[phenixbb] Update waters and chain ID

Scott Lovell swlovell at ku.edu
Thu Jun 19 09:46:07 PDT 2014

Hi All,


I'm refining a structure (dev-1726) that contains 24 protein subunits which
are assigned to chains A-X in the PDB file.  Chains Y and Z are assigned to
a couple of ligands and the ordered solvent molecules are chain w (lower
case).  I decided to give the "Update waters" option a try during refinement
but it seems that the chain ID of the ordered solvent is changed to chain S
by default.  Since I already have a protein subunit assigned to chain S, the
following error is obtained when I try to open the model in Coot (ERROR 39
READ: Duplicate sequence number and insertion code.).  To enable
visualization of the model in Coot, I can of course manually change the
chain ID for the ordered solvent in the output PDB file using a text editor.
However,  is there a way to override the ordered solvent default chain ID in
Phenix to prevent duplication?






Scott Lovell Ph.D., Director

Protein Structure Laboratory

University of Kansas

Del Shankel Structural Biology Center


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