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). Pavel 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 Reply-To: PHENIX user mailing list To: PHENIX user mailing list

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/ ------------------------------------------------------------