great
It worked with the cif file in the end of the command

phenix.refine in_refine.def spp.ligands.cif

thanks every one

> Date: Thu, 13 Aug 2009 10:58:46 +0200
> From: [email protected]
> To: [email protected]
> Subject: Re: [phenixbb] adding sutrates in phenix.refine
>
> Dear Rune
>
> 2009/8/13 Rune wederkinck Andersen <[email protected]>:
> > Hi Nigel
> > Tanks for your quick answer
> > I have tried what you suggested. and ran
> > phenix.ready_set ssp.pdb   (ssp.pdb is my hole protein with my two ligands
> > AMP and RP5)
> >
> > This generate ssp.updated.pdb and ssp.ligands.cif
> >
> > I asume that ssp.ligands.cif is the file containing restraints.
> >
> > This i similar to the  cif file that I  generated  with the comand
> > phenix.elbow  ssp.pdb  --do-all
> >
> > My problem is that I don't know how to  use both files in my later
> > phenix.refine command.
> > I use a in_refine.def file in my refinement command
> >
> > phenix.refine in_refine.def
> >
>
> You could simply add the cif file to that line:
> phenix.refine in_refine.def spp.ligands.cif
> That should work...
>
> If you want to use the updated pdb file (with hydrogens) I would:
>
> Start by stripping your def file:
> phenix.refine --diff-params "in_refine.def"
> To get just your corrections.
> Change the input pdb file in your .def file and then run this as
> mentioned above.
>
> Regards,
>
> Folmer Fredslund
>
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