[phenixbb] Solvent in Auto_Build

[Thomas C. Terwilliger]

Hi Jeff,
I think if you edit the file to replace 'ATOM  ' with 'HETATM' for all the
HOH records then it should work.  Please let me know if it doesn't!
-Tom T

> Dear Dr. Adams, and/or other Phenix experts,
>
>
>
>      I have done water-picking in CNS and some refinement in Refmac-5 in
> ccp4 and subsequent manual adjustments of waters in Coot and O.  I have
> discovered that CNS seems to like the format 'OH2 TIP' for listing waters,
> whereas refmac only likes HOH.  When I then run Auto_Build in the Phenix
> GUI, I get the following error message:
>
>
>
> Input failed
>
> Sorry, the PDB file /path/filename.pdb has an incomplete residue (or
> conformer/residue combination) in conformer ' ' chain S residue HOH 733
> because the conformer is missing the following main chain atoms: [ 'N',
> 'CA', 'C' ].
>
>
>
> The first water in my pdb file is indeed the one in question above.
> Apparently Phenix is thinking that this water should be a protein residue
> instead of solvent.  Can anyone help me with this and tell me what I need
> to
> edit in the pdb file so that Phenix recognizes it as solvent instead of
> protein, or do I need to delete all waters and repick them in Phenix.  I
> have tried changing the segid to from A to S with no success.
>
>
>
> Many Thanks,
>
>
>
> Jeff B.
>
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