setting occupancy for disordered water

From: arka chakraborty
Date: 7 March 2012 13:20


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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From: <Herman.Schreuder

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

 

Good luck!

Herman

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From: Tim Gruene

Dear ARKO,

you can edit the PDB file by doubling the line of the respective water,
assign the the "Alternate location indicator" (column 17) to 'A' and 'B'
(see e.g. http://www.wwpdb.org/documentation/format33/sect9.html#ATOM),
and change the coordinates from 'B' to the second peak.

Make sure that the water is not near a symmetry axis - there are often
artefact of density near symmetry elements.

Tim

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From: arka chakraborty


Hi all,

I apologize for being late in expressing my gratitude. Thanks to Prof. Tim and Prof. Herman, I have fixed the waters and validated the structure.

Cheers,

ARKO