Re: [ccp4bb] Phenix/refmac incompatibility?

[Robbie Joosten]

Hi Eleanor,

This seems to be a caused by a bug in an older version of Phenix. We used to see quite a few examples of this on the PDB-REDO server, but not recently. Renumbering is the only solution I'm afraid.

Cheers,

Robbie

On 30 Dec 2021 20:05, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

I am not sure whether I have this straight but someone has sent a pdb file from phenix refinement with these atoms in the pdb file..

....

ATOM   5580  N   GLY S  18      36.182  44.368  56.021  1.00 79.25           N
ATOM   5581  CA  GLY S  18      37.168  44.349  57.091  1.00 74.78           C
ATOM   5582  C   GLY S  18      37.048  43.211  58.097  1.00 73.20           C
ATOM   5583  O   GLY S  18      37.043  42.043  57.734  1.00 74.31           O
ATOM   5584  N   SER S  19      36.992  43.568  59.375  1.00 75.40           N

...

HETATM11068  O   HOH S  16      68.933  60.684 119.353  1.00 32.35           O
HETATM11069  O   HOH S  17      17.772  20.649  91.306  1.00 40.79           O
HETATM11070  O   HOH S  18      23.684  50.229  65.614  1.00 41.00           O
HETATM11071  O   HOH S  19      45.488  71.114 105.890  1.00 51.50           O

Then REFMAC gets upset because "residue" S 18 appears twice..

Doesnt PHENIX worry about this? or has the user edits these HOH atoms into the file?

And what should we do about it

Eleanor

....

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