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On Wed, Jun 8, 2011 at 4:44 PM, Madhu shankar Madhu shankar < [log in to unmask]> wrote: > I am a beginer in crystallography. I have carried out molecular > replacement in 'phenix' and now want to refine the structure in ccp4. Could > anyone tell me what the proper Rfree_flag value to put in while using > Refmac5(ccp4). I have used 1 and output seems to be fine but I want am not > sure if am going in the right direction. > What program did you use to create the R-free flags? If you used Phenix, this is correct - the rest of the flags will be 0. If you used a CCP4 program, the flags will be a range of integers (depending on what percent of reflections are flagged - if you use 5%, the range will be 0-19), and 0 is usually the test set. In that case, you could still use 1, but I'd recommend sticking to 0, because CCP4 programs will default to using that, and Phenix will recognize that convention in your MTZ file and use 0 too. -Nat PS. If Phenix generated the flags, you can also use the reflection file editor in the Phenix GUI to export them to the CCP4 convention, so CCP4 programs will use the correct set by default.