Jmol users,
Jmol now has DSSP.
For those who don't recognize what this means, it is VERY significant.
It means that Jmol can now use just the ATOM/HETATM records of a PDB file to
calculate the secondary structure (helices of three types, anti-parallel and
parallel sheets, and turns) based on the algorithm described by W. Kabsch
and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637 and implemented by
the DSSP program maintained at http://swift.cmbi.ru.nl/gv/dssp/.
Jmol's ramachandran-angle-based method of calculating structure is still
present, and at least for now it is the default for loading PDB files with
no headers (but I think that should be changed).
Jmol's DSSP implementation has now been verified against a 1769-model
high-resolution data set from
http://dunbrack.fccc.edu/Guoli/pisces_download.php.
This is an authorized implementation; perhaps the first in Java that should
be an exact implementation in conformance with the Apr 1, 2010 version of
dsspcmbi.
Sincere thanks go to Gert Vriend, of the Centre for Molecular and
Biomolecular Informatics, CMBI, for this wonderful contribution to Jmol.
Test files are archived at
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/dssp
Of these models, only one, 2IZQ, fails the test, and it can pass if loaded
with:
set forceAutoBond; load =2izq filter "%A"
(It has whole alternative residues -- three versions of residue 11! --
which Jmol can't handle as a default loading.)
Nico has released Jmol 12.1.14, which has the DSSP capability in it. Jmol
12.1.15_dev makes a few additional fixes for some obscure alt-location
issues. You can pick up a copy at
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
***FEATURE CHANGE***
calculate structure
now uses legitimate, official DSSP. You can get the "old" way using
calculate structure RAMACHANDRAN
There are a few nuances with alternative locations, but they can all be
worked around, and you can use
configuration 1
configuration 2
etc.
to run DSSP analysis on different alt-loc configurations. (This is not
possible using the standard DSSP program, I believe.)
In addition, you can use:
calculate hbonds STRUCTURE
color hbonds type
display backbone
wireframe only
to see a very nice representation of the parallel and antiparallel bonding
in beta sheets.
Documentation to follow.
I think I'd like to add this to 12.0 as well, since it is such a great
feature.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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