[phenixbb] parameters for averaged kick maps

Jose M de Pereda pereda at usal.es
Tue Dec 4 01:12:46 PST 2012

Dear all,

I would like to compare averaged kick maps obtained using different 
“kick sizes”. Is it possible to define the kick size and the number of 
kicks in phenix.refine and/or phenix.maps?

In phenix.refine, the “ordered_solvent” section has keywords to control 
the generation of kick maps:
kick_map {
kick_size = 0.5
number_of_kicks = 100
But, it seems to me that these can not be used during the generation of 
maps or maps’ coefficients.

Related with this issue, does phenix.refine always use the same kick 
size or does it adjust it ad hoc (e.g. based on ML error estimates)?

Thanks a lot,

Jose M de Pereda, PhD
Instituto de Biologia Molecular y Celular del Cancer (IBMCC)
Spanish National Research Council - University of Salamanca
Campus Unamuno s/n
E-37007 Salamanca, Spain
Phone:  +34-923-294817
Fax:    +34-923-294795

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