From: Sara Nichols <sara.nichols@ya...> - 2005-05-23 20:15:57
I was wondering if anyone knew of a way to set a distance measurment
between two aromatic rings, where the distance is measured from the
center of the ring, rather than a specific atom.
I don't think this is directly possible, since the centers of the aromatic
rings are not declared per se. But I see another way to obtain the result
you want, maybe this can be written as a small Python script (sorry I never
wrote any Python scripts, so I can't translate my idea!!).
The idea is the following:
1) declare a function that take two arguments, the id number of the first
Phe (Phe1) and the id number of the second Phe (Phe2).
2) declare two lists of 6 elements containing the string corresponding to
the selection of the atoms of the phenyl rings (i.e. 'resi Phe1 and name
CG', 'resi Phe1 and name CD1', CE1, CZ, CE2, CD2)
3) define two interlaced loops and calculate the distance between all 6
carbons of Phe1 with all 6 carbons of Phe2, either with cmd.dist or with
simple mathematical functions; sum these distances
4) divide the result by 36, and export the data!
Good luck :-)
On Tue, 2005-05-24 at 11:34 +0200, Gr=C3=A9gori Gerebtzoff wrote:
> 3) define two interlaced loops and calculate the distance between all 6
> carbons of Phe1 with all 6 carbons of Phe2, either with cmd.dist or wit=
> simple mathematical functions; sum these distances
> 4) divide the result by 36, and export the data!
Or more simply, once you have selected the 12 atoms, calculate the
centroids of each of the two rings. Then just compute the distance
between these centroids. This is a bit more efficient than doing 36