[Chimera-users] defining a putative binding site

Francesco Pietra chiendarret at gmail.com
Wed Feb 18 00:41:52 PST 2009

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.

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?


francesco pietra

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