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Hi all, recently there was a nice post-10.00 feature development request: support for multiple molecular models - including reading multiple files into one AtomSetCollection - rotation of individual AtomSet's in the Collection - alignment in general Some comments (picked for supporting my suggestion in this email :): "The answer: It depends on the user and the task they're performing." "What happens to the scaling factor? Do things get moved off the screen? What becomes the new center of rotation? What happens to the 'camera' for perspective depth calculations?" "Jmol is a component" "I'm a computer engineer not a chemist" Some applications of support for multiple molecular models: - - manual/algorithmic docking - - superposition of molecules - - fun - - ... I've had an discussion with Miguel about this, and will now explain a few things. PLUGINS FOR JMOL Jmol has a plugin mechanism. This mechanism is aimed to extend the functionality of Jmol 'The Viewer' to do certain things... we all know the DirBrowser plugin. Another plugin that has been around for about a year now is the RSSViewer plugin. Both these extend the core functionality of Jmol with specific features, dir browsing and browsing chemistry enhanced Rich Site Summery feeds, respectively. A full list of plugins is available from: http://www.woc.science.ru.nl/cdk/ The name CDK plugin is used there, as the interface is principally CDK based, but can be used without CDK at all too... Now, the plugin has access to the data classes, and can 'order' Jmol to display new data (the last e.g. used by the DirBrowser). Thus, an alignment plugin could have a button "SuperImpose Molecules in AtomSetCollection" which go through all AtomSet's in the Collection, and align them according to some rules. Thus, 'us' chemistry-pros, would write alignment plugins for certain specific tasks. Plugins that come to mind: - - a super impose the molecules in a SDF file - - place ligand in protein active site with method X - - etc Each plugin would expect certain features of the contents of the AtomSetCollection, but that's all something the Jmol engine need not take care of... Only Jmol has to do, is display the active AtomSetCollection. The current plugin API does not have a script functionality, but this is something we could add quite easily, and, actually, something I have on my TODO list for some time. (off topic: yes, we could thus with this script feature in the plugin API, also make a plugin that will download info from some biochemical database, and use script commands to highlight certain features in the PDB file shown in Jmol... many possibilities come to mind here (e.g. high light of active site)... since a plugin is a self contained component, it can do whatever it want, have custom IO for parsing database specific formats and whatever it needs to do more...) Merging of more than one file can be covered by a plugin too. The big advantage of this setup is that we don't impose many difficult requirements upon the core Jmol development team (aka. Miguel). 2. JMOL AS A JPANEL A second option would be to write a custom application for a certain tasks, but I have a tendency for the above solution, and would like discuss that first. 3. DISCUSSION Ok, so please have a look at one or more plugins, and ask me questions on the above, and let's discuss if the suggested setup would work in the settings you had in mind for multiple models and alignment. Egon - -- [EMAIL PROTECTED] - --------------------------------------- CDK: http://cdk.sf.net/ JChemPaint: http://jchempaint.sf.net/ Jmol: http://www.jmol.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFByC2Yd9R8I9Yza6YRAmlpAKDISUNLbPtKwL7BwpZEA4K1VLLJhACggPzo IH/OFnhY4FOGx6Nwm23nerc= =TEBQ -----END PGP SIGNATURE----- ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
