Dear Phenix Team,

Last week I sent an e-mail to the phenixbb regarding the parameters that control de generation of averaged kick maps. Unfortunately, I have not received any feedback from the community.

I wonder if you could give me some help on this subject.

Probably, the calculation of averaged kick maps is already very well optimized in phenix.refine and phenix.maps. Yet, I am still curious.

Thanks a lot in advance
All the best

   Jose


-------- Original Message --------

Subject:	[phenixbb] parameters for averaged kick maps
Date:	Tue, 04 Dec 2012 10:12:46 +0100
From:	Jose M de Pereda <[email protected]>
Reply-To:	PHENIX user mailing list <[email protected]>
To:	PHENIX user mailing list <[email protected]>

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

-- 
------------------------------------------------------------
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
http://xtal.cicancer.org/
------------------------------------------------------------