[Chimera-users] defining a putative binding site

[Francesco Pietra]

Hi:
I need to define a putative binding site for a smaller protein upon a
larger one. The task is creating a table of likely interactions
between residues of the larger proteinseparated by less than 5 A from
those of the smaller protein. Deriving from molecular dynamics, all
residues for both proteins are in the same pdb file, alongside lipid,
water, etc.

I wonder whether the most appropriate way is to separate in two
different pdb files the lines belonging to the two different proteins.
Then:

sel #0:20,30-40,55 & #1:1701-1793 z<5

where "0" is the larger and "1" is the smaller protein. If OK, can the
results be obtained in a table form?

Thanks

francesco pietra