[phenixbb] combining models from multi-start simulated annealing

[Thomas C. Terwilliger]

Hi James,

You can do this in two ways. Both involve the keyword,

  consider_main_chain_list="pdb1.pdb pdb2.pdb pdb3.pdb"

which lets you suggest a set of models to autobuild to consider in
model-building.

1. You can use this with rebuild_in_place (all your models should have the
same atoms, just with different coordinates):

phenix.autobuild data.mtz  map_file=map.mtz seq_file= seq.dat \
 model=coords1.pdb rebuild_in_place=True merge_models=true \
consider_main_chain_list=" coords2.pdb coords3.pdb" \
 number_of_parallel_models=1 n_cycle_rebuild_max=1

2. You can also use it with rebuild_in_place=False (any fragments or
models are ok):

phenix.autobuild data.mtz  map_file=map.mtz seq_file= seq.dat \
 model=coords1.pdb rebuild_in_place=False \
consider_main_chain_list=" coords2.pdb coords3.pdb" \
 number_of_parallel_models=1 n_cycle_rebuild_max=1

All the best,
Tom T


>> Is there a way to use AutoBuild to combine a set of models created by
>> multi-start simulated annealing?
>>
>> I've used a random number generator to seed different SA runs at two
>> temperatures, as suggested on this bulletin board before ... but can
>> combine the best parts of these models automatically?
>>
>> --James
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