) MIME-Version: 1.0 To: dqujfm0@ps.uib.es Subject: SUMMARY: Animations in Power Point Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Juan Frau Munar wrote: Hello everybody, > > This is the list of messages I got about animations in Power Point. > > Thanks everybody. > > The original question was: > > On Monday, May 10, 1999 3:11 AM, Juan Frau Munar > [SMTP:juan@originqf.uib.es] wrote: > > Hello everybody > > > > I would like to have an active molecule in a Power Point?s slide. We > > would like to get the molecule rotating 360o during the presentation. > > It is something similar to the animations we can see on the web (MDL > > format). Any ideas? > > > > Thanks in advance. > > > > Juan Frau > > > > > > Juan Frau Munar > > Universitat Illes Balears > > Departament de Quimica > > Palma de Mallorca - 07071 > > Baleares. Spain > > > > email: juan@originqf.uib.es > > fax: 971 - 173426 > > telf: 971 - 173254 > > > --------------------------------------------------------------- > > > > Subject: Re: CCL:Animations in Power Point > > Date: Tue, 11 May 1999 11:03:34 -0500 (CDT) > > From: HUTCHINSC@RAND.PPRD.Abbott.Com > > Organization: Abbott Laboratories > > To: juan > > > > Juan, > > > > We have just been dealing with the same problem. Our solution: > > 1) use imgsnap or snapshot to get an rgb image from the SG. > > 2) rotate the molecule and repeat. We do 12 images with 5 degrees between > > frames. > > 3) then create an animated GIF file with the 12 going forward then have > > the twelve in reverse order to give a 24 frame rocking motion animated gif > > file. > > > > One way to do this is to use Ulead GIF Animator from www.webutilities.com > > > > 4) Then read the animated GIF into GIF Animator and export a video .avi file. > > This can be inserted into Powerpoint 97. During a slide show the animation > > can start with a mouse click. Use Edit Movie Object for looping. > > > > I hope the direction are clear; this works for us. > > > > Sorry for the bad typing and Good Luck! > > > > Charlie > > > > --------------------------------------------------------------- > > > > Subject: RE: Animations in Power Point > > Date: Tue, 11 May 1999 09:08:55 -0700 > > From: John Wintersteen > > Organization: Molecular Simulations Inc. > > To: "'Juan Frau Munar'" > > > > Dear Juan, > > > > The WebLab Viewer from Molecular Simulations may be just the application > > for you. Because the WebLab Viewer is OLE2 compliant, you can embed a > > molecule object into a document from other desktop applications like Word, > > Excel, and Power Point. Once embedded, double clicking on the object "in > > place" activates it, giving you access to the WebLab Viewer tool bars and > > commands from within the other application, so that you can interactively > > spin, rotate, change rendering, or otherwise manipulate the structure. > > > > Both the WebLab ViewerLite (freeware) and WebLab ViewerPro can be > > downloaded from MSI's web site at the following address: > > http://www.msi.com/viewer > > > > Regards, > > > > John Wintersteen > > Product Manager, WebLab Viewer Products > > Molecular Simulations Inc.. > > 9685 Scranton Road > > San Diego, CA 92121 > > > > > > --------------------------------------------------------------- > > > > Subject: Re: CCL:Animations in Power Point > > Date: Tue, 11 May 1999 11:19:54 -0500 > > From: Abby Parrill > > Organization: University of Memphis > > To: Juan Frau Munar > > References: <3736B0C3.167E@originqf.uib.es> > > > > Juan, > > > > You will have to record an animation in a format that can be inserted > > into PowerPoint (on a Mac that format is QuickTime, not so sure about > > PC's). The Ball&Stick program will record animations in QuickTime > > format. > > > > Regards, > > Abby > > > > > > _____________________________________________ > > > > Abby L. Parrill (901)678-2638 > > Assistant Professor (901)678-3447 > > Department of Chemistry > > University of Memphis > > Memphis, TN 38152 aparrill@memphis.edu > > > > Computational Research on Materials Institute > > at The University of Memphis (CROMIUM) > > _____________________________________________ > > > > > > --------------------------------------------------------------- > > > > Subject: Re: CCL:Animations in Power Point > > Date: Tue, 11 May 1999 09:39:51 -0700 > > From: "Jeffrey L. Nauss" > > To: Juan Frau Munar > > > > > > WebLab Viewer from MSI > > (http://www.msi.com/solutions/products/weblab/viewer/index.html) can allow > > interactive molecular graphics to be included into PowerPoint presentations. > > > > -- > > Jeffrey L. Nauss, PhD Phone: (619) 799-5555 > > Product Specialist, Simulations Fax: (619) 458-0136 > > Molecular Simulations Inc. E-mail: jnauss@msi.com > > 9685 Scranton Road > > San Diego, CA 92121 > > > > --------------------------------------------------------------- > > > > Subject: Re: CCL:Animations in Power Point > > Date: Tue, 11 May 1999 20:25:33 +0200 > > From: Jordi Villa > > To: Juan Frau Munar > > References: <3736B0C3.167E@originqf.uib.es> > > > > Once you get the frames for the movie you can combine them with the > > GIFCON program in a single movie. This might work. I am sorry I do not > > have any web address for GIFCON. > > > > Jordi > > > > > > -- > > Jordi Vill`a > > Research Group on Medical Informatics > > Carrer del Doctor Aiguader 80 > > E-08003 Barcelona > > Tlf: 34-93-2211009 Fax: 34-93-2213237 > > jvilla@imim.es http://www1.imim.es/~jvilla > > > --------------------------------------------------------------- > > Subject: Re: CCL:Animations in Power Point > Date: Tue, 11 May 1999 11:37:33 -0700 (PDT) > From: Roy Jensen > To: Juan Frau Munar > > Juan > > PowerPoint can present videos in AVI format. > > Does the program you use to visualize the molecule have the capability of > making videos in AVI or MPEG format? There are several conversion > utilities on the 'net if only MPEG. Microsoft Camcorder (distributed with > Office 97) can record off the screen to make a video that can be > subsequently edited. [This information obtained from the PowerPoint help > menu.] > > Roy Jensen > > --------------------------------------------------------------- > > Subject: CCL:Animations in Power Point > Date: Tue, 11 May 1999 12:20:20 -0700 (PDT) > From: Eugene Leitl > To: Juan Frau Munar > References: <3736B0C3.167E@originqf.uib.es> > > Instead of kludging yourself around a proprietary format, why not > using mpg? > > Regards, > Eugene Leitl > > --------------------------------------------------------------- > > Subject: Re: CCL:Animations in Power Point > Date: Wed, 12 May 1999 09:48:48 +0900 > From: Kazuo Teraishi > To: Juan Frau Munar > References: <3736B0C3.167E@originqf.uib.es> > > Hello Juan > > I have done exactly what you want using Chem3D on Macintosh. > Chem3D can rotate the molecule 360 deg. with a given angle step > (you can change the smoothness by changing the step size). > Then you can save it as a QuickTime movie. Then insert the movie > on your PowerPoint slide. You can initiate the animation either opening > that page or clicking once on the page depending on your favor. > > -- > Kazuo Teraishi; Dr. > Nippon Zeon Co. Ltd. > > --------------------------------------------------------------- > > Subject: Re: CCL:Animations in Power Point > Date: Wed, 12 May 1999 12:15:57 +1000 > From: "Kieran F Lim (Lim Pak Kwan)" > To: Juan Frau Munar > > Juan Frau > > I create such animations using Chem3D (from Cambridge Soft, the folk > who also make ChemDraw) and then save the animation as a Quicktime movie. > this can be inserted into PowerPoint using > insert --> movies > > unfortunately the Office 97 version of PowerPoint (for PC's) does NOT > support Quicktime so this will only work for Office 95 (and earlier) > or on Macintoshes (all versions including Office 98). > > Kieran > ------------------------------------------------------------ > Dr Kieran F Lim Biol. and Chemical Sciences > (Lim Pak Kwan) Deakin University > ph: + [61] (3) 5227-2146 Geelong VIC 3217 > fax: + [61] (3) 5227-1040 AUSTRALIA > mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim > > --------------------------------------------------------------- > > Subject: CCL:Animations in Power Point > Date: Wed, 12 May 1999 07:52:08 +0300 > From: Jan Dillen > Organization: University of Stellenbosch > To: Juan Frau Munar > CC: CHEMISTRY@ccl.net > References: <3736B0C3.167E@originqf.uib.es> > > > > Try MSI's WebLab Viewer (http://www.msi.com). > > Greetings > > Jan Dillen. > > --------------------------------------------------------------- > > Subject: Re: CCL:Animations in Power Point > Date: Wed, 12 May 1999 09:21:44 +0100 > From: Mark Forster > Organization: NIBSC > To: Juan Frau Munar > References: <3736B0C3.167E@originqf.uib.es> > > Dear Juan > > If it has to be powerpoint then try the free Weblab ViewerLite from MSI > at the web site http://www.msi.com/download/index.html This allows OLE > to be used to embed a molecule into a Word/Powerpoint/Excel document. > > For a non Microsoft specific solution used an animated GIF in a web page. > > Hope this helps. > > Mark > > -- > > 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 +44 (0)1707 654753 > FAX +44 (0)1707 646730 > E-mail mforster@nibsc.ac.uk > > --------------------------------------------------------------- > > Subject: Re: CCL:Animations in Power Point > Date: Wed, 12 May 1999 14:28:10 -0500 > From: Amit Kulkarni > To: Jan Dillen , Juan Frau Munar > CC: CHEMISTRY@ccl.net > References: <3736B0C3.167E@originqf.uib.es> > > How do you import the moving object from weblab viewer to powerpoint? > > > --------------------------------------------------------------- > > Subject: CCL:Animations in Power Point > Date: Thu, 13 May 1999 09:13:41 +0300 > From: Jan Dillen > Organization: University of Stellenbosch > To: CHEMISTRY@ccl.net > CC: Amit Kulkarni > References: <3736B0C3.167E@originqf.uib.es> <199905121931.OAA29161@email1.cc.uic.edu> > > Amit Kulkarni wrote: > > > > How do you import the moving object from weblab viewer to powerpoint? > > > > 1. I am using the "ViewerPro" version. You pay for it, but I find > it a good investment. My understanding is that the > difference with the free "ViewerLite" version is that the latter > does not have the capability to sketch & build molecules. > 2. Load (or build) the molecule in WebLab > 3. Select it > 4. Edit:Copy > 5. Go to Powerpoint > 6. Edit:Paste Special. This inserts an OLE object. > 7. Selecting the OLE object activates WebLab in the background. You > can now rotate, zoom, translate and even sketch (at least with > ViewerPro). > > Jan. > --------------------------------------------------------------- > > Subject: CCL:Animations in Power Point > Date: Thu, 13 May 1999 11:18:10 +0300 > From: Jan Dillen > Organization: University of Stellenbosch > To: Amit Kulkarni > CC: CHEMISTRY@ccl.net > References: <3736B0C3.167E@originqf.uib.es> <199905121931.OAA29161@email1.cc.uic.edu> > > Amit Kulkarni wrote: > > > > How do you import the moving object from weblab viewer to powerpoint? > > > > As an afterthought I should add that my copy & paste solution may > give you too much of an "active" molecule. > > I you only want a rotating molecule without any need for additional > manipulation, then an animated GIF should do the trick. I have > used WWW Gif Animator 1.1 in the past, and it works well. > > Jan. -- -- Juan Frau Munar Universitat Illes Balears Departament de Quimica Palma de Mallorca - 07071 Baleares. Spain email: juan@originqf.uib.es fax: 971 - 173426 telf: 971 - 173254 --------------19A169D8353C-- From chemistry-request@server.ccl.net Mon May 17 07:34:24 1999 Received: from camdedu9.soongsil.ac.kr (camdedu9.soongsil.ac.kr [203.253.24.214]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA00527 for ; Mon, 17 May 1999 07:34:22 -0400 Received: (from kyn@localhost) by camdedu9.soongsil.ac.kr (950413.SGI.8.6.12/950213.SGI.AUTOCF) id PAA05680 for CHEMISTRY@ccl.net; Mon, 17 May 1999 15:31:51 -0700 Date: Mon, 17 May 1999 15:31:51 -0700 From: kyn@camdedu9.soongsil.ac.kr (Ky-Youb Nam) Message-Id: <199905172231.PAA05680@camdedu9.soongsil.ac.kr> To: CHEMISTRY@ccl.net Subject: Cavitation free energy Dear CCLers, Recently, I calculated relative hydration free energy by molecular dynamics. The relative hydration free energy was corrected by cavitation free energy. I don't know it is right. The relative hydration free energy = d(total energy) + d(cavitation energy) I think the term of caviation energy is included in explicity NPT simulation. I want to know " Is the term of caviation energy included in MD simulation?" or must include the term of caviation energy for correcting hydration free energy. Thank you for your kind attention. Yours sincerely, Ky-Youb Nam From chemistry-request@server.ccl.net Mon May 17 14:49:26 1999 Received: from lauca.usach.cl (root@lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA04989 for ; Mon, 17 May 1999 14:49:22 -0400 Received: from anonimo.usach.cl ([158.170.64.232]) by lauca.usach.cl (8.9.3/8.9.2) with SMTP id OAA12062 for ; Mon, 17 May 1999 14:45:12 -0400 (CST) Message-Id: <1.5.4.32.19990517184821.006a0740@lauca.usach.cl> X-Sender: gcardena@lauca.usach.cl X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 17 May 1999 14:48:21 -0400 To: chemistry@ccl.net From: "Dr. Gloria I. Cardenas-Jiron" Subject: Summary Correlation Electronic Thank you very much to all who replied. The question was: Are there some way to fix the spin in MP or DFT calculations using for example the ROHF command? Answers: 1.- You are correctly concerned about UHF. It is possible to project the UHF wavefunction to get rid of contamination by higher multiplicities, but this changes the wavefunction, and is something I would not recommend. Although Gaussian does not do UHF/MP2 calculations, there are other software packages that do. I would suggest that you investigate these. Good luck. Janet Del Bene 2.- the syntax is ROB3LYP / UB3LYP for example in case of the B3LYP functional. Omitting of RO / U defaults to the unrestricted wavefunction. Cheers, Dominik 3.- Just say ROMP2 or ROB3LYP. Artem 4.- Try ROMP2 or ROBLYP or whatever the functional you want preceded by "RO" Kazuo Teraishi; Dr. Nippon Zeon Co. Ltd. 5.- From: lorentzian.com!csd@lorentzian.com (Cust. Service Doug) Gloria, Gaussian 98 does not implement traditional correlation methods for ROHF references with the exception of ROMP2 energies. There are certainly approaches for doing this but the theory is subtantially more complicated. We have plans for development of the Brueckner Doubles method which does a very good job of removing spin contamination in UHF reference wavefunctions but this will not be available until a future major release of Gaussian. DFT methods can be done with RO- constraints. In place of U you can specify RO to get methods like ROB3LYP for open shell solutions. For most pure DFT functionals, i.e. BLYP or BPW91, spin contamination is small and application of HF style methods to remove it cause more problems than they solve. The hybrid style functionals, B3LYP, do inherit contamination from the the HF exchange contribution. With G98 the method which does best at correcting spin contamination is QCISD and adds the option of gradients. CCSD and the triples corrections are good for cases where you can get by with just energies. 6.- Hola Gloria, La mejor forma de tratar el problema de la correlacion electronica cuando uno tiene metales de transicion es usar una funcion CASSCF como punto de partida. La contaminacion de spin que tiene en una funcion UHF (RHF o DFT) no la puedes eliminar completamente (se puede proyectar el primer contaminante, pero siempre queda bastante) y ademas, se amplifica por el MP2. Un RHOF/MP2 puede no tener contaminacion de spin, pero tu funcion de onda de partida puede participar con un 80% o menos en la expansion MP2, lo que provoca grandes fluctuaciones en la estimacion de la energia de correlacion electronica y grandes errores en propiedades como energias de reaccion, geometrias, frecuencias de vibracion, ... todo lo que dependa de tener siempre la misma cantidad de energia de correlacion incorporada en tu expansion MP2. Volviendo al principio, si tu problema es de metales de transicion (y sobre todo con capas abiertas) usa una funcion CASSCF, al menos. Si tienes alguna duda escribe, intentare contestar pronto. Saludos, Antonio Marquez 7.- Hi Gloria, Gamess (http://www.msg.ameslab.gov/GAMESS/GAMESS.html) does do MP2 on a ROHF wavefunction. I used it, it works great. Greetings, Gert 8.- Hie, You could use ROMP2. It is based on a restricted wave function. Cheers, Theis Soelling 9.- Hola Gloria, Respecto a spin-contamination es un problema mayor ya que los tratamientos UHF siempre sobreestiman el spin. En el caso relativista (Dirac) para open-shell systems este no es problema. Debes recordar que spin esta definido solamente en la Teoria de Dirac y no en la de Schrodinger. Saludos cordiales, Ramiro Arratia Perez, Ph.D. Dr. Gloria I. Cardenas-Jiron Facultad de Quimica y Biologia, Universidad de Santiago de Chile, Santiago, CHILE. From chemistry-request@server.ccl.net Tue May 18 01:21:11 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA11255 for ; Tue, 18 May 1999 01:21:06 -0400 Received: from voxopm-e.csc.fi (voxopm-e.csc.fi [128.214.46.23]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with ESMTP id IAA19891 for ; Tue, 18 May 1999 08:16:36 +0300 (EET DST) Date: Tue, 18 May 1999 08:16:36 +0300 From: Maija Lahtela X-Sender: mlahtela@voxopm.minedu.fi To: chemistry@ccl.net Subject: Free softwares for modelling loop of protein Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am interested in modelling a loop of protein. I have generated different conformations for a loop in a known protein using commercial software (Insight). However, I would like to generate a loop with free academic software. I would appreciate your help in my problem. Yours sincerely, Maija Lahtela-Kakkonen *************************************** Maija Lahtela-Kakkonen Researcher CSC-Center for Scientific Computing Tekniikantie 15 a D P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 FAX 358-9-4572302 E-MAIL mlahtela@csc.fi *************************************** From chemistry-request@server.ccl.net Tue May 18 10:33:29 1999 Received: from pp3.shef.ac.uk (pp3.shef.ac.uk [143.167.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA16555 for ; Tue, 18 May 1999 10:33:26 -0400 From: d.turner@sheffield.ac.uk Received: from pc100182.shef.ac.uk ([143.167.100.182] helo=davets_pc) by pp3.shef.ac.uk with smtp (Exim 2.02 #2) id 10jkrO-0007Ac-00 for chemistry@server.ccl.net; Tue, 18 May 1999 15:28:47 +0100 To: chemistry@server.ccl.net Date: Tue, 18 May 1999 15:28:59 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: SOMFA (sic) and CoMFA 3D-QSAR Priority: normal In-reply-to: <373FEEA1.2D85@originqf.uib.es> X-mailer: Pegasus Mail for Win32 (v3.01a) Message-Id: Hello Has anyone looked at SOMFA from Graham Richards group? (JMedChem,1999,42,573-583). It appears to me that the "new" method described is equivalent to extracting the first PLS latent variable (LV) and no more; ie SOMFA r2 = COMFA PLS LV_1 r2 (for identical fields, resolution and other set up parameters). If I am right then the method is surely limited since many 3D-QSAR models use >one LV?! Can anyone confirm (or deny) my opinion? David Turner Dr David Turner Dept of Information Studies, Sheffield University Sheffield, S10 2TN Tel. 0114 2 222 650 E-mail: D.Turner@sheffield.ac.uk From chemistry-request@server.ccl.net Tue May 18 13:00:46 1999 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA18487 for ; Tue, 18 May 1999 13:00:46 -0400 Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (950413.SGI.8.6.12/8.6.6) with SMTP id MAA02966; Tue, 18 May 1999 12:56:11 -0400 Message-Id: <199905181656.MAA02966@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: Host localhost didn't use HELO protocol Reply-to: bernhold@npac.syr.edu To: chemistry@ccl.net cc: bernhold@npac.syr.edu Subject: XML as program output? MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <2962.927046570.1@snake.npac.syr.edu> Date: Tue, 18 May 1999 12:56:10 -0400 From: "David E. Bernholdt" I'm curious what people think about using XML for the output of chemistry programs? I'd appreciate your response to the scenarios I present below. Lets imagine its a year or two into the future, and you have an XML-capable browser that's as loaded with features as your current HTML browser. You run a chemistry code -- say an SCF calculation, to be concrete. Would you prefer that the primary output of this program be in plain text, as nearly all packages I'm familiar with now produce, or would you prefer it to be thoroughly marked-up XML? The plain text version may be more compact if you page through it using more, or look at it in a text editor, but if you take the XML version, you have all the capabilities of the browser to help you. You could apply different style sheets to highlight different parts of the output. By judicious use of styles & applets, you might even be able to have the molecular geometry rendered with a 3-d viewer, or visualize orbitals, etc. Do the increased presentational possibilities made possible by using XML offset the additional complexity/length of the output file and the need to have an XML browser to view it properly? Now consider the fact that you could also use commodity XML tools to parse the output file & extract specific items for further processing -- perhaps to be stored into a database, a spreadsheet, etc. Does this make XML worthwhile as the primary output format of a chemistry package? How about if the XML conformed to a standardized schema that was used by _all_ SCF programs, so that they all marked up their output the same way? How about if all electronic structure programs conformed to the same schema? Or the unlikely possibility that there was a schema which encompassed "all" chemistry software? What would it take, in your opinion, for XML-based output to be preferrable to the current-day plain text output? Thanks for your thoughts. -- 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 chemistry-request@server.ccl.net Tue May 18 13:59:00 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA19356 for ; Tue, 18 May 1999 13:59:00 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id LAA29564; Tue, 18 May 1999 11:56:18 -0500 Date: Tue, 18 May 1999 11:56:11 +36000 From: Richard Wood To: "David E. Bernholdt" cc: chemistry@ccl.net, bernhold@npac.syr.edu Subject: Re: CCL:XML as program output? In-Reply-To: <199905181656.MAA02966@snake.npac.syr.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I think text is preferable to any other format, IMO, now or in the future. If one needs xml or another format, one can just add the appropriate tags as needed. On Tue, 18 May 1999, David E. Bernholdt wrote: > I'm curious what people think about using XML for the output of > chemistry programs? I'd appreciate your response to the scenarios I > present below. > > Lets imagine its a year or two into the future, and you have an > XML-capable browser that's as loaded with features as your current > HTML browser. > > You run a chemistry code -- say an SCF calculation, to be concrete. > Would you prefer that the primary output of this program be in plain > text, as nearly all packages I'm familiar with now produce, or would > you prefer it to be thoroughly marked-up XML? > > The plain text version may be more compact if you page through it > using more, or look at it in a text editor, but if you take the XML > version, you have all the capabilities of the browser to help you. > You could apply different style sheets to highlight different parts of > the output. By judicious use of styles & applets, you might even be > able to have the molecular geometry rendered with a 3-d viewer, or > visualize orbitals, etc. > > Do the increased presentational possibilities made possible by using > XML offset the additional complexity/length of the output file and the > need to have an XML browser to view it properly? > > Now consider the fact that you could also use commodity XML tools to > parse the output file & extract specific items for further processing > -- perhaps to be stored into a database, a spreadsheet, etc. > > Does this make XML worthwhile as the primary output format of a > chemistry package? > > How about if the XML conformed to a standardized schema that was used > by _all_ SCF programs, so that they all marked up their output the > same way? How about if all electronic structure programs conformed to > the same schema? Or the unlikely possibility that there was a schema > which encompassed "all" chemistry software? > > What would it take, in your opinion, for XML-based output to be > preferrable to the current-day plain text output? > > Thanks for your thoughts. > -- > 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 > -= 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 Tue May 18 15:26:16 1999 Received: from mordor.ai.private (fw.apollo-imaging.com [195.26.208.226]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20662 for ; Tue, 18 May 1999 15:26:14 -0400 Received: from vienna.at (gl@bombadil.ai.private [10.33.246.70]) by mordor.ai.private (8.9.2/8.9.2/Debian/GNU) with ESMTP id WAA04139; Tue, 18 May 1999 22:27:45 +0200 (CEST) Sender: gl@apollo-imaging.com Message-ID: <3741BD3D.DE6C9613@vienna.at> Date: Tue, 18 May 1999 21:19:25 +0200 From: Gerald Loeffler Organization: Apollo Imaging X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry Mailing List CC: "David E. Bernholdt" Subject: Re: CCL:XML as program output? References: <199905181656.MAA02966@snake.npac.syr.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi chemistry-XMLers ! David presents an excellent example, although, IMHO his phrasing is misleading. The _real_ question is whether to go for XML-conformant text-output or for unstructured/arbitrarily structured text-output of chemistry programs. Because XML code _is_ text, i.e. by simply using a plain text editor XML code is as readable and understandable by humans as any other text-output can be. It is only for visually pleasing presentation that you need a helper-application such as a XML-capable web-browser! The _real_ advantage of XML over arbitrarily structured text-output is the fact that XML is easily parseable and, what's more, the meta-information on how to legally form a specific class of XML-documents (e.g. the SCF-output of a Gaussian-run) is standardized and easily parseable as well. These advantages don't even require a commonly agreed-upon format for equivalent information. I.e. Gaussian and its competitors might (and probably will (-: ) output SCF-results as XML-documents of a different type. The interconversion, however, is much more straightforward than now, because 1) the parsing-problem does not exist and 2) there is a strict definition of how the different formats may look like. just my $0.02, gerald "David E. Bernholdt" wrote: > > I'm curious what people think about using XML for the output of > chemistry programs? I'd appreciate your response to the scenarios I > present below. > > Lets imagine its a year or two into the future, and you have an > XML-capable browser that's as loaded with features as your current > HTML browser. > > You run a chemistry code -- say an SCF calculation, to be concrete. > Would you prefer that the primary output of this program be in plain > text, as nearly all packages I'm familiar with now produce, or would > you prefer it to be thoroughly marked-up XML? > > The plain text version may be more compact if you page through it > using more, or look at it in a text editor, but if you take the XML > version, you have all the capabilities of the browser to help you. > You could apply different style sheets to highlight different parts of > the output. By judicious use of styles & applets, you might even be > able to have the molecular geometry rendered with a 3-d viewer, or > visualize orbitals, etc. > > Do the increased presentational possibilities made possible by using > XML offset the additional complexity/length of the output file and the > need to have an XML browser to view it properly? > > Now consider the fact that you could also use commodity XML tools to > parse the output file & extract specific items for further processing > -- perhaps to be stored into a database, a spreadsheet, etc. > > Does this make XML worthwhile as the primary output format of a > chemistry package? > > How about if the XML conformed to a standardized schema that was used > by _all_ SCF programs, so that they all marked up their output the > same way? How about if all electronic structure programs conformed to > the same schema? Or the unlikely possibility that there was a schema > which encompassed "all" chemistry software? > > What would it take, in your opinion, for XML-based output to be > preferrable to the current-day plain text output? > > Thanks for your thoughts. > -- > 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 > -= 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 -- Gerald Loeffler Email: Gerald.Loeffler@vienna.at Smail: Apollo Imaging, Marchettigasse 7, A-1060 Vienna, Austria Phone: +43 676 3289588 (+43 1 5952333 27) Fax: +43 1 5952333 20 Keywords: Java, CORBA, OOA&D, Databases, Bioinformatics, Computational Biology, Computational Biophysics From chemistry-request@server.ccl.net Tue May 18 15:31:07 1999 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20767 for ; Tue, 18 May 1999 15:31:06 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA10518; Tue, 18 May 1999 21:20:38 +0200 Received: from werkman.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA27325; Tue, 18 May 1999 21:26:25 +0200 Date: Tue, 18 May 1999 21:25:58 +0200 (MEST) From: David van der Spoel X-Sender: spoel@werkman.bmc.uu.se To: Richard Wood Cc: "David E. Bernholdt" , chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 18 May 1999, Richard Wood wrote: >I think text is preferable to any other format, IMO, now or in the future. >If one needs xml or another format, one can just add the appropriate tags >as needed. > Text files are usually good for experts, they can interpret output files by reading them. Moreover you can easily post-process text files using small programs or scripts in any language you like. However there is very often reason to visualize results, since in many cases it will give more understanding, but also because some things are hard to grasp from a text file. I prefer to look at a molecule, however small, using rasmol rather than look at the coordinates. When checking the geometry generated using whatever, it is much easier to look at a printed list of bond length and angles than clicking on the atoms in a GUI. Thus I think we want the text files as well as something else, and that something else could well be XML (I don't know it). To have any chance at all to be accepted as "standard" I think the following demands have to be met: - Chemistry/XML format should be non proprietary, i.e. it may not be crippled by browser vendors (like HTML). Ideally the format should be controlled by chemists - There should be a free (GPL'ed) library which programmers can use to write xml output (callable from at least C and fortran, meaning that it should *not* be a C++ library). - There need to be fast portable browsers Looking on the web I found the SGML/XML home page at http://www.oasis-open.org/cover/sgml-xml.html 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 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Tue May 18 15:35:07 1999 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA20876 for ; Tue, 18 May 1999 15:35:07 -0400 Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (950413.SGI.8.6.12/8.6.6) with SMTP id PAA03428; Tue, 18 May 1999 15:30:30 -0400 Message-Id: <199905181930.PAA03428@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: Host localhost didn't use HELO protocol To: chemistry@ccl.net cc: bernhold@npac.syr.edu Subject: Re: CCL:XML as program output? X-followup-to: My message of Tue, 18 May 1999 12:56:10 -0400. <199905181656.MAA02966@snake.npac.syr.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <3425.927055830.1@snake.npac.syr.edu> Date: Tue, 18 May 1999 15:30:30 -0400 From: "David E. Bernholdt" On Tue, 18 May 1999 12:56:10 -0400 I wrote: < I'm curious what people think about using XML for the output of < chemistry programs? I'd appreciate your response to the scenarios I < present below. I realize that I should clarify a little what I meant by XML markup of output. My purpose here is not simply to pretty-print program output -- I envision marking up the actual information content so that it can be unambiguously identified, extracted, and otherwise processed. For example, energies might be marked up as: 101.8303753234 -190.784836075 MO vectors might be marked up like this: -20.65958 ... Molecular structures might be reported using CML's (Chemical Markup Language) construct, dipole moments could be marked up as an array of values. I don't claim that the actual product would look anything like my off the cuff examples here, but the main point is that the markup is not "make this boldface and blue, and that in italics", it actually describes the information content of the document for us. With an appropriate stylesheet, one could arrange that XML-based output look "pretty" in the browser, invoke a 3d viewer for molecular structures, MOs, etc. But more importantly, in my opinion, it now becomes possible to use standard tools for manipulating XML documents to access the information stored within the output file. Right now, this kind of thing can only be done by if you know the output format of a program intimately, and can depend on it not to change with a new release, or on another platform, etc. -- 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 chemistry-request@server.ccl.net Tue May 18 15:52:23 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA21080 for ; Tue, 18 May 1999 15:52:22 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id NAA00088; Tue, 18 May 1999 13:48:25 -0500 Date: Tue, 18 May 1999 13:48:18 +36000 From: Richard Wood To: David van der Spoel cc: "David E. Bernholdt" , chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII But rasmol reads a "text" file format! Why change it and other programs that already read text files? That doesn't make any sense to me. Richard From chemistry-request@server.ccl.net Tue May 18 11:32:28 1999 Received: from outland.cyberwar.com (root@outland.cyberwar.com [206.88.128.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA17521 for ; Tue, 18 May 1999 11:32:27 -0400 Received: from cyberwar.com (ppp04-04.cyberwar.com [206.88.129.89]) by outland.cyberwar.com (8.9.3/8.9.3) with ESMTP id LAA10767 for ; Tue, 18 May 1999 11:27:52 -0400 (EDT) Sender: nathan@cyberwar.com Message-ID: <37418849.BAB9199@cyberwar.com> Date: Tue, 18 May 1999 11:33:29 -0400 From: Nathan Stevens X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: ChemConsole Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have just posted version 0.1 of a Java based Program called ChemConsole, which provides a GUI to legacy Chemistry Applications such as Babel v-1.6 and Mopac. Future versions will add support for Gaussian and give users the ability to run those Applications remotely. You can get the program and Source code at: ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/JAVA/ChemConsole Nathan Stevens From chemistry-request@server.ccl.net Tue May 18 12:35:23 1999 Received: from originqf.uib.es (originqf.uib.es [130.206.133.180]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA18123 for ; Tue, 18 May 1999 12:22:31 -0400 Received: from originqf.uib.es (localhost [127.0.0.1]) by originqf.uib.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id JAA09393 for ; Tue, 18 May 1999 09:22:10 -0700 (PDT) Sender: juan@originqf.uib.es Message-ID: <374193B1.41C6@originqf.uib.es> Date: Tue, 18 May 1999 09:22:09 -0700 From: Juan Frau Munar X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP27) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: [Fwd: Re: CCL:Animations in Power Point] Content-Type: multipart/mixed; boundary="------------167E2781446B" This is a multi-part message in MIME format. --------------167E2781446B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello everybody, When I was summarizing all the answers about animations in Power Point, unfortunately I forgot one of them. Therefore, this file should be inserted in the previous e-mail. -- Juan Frau Munar Universitat Illes Balears Departament de Quimica Palma de Mallorca - 07071 Baleares. Spain email: juan@originqf.uib.es fax: 971 - 173426 telf: 971 - 173254 --------------167E2781446B Content-Type: message/rfc822 Content-Transfer-Encoding: 8bit Content-Disposition: inline Received: from NPD1.NPD.UFPE.BR ([150.161.6.2]) by originqf.uib.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA03722 for ; Thu, 13 May 1999 09:09:22 -0700 (PDT) Received: from npd.ufpe.br (Rlongo2.DQF.UFPE.BR) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01JB5ADDCNWG0002EZ@NPD.UFPE.BR> for juan@originqf.uib.es; Thu, 13 May 1999 11:09:17 GMT-3 Date: Tue, 13 Apr 1999 11:03:00 -0300 From: Gustavo Seabra Subject: Re: CCL:Animations in Power Point To: Juan Frau Munar Message-id: <37134E93.AF62607A@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (Win98; I) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8bit X-Accept-Language: en References: <3736B0C3.167E@originqf.uib.es> Some time go I have a similar problem: I had to animate a MD trajectory in PowerPoint97. But, unfortunately, it is not that easy. PowerPoint does not read animated gifs, the format used in most web animations. So, you have 3 possibilities: (1) use the animations capability of PowerPoint making a number of images of your molecule (in the various degrees of rotation) and then making the images appear one after another, giving the movement impression. The bad part is that PowerPoint uses intervals of integer multiples of 1 second between the frames, so it may become too slow for you. (2) another possibility is to make a movie. The freeware program Gif Construction Set 32, (I do not have the address right now) is able to make animated gifs and change them into movies. The movie format is readable in PowerPoint, but now your problem will be to put a background in the image. This is the option I've chosen, and it had a good effect in the audience. (I just used a black background color.) (3) The last possibility is to wait for the PowerPoint 2000. There are rumours that it'll be able to show animated gifs. I hope this can be of some help. Best regards, Gustavo Seabra. ---------------------------------------------------- Gustavo de Miranda Seabra seabra@npd.ufpe.br Departamento de Quimica Fundamental Universidade Federal de Pernambuco Recife - Pernambuco - Brasil ---------------------------------------------------- Juan Frau Munar wrote: > Hello everybody > > I would like to have an active molecule in a Power Point´s slide. We > would like to get the molecule rotating 360º during the presentation. > It is something similar to the animations we can see on the web (MDL > format). Any ideas? > > Thanks in advance. > > Juan Frau > > -- > > Juan Frau Munar > Universitat Illes Balears > Departament de Quimica > Palma de Mallorca - 07071 > Baleares. Spain > > email: juan@originqf.uib.es > fax: 971 - 173426 > telf: 971 - 173254 > -= 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 --------------167E2781446B-- From chemistry-request@server.ccl.net Tue May 18 15:39:39 1999 Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20951 for ; Tue, 18 May 1999 15:39:36 -0400 Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id VAA03884; Tue, 18 May 1999 21:35:21 +0200 (MET DST) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id TAA03894; Tue, 18 May 1999 19:35:21 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9905182135.ZM3892@torvs.ccc.uni-erlangen.de> Date: Tue, 18 May 1999 21:35:21 -0600 In-Reply-To: Richard Wood "CCL:XML as program output?" (May 18, 11:56) References: Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Richard Wood Subject: Re: CCL:XML as program output? Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On May 18, 11:56, Richard Wood wrote: > Subject: CCL:XML as program output? > I think text is preferable to any other format, IMO, now or in the future. > If one needs xml or another format, one can just add the appropriate tags > as needed. I strongly disagree with this view!!!! It is always easy to strip off tags by a simple procedure, but the automatic addition of tags is often not possible, and manual addition tedious and impractical. >From the standpoint of chemical information processing, there are probably no worse output formats than those written by many QM packages. Anybody who had to adjust scripts which extract some value from these text dumps time after time after a new program version was released, or after some yet unencountered condition led to ever so subtle reformatting of the output, will agree. Output should always be designed to be readable by other programs, and this requires a clearly defined structure. It should be possible to identify the meaning of every piece of output, without human guessing. This is what the tags are primarily for: Not for formatting, but for content description. Many of the standard exchange formats, designed decades ago, such as MDL Molfiles or PDB files, are atrocious with respect to clean design, avoidance of unnecessary limitations and general expressiveness, but they are still far superior to what programs such as Gaussian throw at us. XML is definitely the way to go, because of its general-purpose, flexible design and widespread support (next browser generation, next MS Office generation, plus lots of free tools are available already, for example from IBM alphaworks). By the way, this is not the first time XML has been proposed as chemistry exchange format. Pioneering work was carried out by by Peter Murray-Rust and H. Rzepa on this field. Have a look at www.xml-cml.org for the present status. A first definition of a chemical DTD (document type definition) (CML - Chemical Markup Language) is available, and also an experimental Java Browser for these files. > > On Tue, 18 May 1999, David E. Bernholdt wrote: > > > I'm curious what people think about using XML for the output of > > chemistry programs? I'd appreciate your response to the scenarios I > > present below. > > > > Lets imagine its a year or two into the future, and you have an > > XML-capable browser that's as loaded with features as your current > > HTML browser. > > > > You run a chemistry code -- say an SCF calculation, to be concrete. > > Would you prefer that the primary output of this program be in plain > > text, as nearly all packages I'm familiar with now produce, or would > > you prefer it to be thoroughly marked-up XML? > > > > The plain text version may be more compact if you page through it > > using more, or look at it in a text editor, but if you take the XML > > version, you have all the capabilities of the browser to help you. > > You could apply different style sheets to highlight different parts of > > the output. By judicious use of styles & applets, you might even be > > able to have the molecular geometry rendered with a 3-d viewer, or > > visualize orbitals, etc. > > > > Do the increased presentational possibilities made possible by using > > XML offset the additional complexity/length of the output file and the > > need to have an XML browser to view it properly? > > > > Now consider the fact that you could also use commodity XML tools to > > parse the output file & extract specific items for further processing > > -- perhaps to be stored into a database, a spreadsheet, etc. > > > > Does this make XML worthwhile as the primary output format of a > > chemistry package? > > > > How about if the XML conformed to a standardized schema that was used > > by _all_ SCF programs, so that they all marked up their output the > > same way? How about if all electronic structure programs conformed to > > the same schema? Or the unlikely possibility that there was a schema > > which encompassed "all" chemistry software? > > > > What would it take, in your opinion, for XML-based output to be > > preferrable to the current-day plain text output? > > -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From chemistry-request@server.ccl.net Tue May 18 15:50:44 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA21065 for ; Tue, 18 May 1999 15:50:44 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id NAA29933; Tue, 18 May 1999 13:46:50 -0500 Date: Tue, 18 May 1999 13:46:37 +36000 From: Richard Wood To: Wolf-Dietrich Ihlenfeldt cc: chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: <9905182135.ZM3892@torvs.ccc.uni-erlangen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 18 May 1999, Wolf-Dietrich Ihlenfeldt wrote: > On May 18, 11:56, Richard Wood wrote: > > Subject: CCL:XML as program output? > > I think text is preferable to any other format, IMO, now or in the future. > > If one needs xml or another format, one can just add the appropriate tags > > as needed. > > I strongly disagree with this view!!!! > > It is always easy to > strip off tags by a simple procedure, but the automatic addition of tags > is often not possible, and manual addition tedious and impractical. i think it's just as easy to ADD tags as it is to remove them. text files have the advantage in that they can EASILY be imported into most other applications. Also, to change the output formats of dozens of programs to a format that is not very widely used, especially considering that not everyone is using the same OS and same versions of programs, is daft. Richard From chemistry-request@server.ccl.net Tue May 18 16:08:16 1999 Received: from euch4e.chem.emory.edu (euch4e.chem.emory.edu [170.140.59.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA21271 for ; Tue, 18 May 1999 16:08:16 -0400 Received: (from dima@localhost) by euch4e.chem.emory.edu (AIX4.2/UCB 8.7/8.7) id QAA32996; Tue, 18 May 1999 16:01:15 -0400 (EDT) From: Dmitry Khoroshun Message-Id: <199905182001.QAA32996@euch4e.chem.emory.edu> Subject: Re: CCL:XML as program output? To: dmpc@hugh.chem.uic.edu (Richard Wood) Date: Tue, 18 May 1999 16:01:14 -0400 (EDT) Cc: spoel@xray.bmc.uu.se (David van der Spoel), bernhold@npac.syr.edu (David E. Bernholdt), chemistry@ccl.net In-Reply-To: from "Richard Wood" at May 18, 1999 01:48:18 PM X-Mailer: ELM [version 2.5 PL0b1] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit According to Richard Wood: > > But rasmol reads a "text" file format! Why change it and other programs > that already read text files? That doesn't make any sense to me. This indeed makes not much sense. What use is of introducing a "type" of the energy, like "nuclear repulsion"? You still have to read and understand it, not just click on it with a mouse. Unix scripting possibilities allow for many many things like sorting or similar. And of course programs such as molden have no problems with reading text files. I guess the next step would be implementing surrounding sound into Gaussian. Sincerely, Dmitry Khoroshun dima@euch4e.chem.emory.edu From chemistry-request@server.ccl.net Tue May 18 16:21:14 1999 Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA21673 for ; Tue, 18 May 1999 16:21:08 -0400 Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id WAA04014; Tue, 18 May 1999 22:16:53 +0200 (MET DST) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id UAA03942; Tue, 18 May 1999 20:16:53 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9905182216.ZM3940@torvs.ccc.uni-erlangen.de> Date: Tue, 18 May 1999 22:16:53 -0600 In-Reply-To: Richard Wood "Re: CCL:XML as program output?" (May 18, 13:46) References: Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Richard Wood Subject: Re: CCL:XML as program output? Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On May 18, 13:46, Richard Wood wrote: > Subject: Re: CCL:XML as program output? > > On Tue, 18 May 1999, Wolf-Dietrich Ihlenfeldt wrote: > > > On May 18, 11:56, Richard Wood wrote: > > > Subject: CCL:XML as program output? > > > I think text is preferable to any other format, IMO, now or in the future. > > > If one needs xml or another format, one can just add the appropriate tags > > > as needed. > > > > I strongly disagree with this view!!!! > > > > It is always easy to > > strip off tags by a simple procedure, but the automatic addition of tags > > is often not possible, and manual addition tedious and impractical. > > i think it's just as easy to ADD tags as it is to remove them. No, this is certainly not true. I doubt that anybody really wants to do this. We are not talking about something simple like adding an HTML header and a few paragraph breaks for a quick publication of a text as a web page, but about a careful markup, identifying and classifying each and every number, procedure, etc. text > files have the advantage in that they can EASILY be imported into most > other applications. Not true either. Into what applications? Word processors? Maybe. But who wants to do that? If you count the number of applications which can read a PDB file, compared to those who are able to understand the typical textual output of some popular QM application (with all its variants, platform-dependend formatting varations, version changes, etc.) you will have to agree that is is a very good thing to have a standard. > > Also, to change the output formats of dozens of programs to a format that > is not very widely used, especially considering that not everyone is > using the same OS and same versions of programs, is daft. Better change them now, instead of adding another undocumented output variation because you hacked some additional feature, or change a column width because your new 64-bit machine gives you better precision. The idea of tagging is that the second set of programs, which process the output of the first set, can easily extract from the data the part they can handle, without having to understand all intricacies of a text dump, using only one XML parser. If new output data is encapsulated into its own tags, it is easy to ignore. Adding another column to a text dump is very dangerous, because it will desynchronize scripts which cannot do anything more intelligent than counting columns until they find their data. This has nothing to do with platform independence. XML IS platform-independent, since it is ASCII and does not suffer from any byte ordering or FP representation issues. > -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From chemistry-request@server.ccl.net Tue May 18 16:32:12 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA22158 for ; Tue, 18 May 1999 16:32:12 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA00292; Tue, 18 May 1999 14:28:05 -0500 Date: Tue, 18 May 1999 14:27:57 +36000 From: Richard Wood To: Wolf-Dietrich Ihlenfeldt cc: chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: <9905182216.ZM3940@torvs.ccc.uni-erlangen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII But isn't typing as difficult as typing ? On Tue, 18 May 1999, Wolf-Dietrich Ihlenfeldt wrote: > No, this is certainly not true. I doubt that anybody really > wants to do this. We are not talking > about something simple like adding an HTML header and a few > paragraph breaks for a quick publication of a text as > a web page, but about a careful markup, identifying and > classifying each and every number, procedure, etc. > > text > > files have the advantage in that they can EASILY be imported into most > > other applications. > > Not true either. Into what applications? Word processors? Maybe. > But who wants to do that? A lot of people do, myself included. Does MS Excel read xml files? No, yet it reads text files. > If you count the number > of applications which can read a PDB file, compared I don't use pdb files. PDB files are generally useless because of their lack of connectivity tables, at least in the programs i use. From chemistry-request@server.ccl.net Tue May 18 16:51:50 1999 Received: from charleston.softhome.net (qmailr@charleston.SoftHome.net [204.144.231.41]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA22620 for ; Tue, 18 May 1999 16:51:50 -0400 Received: (qmail 2088 invoked by uid 417); 18 May 1999 21:08:43 -0000 Received: from 1cust246.tnt1.det1.da.uu.net (HELO kressj.www.microsoft.com) (153.34.15.246) by smtp.softhome.net with SMTP; 18 May 1999 21:08:43 -0000 Message-ID: <004d01bea16f$964b1f60$f60f2299@kressj.www.microsoft.com> From: "Jim Kress" To: "Dmitry Khoroshun" , "Richard Wood" Cc: "David van der Spoel" , "David E. Bernholdt" , Subject: Re: CCL:XML as program output? Date: Tue, 18 May 1999 16:47:03 -0400 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 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 1) Having an XML POSTprocessor would be great. Modifying the QC or SM (or whatever) code would be a real pain. 2) If Gaussian put surround sound into their product a) You'd probably only get sound out of 1.5 speakers and b) They'd still have a manual that claimed full feature content but software that did not live up to the manual's claims. Jim Check out my web site http://www.kressworks.com/ It'll blow your mind (politically), stimulate your senses (artistically) and provide scientific insights that boggle the mind!! -----Original Message----- From: Dmitry Khoroshun To: Richard Wood Cc: David van der Spoel ; David E. Bernholdt ; chemistry@ccl.net Date: Tuesday, May 18, 1999 4:29 PM Subject: CCL:XML as program output? >According to Richard Wood: >> >> But rasmol reads a "text" file format! Why change it and other programs >> that already read text files? That doesn't make any sense to me. > >This indeed makes not much sense. What use is of introducing a "type" >of the energy, like "nuclear repulsion"? You still have to read and >understand it, not just click on it with a mouse. Unix scripting >possibilities allow for many many things like sorting or similar. And of course >programs such as molden have no problems with reading text files. > >I guess the next step would be implementing surrounding sound into Gaussian. > >Sincerely, >Dmitry Khoroshun >dima@euch4e.chem.emory.edu >-= 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 Tue May 18 16:54:31 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22715 for ; Tue, 18 May 1999 16:54:31 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA19898; Tue, 18 May 1999 16:48:54 -0400 (EDT) Date: Tue, 18 May 1999 16:48:54 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: XML in output/input files for Comp. Chem. Codes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Partially from conviction, and partially to prevent a flame war on the list, I want to point out that we will have to live for a long time with the presence of "legacy formats". So, let the programs produce and process legacy formats too, but I would love to have also a file: output.xml produced, and file input.xml accepted for input. The number of various something2somethingother.pl (awk, sed, etc.) scripts which I produced over the years is in hundreds. I wish I could have spent this time reading something interesting or thinking about the data I produced. In short... I do believe that we cannot abandon legacy formats overnight. It would make me use a few #@!&? words exactly the same way, as when the new release of "well known" quantum chemistry workhorse comes out. However, I would be happy, if beside the *.out, I also had *.xml. It does not have to be a fancy XML... Let them design their own tags and attributes to kill the competition and to feed the sense of being right, but let the tags be closed and properly nested. I will do the rest. Over the years I lost any hope that Computational Chemistry formats for input or output can be standardized. Egos, and commercial interests will not allow it. But at least, if there was a companion XML file with the same info as in traditional legacy input or output file, it would make my life easier (as well as many others, I hope). Disk space is cheap, and putting additional WRITE or fprintf statements is not a big deal. The funny thing is that chemists were the first to see the opportunity with Peter Murray-Rust and Henry Rzepa advocating CML. And what? Depends whom you ask, but on average, we as a professional group can claim foresight, but not wide spread practice. Jan jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Tue May 18 17:00:16 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA22887 for ; Tue, 18 May 1999 17:00:15 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA00473; Tue, 18 May 1999 14:56:16 -0500 Date: Tue, 18 May 1999 14:56:09 +36000 From: Richard Wood To: Wolf-Dietrich Ihlenfeldt cc: chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: <9905182249.ZM3968@torvs.ccc.uni-erlangen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Well, the notion of coming up with a NEW file format to replace 10++ file formats confuses me even more. Richard From chemistry-request@server.ccl.net Tue May 18 17:05:17 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA23107 for ; Tue, 18 May 1999 17:05:16 -0400 Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id OAA07136; Tue, 18 May 1999 14:00:36 -0700 (PDT) Received: from localhost by redox.scripps.edu (8.9.1/TSRI-2.8) with SMTP id OAA01419; Tue, 18 May 1999 14:00:34 -0700 (PDT) Date: Tue, 18 May 1999 14:00:34 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: Richard Wood cc: chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Richard and all, It is not more that you need to change the internal format of programs like Rasmol. Think of XML as a data encapsulation format, which can be filtered to any other proprietary or widely used format. The idea of XML is to be not only markup, but that the markup will have meaning. So XML is not only for information about the structure of a document, it can also be treated as data. Two of the examples of XML application I know are: WDDX: http://www.wddx.org/ (Wed Distributed Data eXchange) CML: http://www.xml-cml.org/ (Chemical Markup Language) The latter has been for about 2 years already and there is ever a CML/XML java browser (and sort of editor) by one of the proponents of CML (Peter Murray-Rust) named "Jumbo". Now XML is not only a text file format, if contains meta-information about the data in it. And if your have a DTD (Document Type Definition) for the markup, the validity of the information/structure can be validated too. There is a great push for using XML and Java, or uxing XML as a CORBA container. Imagine you have an agent program that understands XML, you can ask it to go and fetch information from dissimilar sources, and then put it into XML, which then can be both displayed on your computer and put into an XML-object into a database (or translated into an SQL string for an SQL database). Or maybe think of XML as a general description format from which you can translate to/from to your favorite program. On Tue, 18 May 1999, Richard Wood wrote: > Date: Tue, 18 May 1999 13:48:18 +36000 > From: Richard Wood > To: David van der Spoel > Cc: "David E. Bernholdt" , chemistry@ccl.net > Subject: CCL:XML as program output? > > But rasmol reads a "text" file format! Why change it and other programs > that already read text files? That doesn't make any sense to me. > > Richard Hope I dit not bore you to death with my rant. Best regards. -- Jesus M. Castagnetto, PhD - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@server.ccl.net Tue May 18 17:08:43 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA23194 for ; Tue, 18 May 1999 17:08:43 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA00626; Tue, 18 May 1999 15:05:58 -0500 Date: Tue, 18 May 1999 15:05:35 +36000 From: Richard Wood To: "Jesus M. Castagnetto" cc: chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It just seems like someone created a "new" file format without any apps to use it and is now trying to ram it down our throats. Richard From chemistry-request@server.ccl.net Tue May 18 16:59:55 1999 Received: from nickel.camsoft.com ([198.112.109.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22866 for ; Tue, 18 May 1999 16:59:54 -0400 Received: from 198.112.109.83 by nickel.camsoft.com with SMTP (QuickMail Pro Server for MacOS 1.0.3); 18 MAY 99 16:48:40 UT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: Jonathan Brecher@nickel.camsoft.com Message-Id: In-Reply-To: References: <9905182135.ZM3892@torvs.ccc.uni-erlangen.de> Date: Tue, 18 May 1999 16:55:38 -0400 To: chemistry@ccl.net From: Jonathan Brecher Subject: Re: CCL:XML as program output? At 1:46 PM -0400 5/18/99, Richard Wood wrote: >On Tue, 18 May 1999, Wolf-Dietrich Ihlenfeldt wrote: > >> On May 18, 11:56, Richard Wood wrote: >> > Subject: CCL:XML as program output? >> > I think text is preferable to any other format, IMO, now or in the future. >> > If one needs xml or another format, one can just add the appropriate tags >> > as needed. >> >> I strongly disagree with this view!!!! >> >> It is always easy to >> strip off tags by a simple procedure, but the automatic addition of tags >> is often not possible, and manual addition tedious and impractical. > >i think it's just as easy to ADD tags as it is to remove them. text >files have the advantage in that they can EASILY be imported into most >other applications. This is a pointless discussion. I'm seeing two main threads: A) Adding vs removing tags: The presence or absence of tags is irrelevent; the only issue is how well-formatted the text is to start with. o It is easy to add tags to well-formatted raw text o It is easy to remove tags from well-formatted tagged text o It is difficult to add tags to poorly-formatted raw text o It is difficult to remove tags from poorly-formatted tagged text (Spoken from the perspective of someone who spent the last several years doing all four). XML would be appealing if it required that well-formatted files. Unfortunately, it doesn't, or at least it doesn't any more than HTML does. Look at all the crappy HTML that is out there. Look at the garbage produced by PageMill or FrontPage or most any other commercial program. Look through release notes for earlier versions of Netscape or MSIE and see the hoops those developers had to go through to deal with all the creative html that people cooked up. All arguments I've seen for XML take it as an implicit fact that XML-compliant files will magically be well-formatted and easily understandable. Guess what folks; it ain't gonna happen. B) Text vs non-text This is even more pointless. "Text" is a description of the character set used, and not even a very good description. There is no such thing as a program that "understands text" any more than there is a person who "understands speech". Traditionally, "text" files are written with the 96 ASCII characters from 32 to 127. The Gaussian file format is one such file type. It is possible to say that "a program interprets the Gaussian file format." Saying so does not in any way imply that it will interpret the MOPAC file format or the PDB file format -- any more than saying that someone understands English implies that he also understands French. XML files *are* text in that they are written using those 96 printable ASCII characters. So are HTML files. So is this message. So what? Programmatically, "text" files are often *less* easy to interpret than binary files. There are lots of benefits to using binary file format, including density of data and speed of interpretation. The major drawback is that they are not readily interpretable by unassisted humans. XML is "just another file format". There is no program in the world that will magically be able to interpret XML without specific programming effort. The programming effort to interpret XML is neither significantly more nor significantly less than that required to interpret any other file format (assuming a similar number of data *types* in both cases). The major benefit of XML -- or any other file format -- would be in how widely it is accepted. Converting between file formats is a bitch, and often involves some sort of data loss. *IF* (and it's a big if) XML becomes widespread, it would be a big win for everyone. On the other hand, the exact same thing could be said for any file format. The name of the game is communication, and anything that improves communication, including a widely-understood file format, would be a Good Thing. People have high hopes that XML will indeed become such a lingua franca. I agree that it would be a great thing if it did. However, it hasn't yet, and it won't at any time in the near future, and anything beyond the near future is in the realm of guesswork. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From chemistry-request@server.ccl.net Tue May 18 17:01:03 1999 Received: from faui45.informatik.uni-erlangen.de (root@faui45.informatik.uni-erlangen.de [131.188.2.45]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA22913 for ; Tue, 18 May 1999 17:01:00 -0400 Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.212]) by faui45.informatik.uni-erlangen.de (8.9.1/8.1.49-FAU) with ESMTP id WAA16785 for ; Tue, 18 May 1999 22:49:04 +0200 (MET DST) Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id WAA04117; Tue, 18 May 1999 22:49:23 +0200 (MET DST) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id UAA03970; Tue, 18 May 1999 20:49:23 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9905182249.ZM3968@torvs.ccc.uni-erlangen.de> Date: Tue, 18 May 1999 22:49:23 -0600 In-Reply-To: Richard Wood "Re: CCL:XML as program output?" (May 18, 14:27) References: Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Richard Wood Subject: Re: CCL:XML as program output? Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On May 18, 14:27, Richard Wood wrote: > Subject: Re: CCL:XML as program output? > But isn't typing as difficult as typing src="mypicture.gif">? > > On Tue, 18 May 1999, Wolf-Dietrich Ihlenfeldt wrote: > > text > > > files have the advantage in that they can EASILY be imported into most > > > other applications. > > > > Not true either. Into what applications? Word processors? Maybe. > > But who wants to do that? > > A lot of people do, myself included. Does MS Excel read xml files? No, > yet it reads text files. It does not read text files in general, only tab-separated (or similarily structured) table data files, if you want a sheet you can reasonably work with. It does not read the atomic charges from a MOPAC result file, or a series of such files. You have to prepare the output by going through the result file and extract it into an intermediate file, manually, if you do not have a converter script which needs constant maintenance. And a simple tab-sep table is certainly not useful as a general output format. Office 2000 will presumably parse an XML-file of any origin and let you graphically pick the data columns which should be imported. > > > If you count the number > > of applications which can read a PDB file, compared > > I don't use pdb files. PDB files are generally useless because of their > lack of connectivity tables, at least in the programs i use. a) PDB can encode connectivity (though not bond orders) (No, I am not defending PDB - I think PDB should also be abolished in favor of a more flexble approach ASAP) b) How do you encode connectivity in your 'text-file' tables? And how do you obtain this information from, say, Gaussian? What kind of format do you use? To me, it is not yet clear how do you think an output should look like. Your notion of a 'text file' confuses me. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From chemistry-request@server.ccl.net Tue May 18 17:35:31 1999 Received: from acaix1.ucis.dal.ca (acaix1.UCIS.Dal.Ca [129.173.1.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA24233 for ; Tue, 18 May 1999 17:35:30 -0400 Received: from is2.dal.ca (murashov@IS2.Dal.Ca [129.173.1.66]) by acaix1.ucis.dal.ca (8.9.0/8.9.0) with ESMTP id SAA30166 for ; Tue, 18 May 1999 18:07:36 -0300 Received: from localhost (murashov@localhost) by is2.dal.ca (8.9.0/8.9.0) with SMTP id SAA91424 for ; Tue, 18 May 1999 18:07:35 -0300 Date: Tue, 18 May 1999 18:07:34 -0300 (ADT) From: Vladimir Murashov To: chemistry@ccl.net Subject: Ellipsoids in OpenGL Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I was wondering if some kind soul can direct me to an optimized subroutine for OpenGL/GLUT that draws an arbitrary ellipsoid. Thanks, Vladimir Dr. Vladimir V. Murashov Dept. Chemistry University of British Columbia Vancouver, BC V6T 1Z1 From chemistry-request@server.ccl.net Tue May 18 18:05:25 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA24963 for ; Tue, 18 May 1999 18:05:25 -0400 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id QAA01007; Tue, 18 May 1999 16:02:48 -0500 Date: Tue, 18 May 1999 16:02:36 +36000 From: Richard Wood To: Jonathan Brecher cc: chemistry@ccl.net Subject: Re: CCL:XML as program output? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I still say why convert many file formats to one if you don't have to/not all applications curently being used will handle them. It's like assuming that everyone using a PC is using Windows 95/98, when the fact is that some are still using Windows 3.1. Richard From chemistry-request@server.ccl.net Tue May 18 18:26:38 1999 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA25147 for ; Tue, 18 May 1999 18:26:37 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 10jsF2-0004vB-00; Tue, 18 May 1999 22:21:40 +0000 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 10jsEN-0000H9-00; Tue, 18 May 1999 22:20:59 +0000 Received: from [155.198.8.49] by cscmgb.cc.ic.ac.uk (980427.SGI.8.8.8/4.0) id XAA09902; Tue, 18 May 1999 23:20:37 +0100 (bst) Mime-Version: 1.0 X-Sender: rzepa@155.198.63.8 Message-Id: In-Reply-To: References: Date: Tue, 18 May 1999 23:19:23 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Re: CCL:XML in output/input files for Comp. Chem. Codes Content-Type: text/plain; charset="us-ascii" >The funny thing is that chemists were the first to see the opportunity >with Peter Murray-Rust and Henry Rzepa advocating CML. >And what? Depends whom you ask, but on average, we as a professional >group can claim foresight, but not wide spread practice. Since Jan was kind enough to quote Peter and myself, I note here that Part 1 of an article on XML and CML just been submitted for publication in JCICS by Peter and myself (but not yet refereed or accepted). Due to the policy of the ACS, I cannot place the entire article on the Web, since that would constitute prior publication. However, I will seek guidance from Bill Milne of JCICS to see whether the CML tagset, the attribute list, six examples and the DTD could be published in the interests of the community and of "OpenSource" software. Peter has also written around 8 "legacy" to CML converters (ie Gaussian, GAMESS, MOPAC, PDB,, etc etc) and he is happy to make these available to anyone who wishes to test/improve/add to them. This will all be made available via http://www.xml-cml.org/ Finally, we hope to be shortly releasing an XML-CML repository server with some interesting and we hope novel features, which will really allow the true potential of XML to be demonstrated. We would invite the community to comment on this formal CML definition, and to contribute to the development of chemical markup languages in general in the sprit of OpenSource. I might also add that CML was first proposed in August 1995 (well before XML itself!) and a special version of MOPAC capable of producing program output in CML was made available, thus anticipating the thread of this discussion. Its still up at http://www.ch.ic.ac.uk/cml/ where you can try it for yourselves. The CML was a very early draft, and might differ slightly from the version proposed in the JCICS article. In particular, it was not XML conformant for obvious reasons. Finally, I am sure you are all aware of it, but the principle XML discussion forum is at http://www.lists.ic.ac.uk/hypermail/xml-dev/ and contains some 13,000 postings from Feb 97 to present. It is indexed, so anyone wishing to search for specific terms can do so. Henry Rzepa. +44 171 594 5774 (Office) +44 171 594 5804 (Fax) http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Tue May 18 18:51:26 1999 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA25403 for ; Tue, 18 May 1999 18:51:25 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 10jsdJ-00050r-00 for CHEMISTRY@ccl.net; Tue, 18 May 1999 22:46:45 +0000 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 10jsdI-0000Of-00 for CHEMISTRY@ccl.net; Tue, 18 May 1999 22:46:44 +0000 Received: from [155.198.8.49] by cscmgb.cc.ic.ac.uk (980427.SGI.8.8.8/4.0) id XAA10529; Tue, 18 May 1999 23:46:42 +0100 (bst) Mime-Version: 1.0 X-Sender: rzepa@155.198.63.8 Message-Id: In-Reply-To: References: <9905182135.ZM3892@torvs.ccc.uni-erlangen.de> Date: Tue, 18 May 1999 23:48:56 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Re: CCL:XML as program output? Content-Type: text/plain; charset="us-ascii" >...XML would be appealing if it required that well-formatted >files. Unfortunately, it doesn't, or at least it doesn't any more than >HTML does. ...All arguments I've seen for XML >take it as an implicit fact that XML-compliant files will magically be >well-formatted and easily understandable. Guess what folks; it ain't gonna >happen. A full answer to Jonathan's point is deserved, but for the time being I will confine myself to saying that comparing HTML and XML is unfair. The comparison should really be with XML and SGML (which is widely regarded in document publishing as a great success and has been around for 15 years). A HTML server accepts any document, well formed or not; an XML repository will accept only a well formed (ie balanced tags) and valid (ie conforming to a specified DTD) XML document; Arguably, an XML repository is closer to an object-oriented database than a HTML server., but with style sheets there is no reason it cannot be more powerful than HTML. XML IS much better formed and structured than HTML (HTML itself is migrating to XHTML in recognition of this) and I think Jonathan is wrong about XML not making it in the near future. The last 3 months have seen a remarkable uptake, although not obvious to the public at large. See http://www.lists.ic.ac.uk/hypermail/xml-dev/ for examples. Although much XML development is taking place in commercial environments, we should encourage OpenSource thinking in an area such as chemistry, since it is only by such collaborative efforts that it will succeed in our community. I might also add that a lamentably unlauded project called HyperWave (originally HyperG) solved many of the problems of "bad" HTML and broken servers by only allowing well formed marked up documents to be entered and served. It also handled links correctly, as well as metadata, queries, and many other things now considered good practice! It was introduced ONE year before Tim Berners-Lee invented the Web at CERN, and had IT caught on instead, things might have been a little different! It was literally ahead of its time, and the World was not ready for it. Henry Rzepa. +44 171 594 5774 (Office) +44 171 594 5804 (Fax) http://www.ch.ic.ac.uk/rzepa/