Again, Bob, many thanks for taking the time.
For method2 (the q-map), I will have to do the requisite background reading -
thanks for the directional signal.
However, method1 is closer (I think) to what I need, as the following should
make clear (I hope!).
What I would do is derive the initial set of "driver" vectors by an algorithm
over the pair of linear DSSP or STRIDE segments Sa and Sb corresponding to the
tertiary substructures A and B. (One can easily image how such an algorithm
would work:
1) first arrange the helices and strands of the smaller DSSP/STRIDE segment so
that they are (linearly) "on-center" with the corresponding helices and
strands of the larger DSSP/STRIDE segment;
2) then work on each helix of the smaller DSSP/STRIDE segment so that its start
and end residues coincide (linearly) with the start and end residues of the
corresponding helix in the larger DSSP/STRIDE segment; then, for each helix in
the smaller segment, space its residues evenly between the new positions of its
start and end residues;
3) do (2) for strands as well as helices.
4) then "space" residues in the intervening "turns" or :"loops" joining the
strands and helices.
Once (1-4) are completed, it would be trivial (I think) to derive the "driver"
vectors required for the JMol deformation.
Reason why I prefer this approach, at least initially, is that I can: do a
visual superimposition to see which residues of the larger (unscaled)
substructure line up closely with which residues of the smaller (scaled)
structure, followed up by a "calculated" superimposition to make a table of
corresponding residues.
And then, this table of corresponding residues might provide a way to refine
and elaborate the original "sparse" primary structure patterns that led to the
initial identification of substructrues A and B in the first place, i.e. make
these primary structure patterns less "sparse" and therefore increase their
usefulness as probes back into the PDB.
Anyway, thanks very much again for providing direction here.
djh
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
