[Jmol-users] [Fwd: Re: [Open Babel] vdw radii in openbabel (long reply)]
For those of you interested in the vdw radius question ... I posted an inquiry to the Open Babel mailing list asking about the source of the vdw radius values that are in the Open Babel source code. Geoff Hutchison replied with the message below. Thoughts? Comments? Miguel Mensaje original Asunto: Re: [Open Babel] vdw radii in openbabel (long reply) De: "Geoff Hutchison" <[EMAIL PROTECTED]> Fecha: Vie, 21 de Enero de 2005, 18:12 Para: "Miguel" <[EMAIL PROTECTED]> Cc: [EMAIL PROTECTED] -- On Jan 21, 2005, at 8:39 AM, Miguel wrote: > Q: Are the van der Waals radius values even used in OpenBabel? No, the VdW radii are not used directly in Open Babel--but that doesn't mean we're suddenly going to get rid of them. There is code and data in Open Babel that's intended for others to use, which goes along with the spirit of the project and the fact that Open Babel is a library for building chemistry applications. I like having a good set of chemical data for other programs. > My question relates to the van der Waals radii values in OpenBabel. webelements says that their reference for vdw radii is: > A. Bondi, J. Phys. Chem., 1964, 68, 441. > Q: What is the source of the vdw radii values in OpenBabel? Now you want to know where the VdW radii come from for Open Babel. Therein lies a story. See, the problem is that lots of people say they use Bondi's paper from JPC 1964. Then they go off and quote VdW radii that aren't in the paper. Bondi doesn't cover the whole periodic table (only 38 elements by my count)--so if you want the vdW radius for Fe, you're outof luck. Somehow WebElements and others give values and don't usually say where they come from. (I can't say that I've gone through everything on the WebElements site -- he's usually pretty good about giving citations.) Worse, there are a lot of inconsistent sets of VdW radii--some may look like Bondi's values for a few elements, but then *wham* they've changed a few elements with no explanations. Part of the problem is that "van der Waals radius" sounds like such a nice simple value in intro chemistry class. But then you realize that people have defined it for crystals (supposedly why people use Bondi's radii), gas phase (for the van der Waals equation), or equilibrium calculations (i.e., conformation, molecular mechanics) and a few other areas. And these don't always match: Zefirov YV RUSSIAN JOURNAL OF INORGANIC CHEMISTRY 46 (4): 568-572 APR 2001 (quite a readable article if you have the time -- it's in English) I've really hunted and hunted to find an actual academic source for a consistent set of VdW radii across the periodic table. The closest I came (besides Bondi's incomplete set): Batsanov SS, INORGANIC MATERIALS 37 (9): 871-885 SEP 2001 Now there's also this Chinese paper that looks somewhat interesting, but I can't get it (or read it): Hu SZ, Zhou ZH, Tsai KR, ACTA PHYSICO-CHIMICA SINICA 19 (11): 1073-1077 NOV 2003 Batsanov gives some fairly reasonable numbers, IMHO, and defines them for 65 elements--basically everything except the lanthanides and actinides and the nobel gases. So I used the nobel gas values from Bondi and generally the rest of them from Batsanov. I'm open to other suggestions. -Geoff - Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] - --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Re: two targets on the same page
Henw wrote: > document.jmol1.script('script1...'); > document.jmol2.script('script2...'); Or, using Jmol.js one can call: jmolScript('script1', 1); jmolScript('script2', 2); > In this way one can construct toggle buttons as well, which I don't find > in the current jmol.js These 'toggle' buttons are available in Jmol.js as jmolCheckbox('script-when-checked', 'script-when-unchecked', 'label-name', booleanIsCheckedByDefault); Miguel --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] two targets on the same page
>Hi > > Is there any way to send a command (script) to two different > jmolapplets on the same page by the way of one single button, radio > group, checkbox or menu ? > Or even better send to different commands to two applets on the same > page? > I have tried several synthaxes but I couldn't get it. The standard 'control' functions in the Jmol.js JavaScript library (jmolButton, jmolCheckbox, etc.) do not provide this functionality. You can easily construct this by yourself: 0. create your jmolApplet s with names "target1" and "target2" 1. create your own html form controls: 2. have "myFunction" call jmolScript("script1", "target1") jmolScript("script2", "target2") Miguel --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fwd: [Biojava-l] BOSC 2005
Presence of Jmol and/or CDK would be nice... Egon -- Forwarded Message -- Subject: [Biojava-l] BOSC 2005 Date: Thursday 20 January 2005 06:58 pm From: Darin London <[EMAIL PROTECTED]> To: open-bioinformatics-foundation@open-bio.org, [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], biojava-l@biojava.org, [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED] {Please pass the word!} MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2006, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Email: [EMAIL PROTECTED] FEES TO BE ANNOUNCED. Watch the bosc website for more information. SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited. SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2005. If you are interested in giving a software demonstration at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php SESSION CHAIRS WANTED If you would like to be involved BOSC 2005, we invite you to chair a session. This will not require much of your time. You will be given a schedule of presenters during your session. You simply introduce each speaker, and manage the time of their presentation (25 minutes for full presentations, 5-10 minutes for lightning talks/demos, depending on the number of entries). If you are i
[Jmol-users] Re: two targets on the same page
Hervé, Let your button call a javascript function, and in this function you send any script to any applet you like document.jmol1.script('script1...'); document.jmol2.script('script2...'); In this way one can construct toggle buttons as well, which I don't find in the current jmol.js Is this what you meant? Hens Hi Is there any way to send a command (script) to two different jmolapplets on the same page by the way of one single button, radio group, checkbox or menu ? Or even better send to different commands to two applets on the same page? I have tried several synthaxes but I couldn't get it. Hervé --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] two targets on the same page
Hi Is there any way to send a command (script) to two different jmolapplets on the same page by the way of one single button, radio group, checkbox or menu ? Or even better send to different commands to two applets on the same page? I have tried several synthaxes but I couldn't get it. Hervé --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: Sliders to control Chime -> Jmol?
It was Bob Hanson who once provided me with fully Javascript based sliders to control background colour, atom size and bond size, and with some tinkering any numerical value being sent to Jmol (or Chime) by script. See for a kind of demo http://cheminf.cmbi.ru.nl/wetche/organic/cyclohexane/jm/chxjmol.html Hens The sliders are fantastic for easy exploring. So many times the atoms are too large or too small or the bonds get in the way, etc. With the sliders I could easily (emphasize easily) set things the way I want to see it. I would think it would be great for a beginning student. So yes. I am interested! Charles Sundin University of Wisconsin-Platteville --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users