[phenixbb] Fwd: parameters for averaged kick maps

Pavel Afonine pafonine at lbl.gov
Mon Dec 10 15:15:11 PST 2012

Hi Jose,

kick-map related parameters in ordered_solvent scope of parameters are 
leftover that I forgot to remove back when I was working on it. So you 
can see it as a minor bug. And yes, you can't change them. Sorry about 
delayed answer (I saw the email on phenixbb but did note reply 
immediately and it sank in the flood of other stuff).


On 12/10/12 11:04 AM, Jose M de Pereda wrote:
> 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 <pereda at usal.es>
> Reply-To: 	PHENIX user mailing list <phenixbb at phenix-online.org>
> To: 	PHENIX user mailing list <phenixbb at phenix-online.org>
> 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/
> ------------------------------------------------------------

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