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Probably, you have built water molecules that are associated with symmetry-related macromolecules rather than the host molecule.  Turn symmetry on, check the nearest neighbors of the offending waters, and move the waters close to the host molecule if appropriate.  I believe you can do this with the CCP4 program watertidy.

kmj

On Thu, Mar 11, 2010 at 12:15 PM, Azadeh Shahsavar <[log in to unmask]> wrote:
Dear All,

In depositing a pdb file, after validation step, an error comes up:

Solvent Atoms

The following solvent molecules lie farther than expected from the protein.

Can any one give me some advice about it?
deleting these water molecules results in a large increase of R factor, by the way.

Thank you in advance,

A