[phenixbb] Two groups per residue and multiple trajectories for simulated annealing

Stephen Graham stepheng at strubi.ox.ac.uk
Fri Mar 2 02:39:34 PST 2007

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?



P.S.  My .def file is the default (from phenix.refine --dry-run) w/
the following changes:

<   refine_adp_individual = True
<   refine_adp_group = False
>   refine_adp_individual = False
>   refine_adp_group = True
<   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

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