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
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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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]mailto:[email protected]] Verzonden: dinsdag 24 juni 2014 14:31 Aan: Elke De Zitter; [email protected]mailto:[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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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 [[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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Elke De Zitter -
Pavel Afonine