Hi all, I am taking my first tentative steps into the world of phenix.refine with a somewhat problematic 3 A data set and I had a few questions that Google couldn't answer. I am running phenix.refine version 1.24.1b (intel-linux-2.6) from the command line. Firstly, is it possible to do 'grouped' adp refinement with 2 groups per residue (like the good old bgroup.inp of CNS)? Secondly, is it possible to specify multiple starting trajectories for simulated annealing? I often find it handy to do 10 runs of simulated annealing and overlay the output co-ordinates to see where the 'wobbly' bits are. Lastly, can the latest version of phenix.refine do SA omit maps? Thanks, Stephen P.S. My .def file is the default (from phenix.refine --dry-run) w/ the following changes: 86,87c86,87 < refine_adp_individual = True < refine_adp_group = False ---
refine_adp_individual = False refine_adp_group = True 92c92 < simulated_annealing = False
simulated_annealing = True
-- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549