[Jmol-users] How difficult this feature might be?

[<ppa...@no...>]

Hello.
Sorry for contributing not with the technical questions/solutions, but with
"user would like to....".

In your expert opinion how difficult would be to implement the following
functionality to Jmol (polymers=proteins again, my nemesis):

INPUT:
a.  pdb file of a protein (no indexing issues, ideal case) of N residues
(amino acids).
b. NxN matrix relating somehow all pairs of residues i<>j in the N-mer.
This is flat text file (any format, user is responsible for it)

GOAL:
c. Load the protein to Jmol as usual.

d. Tell Jmol that the NxN file related to the protein should be loaded to
say internal matrix M (Menu item)

e. Create a window  WM (WM is connected to the protein plot in Jmol window
see below) with contour plot of the profile defined by M and allow user to
vary the z-axis threshold (goal: If maxima of M-defined profile is what I
need to see, it would be nice to have a slider with Zmax-Zmin interval,
that I can drag and the contours would start from the z-threshold thus
defined..optimally, one can move both lower and upper threshold to see a
"slice").

f. If I (left-?)-click on the feature  in WM, the i and j coordinates (in
real units, i.e. in the indices of monomers i and j, corresponding to the
selected element of M) are read, and transferred to the "select i,j"
command issued for the protein. At the same time, the selection should be
somehow visualized, either by immediate (automatic) coloring of the
residues i and j or by rendering them in stick or CPK. Toggle by
right-click this would de-select the residues in mol. plot and restore
previous rendering of them.

g. If I drag a rectangle in WM window, the boundaries of that rectangle
would be identified as i and j and transferred to protein structure plot by
"select i-j" with the similar visualization (color, residue rendering).
Somehow then I should be able to de-select the region again from the WM
window (say by left click inside the rectangle?).

Any one knows about a viewer with such a functionality? VM had something
like that but not very flexible and handy.

What I am using to emulate this functionality is sort of "off-line"
combination of a script in R which I run parallel to Jmol. R reads the
matrix, generates the plot, allows me to do the z-clipping and reads-out
the features in terms of residue i, residue j pairs with printing them in
R-text window as "select i,j" or "select i-j".  I then copy/paste those to
Jmol/Rasmol command line window + some additional clicking.

If this sounds doable, where to start? Not much experience with Jmol code,
so most probably I need to learn a lot first....

Thanks, PP



Dr. Petr Pancoska
Department of Pathology
SUNY Stony Brook, NY 11794
phone:          (631)-444-3030

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