[phenixbb] Solvent in Auto_Build

Jeff Bush jbush at chemmail.chem.fsu.edu
Sun Sep 10 09:44:47 PDT 2006

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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