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 [[email protected]]
Verzonden: woensdag 25 juni 2014 18:22
Aan: Elke De Zitter; [email protected]
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 [[email protected]]
Verzonden: dinsdag 24 juni 2014 14:31
Aan: Elke De Zitter; [email protected]
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
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