Re: [phenixbb] refinement at 3.7A

Hi Vincent, I can tell you from my work with a 5A virus capsid that NCS can make your maps look much better than the resolution dictates. You didn't say how much NCS you have, but you may also consider NCS averaging as a tool. Also be aware of high NCS contaminating the free set of reflections- I think Phenix can auto-magically pick in thin shells to mitigate this effect. -Christina ________________________________ From: vincent Chaptal To: PHENIX user mailing list Sent: Fri, April 9, 2010 12:35:15 PM Subject: [phenixbb] refinement at 3.7A Hello list, i would like to add a following discussion to yesterday's low resolution refinement question: What is low res? at what resolution should we use only rigid body refinement or can we use minimization as well? In my case, i have a 2.7A and a 3.7A structures, of 2 different mutants, in the same space groups and cell parameters. After refining the high res one, i'm wondering what is the best strategy to refine the low res one? If i do a simple rigid body refinement, I have R=32.1, Rfree=35.8. If i use individual site refinement, i have R=30.7, Rfree=35.8. (both with group ADP, TLS and NCS). The statistics look good and the maps look great. There isn't any feature in the difference map so i'm guessing i'm done with refinement? (I'm afraid of over-refining it as the map look too good for this resolution. ) I was also advised to add hydrogen bond restraints to maintain secondary structures, I guess upon using minimization refinement? Basically, could you update me on what's today's dogma on what type of refinement we should use at what resolution? ( i couldn't find this info on the phenix web site, sorry if i missed it) thank you very much. vincent Pavel Afonine wrote:

Hi,

rigid body refinement does not employ any restraints. You can use secondary structure restraints in refinement of individual coordinates.

Actually, you can use secondary structure restraints in constrained rigid body refinement (SA in torsion angle space).

To use secondary structure restraints: "secondary_structure_restraints=true". phenix.refine GUI should have an option for this too.

Pavel.

On 4/7/10 4:38 PM, r n wrote:

...

Hi I wanted to do low resolution rigid body refinement with secondary structural restrain. I have not seen any command or information in the phenix document? any help Thanks ram****

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