This is terrific. Suggestions:
-test this on a 1024x768 screen. Is this the way you want it, with the table going off the edge so tha last columns are not visible? On the pop-up, my "Start" menu hides the bottom of the window. Does it have to be quite that large?
-When I called up hemoglobin, I can't see the nonprotein parts. There should be some way to do this.
-You can now put "width=" in <input type=button> elements. This gives a cleaner look. Perhaps these buttons could go down the side of the applet in a table.
-Add some more viewing options -- not too many -- but some.
-Custom script generates an error PDB ID: None ... ERROR - NO PDB ID SPECIFIED when ENTER is pressed instead of using the OK button. The <form> tag needs action="javascript:scriptMe(document.myform.Script.value)"
Bob Hanson
Raphael A. Bauer wrote:
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Hi list,
As I promised in my last postings, I want to announce how our project "Columba" uses 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.
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.
Thanks - I hope this is interesting for the list and not too OT!
Raphael - -- // privacy is no feature! // public key www.informatik.hu-berlin.de/~rbauer/10F67206.gpg // www.gnupg.org -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
iD8DBQFBa9dI+rfCoBD2cgYRAm4MAJ0U0dQ5pn0GsnCv/i+4DpiYt/iXkgCcC9P+ wTBXJ2M8m1JWaialEIev5Bc= =MZZO -----END PGP SIGNATURE-----
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-- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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