Re: [phenixbb] Selection of R-free set for twin refinement

Hi Boaz, The two options are equivalent and no twin law needs to be specified in either case. SA should be possible with twin refinement. Cheers Peter 2009/5/6 Boaz Shaanan :

Hi,

If I understand correctly, the Phenix manual suggests two options for selecting the R-free set for twin refinement. One is to do this using the phenix.reflection_file_converter with the parameter

--use-lattice-symmetry-in-r-free-flag-generation

which I suppose does not require input of the twin law. The second is in the actual refinement using the parameter

xray_data.r_free_flags.generate=True

in which case the twin law is part of the input. My first question is whether the two options are truly equivalent. The second question is whether one can go into either of them with an mtz file in which R-free set reflections have already been selected (e.g. in scala or XDS) without any twinning assumption, or should one use a file without any R-free set altogether and let the phenix script choose it from scratch, under the twinning assumption.

Another (related) question is whether simulated annealing is possible in conjunction with twin refinement.

Thanks,

Boaz

----- Original Message ----- From: Pavel Afonine Date: Tuesday, May 5, 2009 4:53 Subject: Re: [phenixbb] ncs To: PHENIX user mailing list

...

I see. I suggest to run two refinements:

- with NCS and "optimize_wxc=true optimize_wxu=true" options, and

- without NCS and with "optimize_wxc=true optimize_wxu=true".

This will make it weight-choice independent and so easier to understand. Otherwise, since NCS term is included in weights calculation, using or not using NCS may change the X-ray/Restrains weight which may have larger effects than using/not using NCS itself.

Pavel.

On 5/4/09 6:48 PM, Maia Cherney wrote:

...

Hi Pavel, The resolution is 2.15 A. The NCS was always on during the refinement until we got low R factors (19.2% and 21.2%). Then the NCS was turned off for the final refinement and the R factors increased, which is strange as they should be going down when you apply less restraints. There are five restraint groups in the asym. unit.

Maia

Pavel Afonine wrote:

...

Hi Maia,

- I'm wondering why this puzzles you?

- The gap Rfree-Rwork seems suspiciously small, although I can't tell without knowing the resolution.

- Overall, better R-factors (Rwork, Rfree and Rfree-Rwork) mean that among many possible refinement strategies you have chosen the one that is better than the others.

What is the resolution? What are the R-factor  before using NCS? What will be the R-factors after you turn NCS back off?

Pavel.

On 5/4/09 12:27 PM, Maia Cherney wrote:

...

Hi everybody, I am wondering why my final structure refined with NCS=True has lower  R factors (19.2% and 21.2%) than without NCS by approximately 1.5%.

Leo _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎ _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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