Hi,
What happens usually is that some solvent atoms are in fact closer to a
symmetry-related molecule than the one you are working on. The PDB has
programs to reposition these water molecules closer to the "correct"
macromolecule or subunit, and they will provide you with the modified
waters and ask you to approve (or not).
So I personally ignore these warning messages until I receive news from
the PDB.
HTH,
Fred.
Azadeh Shahsavar 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
