When I deposit at the EBI the deposition software moves solvent to
assocoiate with a protein molecule. If that has been done, those
messages would mean that the solvent is indeed unconnected to anything.
It seems a bit unlikely chemically - and I would check the maps..
has something beem missed?
Eleanor
Kevin Jude wrote:
> 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
>>
>
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