[phenixbb] Anisotropic B-factor restraints

[Pavel Afonine]

Hi Elke,

you can make ADP restraints stronger by making X-ray target weight 
smaller, for example, set wxu_scale weight to something smaller than the 
default (1.0). You may need to try a few values to see which one works best.

Alternatively, you can make ADP restraints weight, wu, larger than the 
default (1.0), which is equivalent.

Let me know if you have any questions or need help with this!

Pavel

On 6/25/14, 7:18 AM, Elke De Zitter wrote:
> Dear Pavel
>
> Thank you for the quick response. After reading this paper and some of 
> its references, I suppose that Phenix.refine automatically restraint 
> the anisotropic B-factor calculation. However, I want to restraint it 
> more because certain atoms have very long small ellipsoids and atoms 
> in some tyrosine rings are moving in different directions. Is there a 
> way to play with the restraints manually?
>
> Kind regards
> Elke
>
> Elke De Zitter
>
> PhD student, KU Leuven
>
> Biochemistry, Molecular and Structural Biology
>
> Celestijnenlaan 200f - bus 2404, 3001 Leuven
>
> Room 00.84, +32 16 3 26530
>
> ------------------------------------------------------------------------
> *Van:* Pavel Afonine [pafonine at lbl.gov]
> *Verzonden:* dinsdag 24 juni 2014 14:31
> *Aan:* Elke De Zitter; phenixbb at phenix-online.org
> *Onderwerp:* Re: [phenixbb] Anisotropic B-factor restraints
>
> Hi Elke,
>
> phenix.refine uses similarity restraints on anisotropic ADPs as 
> described here:
>
> http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf
>
> Pavel
>
> On 6/24/14, 5:03 AM, Elke De Zitter wrote:
>> Dear All
>>
>> I'm refining a protein structure with a resolution of 1.25 A, using 
>> Phenix GUI version 1.9. I am refining the B-factors for the protein 
>> atoms anisotropic and those for the water molecules isotropic. How 
>> can I restrain the anisotropic B-factors so that bonded atoms have 
>> similar ellipsoids (like the SIMU and DELU commands in Shelx making 
>> the atoms moving similarly in direction and amount)?
>>
>> Thanks
>> Elke
>>
>> Elke De Zitter
>>
>> PhD student, KU Leuven
>>
>> Biochemistry, Molecular and Structural Biology
>>
>> Celestijnenlaan 200f - bus 2404, 3001 Leuven
>>
>> Room 00.84, +32 16 3 26530
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>

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