Hi all,
I am currently developing a new Jmol-based user interface for the "Jena
Image Library of Biological Macromolecules". An underlying database
integrates information from the following structure and sequence databases:
- PDB: Protein Data Bank (http://www.rcsb.org/pdb/)
- SCOP: Structural Classification of Proteins
(http://scop.mrc-lmb.cam.ac.uk/scop/)
- UniProtKB/Swiss-Prot:
including information on SNPs/SAPs (Single Amino Acid Polymorphisms)
(http://www.expasy.org/sprot/)
- PROSITE: Database of protein families and domains
(http://www.expasy.org/prosite/)
Sequence information is mapped onto 3D structures via sequence alignment.
The interface visualizes/highlights both structural features such as
secondary and domain structure information, hetero components, active
sites, disulphide bonds and results of the 3D mapping of sequence
information such as functional sequence motifs and SNPs or SAPs.
The key features are:
1) simultaneous access to all this structure-based and sequence-based
information through a (hopefully) user-friendly interface
2) two interface types
- "basic", designed for convenience
- "advanced", designed for maximum flexibility
3) the two interface types are freely interchangeable at any time,
without loosing any previous work
4) standard views
Default, Hetero/Site, SNP, PROSITE, SCOP, Model (NMR models)
5) compact design, allowing to hide currently unused parts
6) a hidable information table for each data type, crosslinked to other
resources
7) easily extendable to other data types
We just released a beta version and would greatly appreciate it if you
could have a look at it and provide some feedback. Comments,
suggestions, bug reports, compatibility reports etc. would be great.
The interface should work for all of the currently 32520 PDB entries (as
of 06-09-2005). The underlying database is updated on a regular basis.
Below a few PDB examples are listed, illustrating some of the features.
But feel free to use any valid PDB codes you like for testing. Just
replace the PDB code in the URL after "CODE=" by another one. The
interface is also accessible through the atlas pages at
"http://www.fli-leibniz.de/IMAGE.html";
(e.g.: http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1deh).
http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh
http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1spd&VIEW=prosite
http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1vyn&VIEW=model
http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1evr&VIEW=SCOP
http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1axi&VIEW=prosite&SIZE=max
The interface uses only the basic functions of a slightly modified
version of the "jmol.js" javascript library.
The modifications are:
1) added the message callback function (absolutely needed!)
2) each script send by "jmolScript" is accompanied by a wait message
(provides rudimentary feedback even if the message callback doesn't work
properly or the log is currently invisible)
3) disabled absolute path alert (I disagree with Miguel on this point)
Thank you in advance,
Rolf
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