Water picking

[Robert D Scavetta]

Hi all,

I'm in the process of picking waters, but I am experiencing some problems that
I hope some of you out there have experienced and found solutions for.


For the basic run I do the following:

Once I have my protein model, and am confident that the coordinates are
correct, I obtain an Fo-Fc map (from x-plor).  This map I am running through
mapman to generate a peak.pdb file.  I then run this peak.pdb file along with
the protein.pdb file through a program that was obtained from Carl Sprang
called WATERSELECT, which throws out waters that are sym-related and outside an
angstrom range from the protein.

I then run this modified peak.pdb file through x-plor.

This is where I start having problems.  Should I constrain the waters at this
point or not?  When should I constrain waters?

I get s 2Fo-Fc map out, and I check my waters.  My criteria for keeping them
is:

In 2Fo-Fc density
B-factor less than 60
At least 2 H-bonding neighbors

I have ran the cycle several times to generate 200 waters in the protein.  I am
finding out that waters in earlier cycles that meet the criteria are moving out
of density in later cycles.

Any and all help is greatly appreciated.



-- 
Robert D Scavetta
Dr. Francis Jurnak's Laboratory
Department of Biochemistry
University of California, Riverside
scavetta at xtreme.ucr.edu   or    scavetta at ucrac1.ucr.edu