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
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