[phenixbb] adding sutrates in phenix.refine
Rune wederkinck Andersen
andersenrune at hotmail.com
Thu Aug 13 02:57:42 PDT 2009
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: folmerf at gmail.com
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] adding sutrates in phenix.refine
> 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
> phenixbb mailing list
> phenixbb at phenix-online.org
Share your memories online with anyone you want.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb