Re: [phenixbb] adding sutrates in phenix.refine

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 :

...

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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