[phenixbb] phenix error

Nathaniel Echols nechols at lbl.gov
Fri Oct 17 08:12:38 PDT 2014

On Thu, Oct 16, 2014 at 7:36 AM, Ivan IVANOV <ivanov at embl.fr> wrote:

>   I have an error appearing in phenix. I think it is a problem of my pdb
> file. I do not know how to change it.
>   Error:
>  residue.id_str(suppress_segid=false):segid is not unique: pdbres=ATP C
> 1 "segid= "O"
>    Does anyone can help me??
>    Where is the mistake and how to solve it ??

This means that within a single "residue" (I guess an ATP ligand?), the
unofficial segID field (columns 72-76, I think) that is sometimes use as an
alternative to chain ID has multiple values for the different atoms.  This
tends to break other code so it's checked when the file is read in.  There
are several ways to fix this, but probably the easiest is to run
phenix.pdbtools and tell it to clear the segID - on the command line this
would be:

phenix.pdbtools model.pdb clear_segid=True

and in the GUI it should be pretty obvious which box to check.

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