From the user's point of view one of the most serious disadvantages of
the current Jmol version is the strange internal mechanism for
protein secondary structure determination.
One example is the structure 1srb.
RasMol/Chime give for all 10 models one helix in the middle of the sequence.
On the contrary, Jmol yields
Model Sheets (S), Helices (H)
1 2 S
2 2S,1H
3 0S,0H
4 1S
5 1S
6 2S
7 1S,1H
8 1S
9 2S
10 2S
You may want to contact G. Vriend at the CMBI in Nijmegen/The Netherlands.
He seems to take care of the DSSP program written by W. Kabsch and C.
Sander.
(http://swift.cmbi.ru.nl/gv/dssp/).
A further suggestion refers to the rendering of SS bonds. Currently,
these bonds
link either sidechain or backbone atoms. A third useful option would be to
extend the lines to the cartoon ribbon.
An example, how this could look like, can be found here:
http://www.imb-jena.de/cgi-bin/htmlit.pl?color=white&id=1pi2&src=1pi2_prepi_1.gif&name=mono%201pi2
Regards.
js
--
Dr. Juergen Suehnel
Biocomputing Group
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
[formerly Institute of Molecular Biotechnology (IMB)]
Jena Centre for Bioinformatics
Beutenbergstr. 11
D-07745 Jena/Germany
fon: +49 (0)3641 65 6200
fax: +49 (0)3641 65 6210
e-mail: [EMAIL PROTECTED]
web: www.fli-leibniz.de/www_bioc/js/
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