I would use in coot: calculate - model/fit/refine - add alt conf. This should generate a correctly defined alternative water.

Good luck!

Herman

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of arka chakraborty
Sent: Wednesday, March 07, 2012 2:21 PM
To: [log in to unmask]
Subject: [ccp4bb] setting occupancy for disordered water

Hi all,

I am having a structure where there is a disordered water .I have fixed one water into the density, yet there is a positive density about 1.6 ang away. I want to put in another water and attribute 0.50 occupancy to each of the the waters while attributing them to one water in reality. I would like to know how to modify the pdb so that phenix.refine accepts it.

Thanks in advance,

Regards,

ARKO

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ARKA CHAKRABORTY

CAS in Crystallography and Biophysics

University of Madras

Chennai,India