[phenixbb] adding sutrates in phenix.refine

Folmer Fredslund folmerf at gmail.com
Thu Aug 13 01:58:46 PDT 2009

Dear Rune

2009/8/13 Rune wederkinck Andersen <andersenrune at hotmail.com>:
> 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.


Folmer Fredslund

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