Hi Vincent,
I think the consensus often varies on what is considered high resolution, though I have heard that anything better than 2A is considered high resolution. I suppose if ask 10 different people, you may get 10 different answers :)
As for refinement strategies, I think the main thing to consider is maintaining a proper data-to-parameter ratio with a safety factor around 3. With that said, you should be able to do rigid-body refinement with group ADPs and simulated annealing at 3.7 A. You should be add in TLS groups at the end as well. Given that the refinement will be done in "groups", you can easily manipulate the number of groups to maintain a legal data-to-parameter ratio. For example, one rigid group requires 6 parameters, and a single TLS group requires 20. All of this can be done easily in Phenix.
I hope this helps. I'm sure Pavel or someone else from the Phenix group will add their expertise.
Best regards,
Jason Porta
Graduate Student
Eppley Structural Biology Facility
Dept. Biochemistry & Molecular Biology
University of Nebraska Medical Center
Omaha, NE 68198
402-559-5533
-----phenixbb-bounces@phenix-online.org wrote: -----
To: PHENIX user mailing list <phenixbb@phenix-online.org>
From: vincent Chaptal <vchaptal@mednet.ucla.edu>
Sent by: phenixbb-bounces@phenix-online.org
Date: 04/09/2010 12:35PM
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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--
Vincent Chaptal
Dept. of Physiology at UCLA
http://www.physiology.ucla.edu/Labs/Abramson/index.html
<http://www.physiology.ucla.edu/Labs/Abramson/index.html/>
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