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great <br>It worked with the cif file in the end of the command <br><br> phenix.refine in_refine.def spp.ligands.cif<br><br>thanks every one<br><br>> Date: Thu, 13 Aug 2009 10:58:46 +0200<br>> From: folmerf@gmail.com<br>> To: phenixbb@phenix-online.org<br>> Subject: Re: [phenixbb] adding sutrates in phenix.refine<br>> <br>> Dear Rune<br>> <br>> 2009/8/13 Rune wederkinck Andersen <andersenrune@hotmail.com>:<br>> > Hi Nigel<br>> > Tanks for your quick answer<br>> > I have tried what you suggested. and ran<br>> > phenix.ready_set ssp.pdb (ssp.pdb is my hole protein with my two ligands<br>> > AMP and RP5)<br>> ><br>> > This generate ssp.updated.pdb and ssp.ligands.cif<br>> ><br>> > I asume that ssp.ligands.cif is the file containing restraints.<br>> ><br>> > This i similar to the cif file that I generated with the comand<br>> > phenix.elbow ssp.pdb --do-all<br>> ><br>> > My problem is that I don't know how to use both files in my later<br>> > phenix.refine command.<br>> > I use a in_refine.def file in my refinement command<br>> ><br>> > phenix.refine in_refine.def<br>> ><br>> <br>> You could simply add the cif file to that line:<br>> phenix.refine in_refine.def spp.ligands.cif<br>> That should work...<br>> <br>> If you want to use the updated pdb file (with hydrogens) I would:<br>> <br>> Start by stripping your def file:<br>> phenix.refine --diff-params "in_refine.def"<br>> To get just your corrections.<br>> Change the input pdb file in your .def file and then run this as<br>> mentioned above.<br>> <br>> Regards,<br>> <br>> Folmer Fredslund<br>> <br>> _______________________________________________<br>> phenixbb mailing list<br>> phenixbb@phenix-online.org<br>> http://www.phenix-online.org/mailman/listinfo/phenixbb<br><br /><hr />Share your memories online with anyone you want <a href='http://www.microsoft.com/middleeast/windows/windowslive/products/photos-share.aspx?tab=1' target='_new'>anyone you want.</a></body>
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