-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Tuesday 12 October 2004 15:08, Raphael A. Bauer wrote: > As I promised in my last postings, I want to announce how > our project "Columba" uses Jmol.
It seems very basic use... i.e. it only displays the PDB structure. It would be nice to have buttons as well that color for example the active site, though I do not know wether that info is in one of the integrated databases... Who was using automatically created scripts again for displaying database extracted info with Jmol? > In general our project, the www.columba-db.de is a > data integration project, aiming towards the integration of > several different protein related data sources. Our > main data source is the PDB. Currently we integrated swissprot, scop, cath, > dssp, GeneOntology, pisces, kegg, Ncbi Taxonomy ExPasy and the PDB. I'm no expert in bio databases, but I think there are other systems that integrate several databases... SRS is one, right? What does Columba offer over already existing solutions? > The main aim of our project is to serve as a quick and simple > possibility for biochemistry people that search for specific > knowledge about a protein. > > Jmol is so to say a nice to have feature for us. If you > found a matching PDB entry you can select it and view > it's 3D structure via Jmol, change the coloring and the viewing method. > > It is not officially released yet, but you can have a look at > the "beta" version at "www.columba-db.de/dev3/columba.cgi". > Search for eg "1mnm" (a pdb entry). Click on "1mnm" and then click on > "3D View of this molecule" right in the upper middle. > A pop up window with Jmol appears and you can select coloring and > structural options or type in some custom script. > > Technically speaking: > - I use the javascript pop-up to have a windows of it's own. > - The version is Jmol10pre11 (that is much better than v9 and never > crashed). - The buttons are connected via liveconnect javascript (yes I had > problems with safari, ~ but after the last update it now works fine) > - I use the perl proxy supplied in the CVS and fetch the pdb 3D Data from > the pdb server - All calling thing is done via a pyhton cgi. (As our > complete Columba Web Interface works ~ with pyhton) > > If you have any questions, requests, suggestions, critics let me hear about > it. It's always important to hear about other people's opinions. Especially > in this beta testing phase. > > If you want to use code of the project or want to know how we did this or > that feel free to use our code or just ask me. What's the license of the website source code? > Thanks - I hope this is interesting for the list and not too OT! It is interesting indeed. As someone already said today, having examples of how others use Jmol makes it easier to use it yourself too... 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) iD8DBQFBa+Wud9R8I9Yza6YRAuvUAKCJjIzH+ikyt0bnOIpVYk7iqCBk0ACfW2k3 N5K+ftljItSBz16Gocgxcec= =Elf6 -----END PGP SIGNATURE----- ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
