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Hi Preeti, In addition to Roberto's explanantion: Refmac's occupancy refinement is also automatically used in PDB_REDO if your ligand has one or atoms with occupancy set to 0.01 or 0.00 (unless your model comes straight out of PHASER). Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > Preeti Satya > Sent: Thursday, May 05, 2016 10:44 > To: [log in to unmask] > Subject: [ccp4bb] regarding occupancy refinement > > Hi All, > > Could anyone please tell me how we can do occupancy refinement in ccp4. > Actually I have a structure with ligand bound to it. The density seems to be > quiet clear at that region at sigma cut off 1.0, but when I am doing density > validation as well as temperature factor validation it is shown to be very high > as compared to other amino acid residues in protein. The site where I have > fitted the ligand is exactly the place where the ligand should be (known from > other ligand bound structures). I think there is some problem with the > occupancy of this ligand as my crystals were soaked ones. So I need to know > about occupancy refinement in CCP4. > > > > -- > > Regards, > Preeti > > PI - Dr. S .Gourinath > School Of life sciences > JNU > N.Delhi 110067 > > http://www.jnu.ac.in/Faculty/gourinath/Lab_Members.htm > .... > knowledge is power. So go on achieving knowledge through out your life > time.