hi all,
with Miguel's help, I have installed a new method for assigning
protein secondary structure in Jmol. it represents a first attempt,
and I will be refining it greatly over the next few days/weeks.
details are below. anyone interested in trying it can download and
build the latest from CVS. in addition, I have added a few test
structures to samples/pdb. these are pdb structures that have their
structure records removed. you can compare them with their originals
(also in samples/pdb) to gauge the effectiveness of the assignments.
(the file names should be self-explanatory.)
details.
the new algorithm currently uses the dihedral angles of each
successive residue pair in a monomer to determine the local
conformation, then compares the values to standard dihedral ranges
for regular secondary structure. four or more consecutive helical-
like dihedrals defines a helix, and three or more consecutive strand-
like dihedrals define a beta strand.
direction.
I plan to use the dihedral-based assignments as a platform for a more
complex scoring system that takes into account dihedrals, hydrogen
bonding, and primary sequence. I think the current approach allows
too much leeway, and it doesn't take into account special cases that
are generally accepted by the community. for example, an
unstructured residue in the middle of a long stretch of structure
adopting the structure of its neighbors.
also, I think we can add assignments for other protein SS (turns,
3-10 helices, etc.), and extend out to nucleic acid SS in the future
(using different torsion angles, of course ;-).
if you are interested in contributing ideas, opinions, test cases
(very helpful!), or literature references (extremely helpful!) that
pertain to secondary structure assignment, please do so. the more
help, the better. you can send offlist to me, or keep it on list for
now.
regards,
tim
--
Timothy Driscoll
molvisions - see. grasp. learn.
<http://www.molvisions.com/>
earth:usa:virginia:blacksburg
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