Tight Waters

[Andrew Orry]

Q. When I convert a protein structure there is an option called "keep tight waters". What defines a tight water?

A.

Tightly bound water molecules are identified by the total strength of hydrogen bonding, calculated as described:

http://www.molsoft.com/man/icm-commands.html#hbond-color

Default cutoff is 5.0, which typically means three or more hydrogen bonds; some water molecules with two hydrogen bonds at near-ideal coordination geometries also can reach the cutoff.