Hi Bill, In PHENIX you can use the following commands for making different omit maps:
A simple composite omit map can be made by: phenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=simple_omit An iterative build omit map: phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=target.pdb \ composite_omit_type=iterative_build_omit SA omit map: phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=coords.pdb \ omit_res_start_list=3 omit_res_end_list=4 omit_chain_list=A \ composite_omit_type=sa_omit phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit For more details: http://www.phenix-online.org/documentation/autobuild.htm#anch159 Regards, Debanu. -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of William G. Scott Sent: Saturday, July 26, 2008 11:12 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] question about getting rid of model bias in refinement Hi Sun: It might be worth doing a simulated annealing omit refinement in phenix or CNS, with the residues in question omitted. CNS also allows you to make a composite-omit map. I haven't seen that in phenix yet but presumably it is doable. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 25, 2008, at 10:53 PM, Sun Tang wrote: > Hello Everyone, > > I have a question about getting rid of model bias in refinement with > refmac. I solved the structure with molecular replacement. After final > refinement of the structure, I found out some key amino acids in the > structure and wanted to make sure their conformations are correct. I > omitted these amino acids (by setting occupancy to zero) and refined > the structure. I manually fit the amino acids into the density and > refined the structure again. I found these amino acids return to the > precious conformations even though the conformations I fit were > different. Should I omit these amino acids from the beginning of the > refinement? What is the best way to get rid of the model bias? Your > suggestions are greatly appreciated! > > Best, > > Sun > > >
