VMD-L Mailing List

From: divya nayar (divya.alchemist_at_gmail.com)
Date: Mon Jun 27 2011 - 01:15:21 CDT

Hi,
I want to calculate the protein-water (oxygen) RDF from the VMD GUI Plugin
of RDF. I give "protein" in selection 1 and "name OH2" in selection 2. The
keyword "protein" over here means that the center of mass of protein will be
taken into consideration or it will take any heavy atom of protein because
in Tcl script if "protein" keyword is given in any selection ,it means any
heavy atom of protein.
Somebody please clear my doubt as to what exactly is taken as selection in
VMD RDF if "protein" is written.

Morevover, from where can I obtain the in-built tcl script for calculation
of RDF that VMD uses?

Thanks,
Divya