[phenixbb] Update waters and chain ID

Pavel Afonine pafonine at lbl.gov
Thu Jun 19 17:49:10 PDT 2014

Hi Scott,

you can specify new solvent chain ID, it is under solvent parameters:

Refinement settings -> All parameters -> Ordered solvent -> Output chain id


On 6/19/14, 9:46 AM, Scott Lovell wrote:
> 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?
> Thanks,
> Scott
> __________________________________
> Scott Lovell Ph.D., Director
> Protein Structure Laboratory
> University of Kansas
> Del Shankel Structural Biology Center
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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