[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
Pavel
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
>
>
>
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> phenixbb at phenix-online.org
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