[phenixbb] Anisotropic B-factor restraints

[Pavel Afonine]

Hi Elke,

could you please send me data and model files, and indicate residues 
that you think have incorrect B-factors?

Thanks,
Pavel

On 6/26/14, 6:31 AM, Elke De Zitter wrote:
> Dear Pavel
>
> I played with wxu_scale and wu several times. When wu = 0, this 
> unrestrained refinement results in totally unrealistic ADP's. However, 
> if I use wu = 1, wu = 5 or wu = 20, I always get the same results. Is 
> this normal? On the bottom of this e-mail, you can find the target 
> weight settings (for wu = 20).
>
> Kind regards
> Elke
>
> target_weights {
>     optimize_xyz_weight = False
>     optimize_adp_weight = False
>     wxc_scale = 0.5
>     wxu_scale = 1
>     wc = 1
>     wu = 20
>     fix_wxc = None
>     fix_wxu = None
>     shake_sites = True
>     shake_adp = 10
>     regularize_ncycles = 50
>     verbose = 1
>     wnc_scale = 0.5
>     wnu_scale = 1
>     rmsd_cutoff_for_gradient_filtering = 3
>     force_optimize_weights = False
>     weight_selection_criteria {
>       bonds_rmsd = None
>       angles_rmsd = None
>       r_free_minus_r_work = None
>       r_free_range_width = None
>       mean_diff_b_iso_bonded_fraction = None
>       min_diff_b_iso_bonded = None
>
> 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:* woensdag 25 juni 2014 18:22
> *Aan:* Elke De Zitter; phenixbb at phenix-online.org
> *Onderwerp:* Re: [phenixbb] Anisotropic B-factor restraints
>
> 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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