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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font face="Arial" size="2">Dear Pavel</font>
<div><font face="Arial" size="2"><br>
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<div><font face="Arial" size="2">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).</font></div>
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<div><font face="Arial" size="2">Kind regards</font></div>
<div><font face="Arial" size="2">Elke</font></div>
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<div>target_weights {</div>
<div> optimize_xyz_weight = False</div>
<div> optimize_adp_weight = False</div>
<div> wxc_scale = 0.5</div>
<div> wxu_scale = 1</div>
<div> wc = 1</div>
<div> wu = 20</div>
<div> fix_wxc = None</div>
<div> fix_wxu = None</div>
<div> shake_sites = True</div>
<div> shake_adp = 10</div>
<div> regularize_ncycles = 50</div>
<div> verbose = 1</div>
<div> wnc_scale = 0.5</div>
<div> wnu_scale = 1</div>
<div> rmsd_cutoff_for_gradient_filtering = 3</div>
<div> force_optimize_weights = False</div>
<div> weight_selection_criteria {</div>
<div> bonds_rmsd = None</div>
<div> angles_rmsd = None</div>
<div> r_free_minus_r_work = None</div>
<div> r_free_range_width = None</div>
<div> mean_diff_b_iso_bonded_fraction = None</div>
<div> min_diff_b_iso_bonded = None</div>
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Elke De Zitter</p>
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PhD student, KU Leuven</p>
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Biochemistry, Molecular and Structural Biology</p>
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<div id="divRpF642615" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>Van:</b> Pavel Afonine [pafonine@lbl.gov]<br>
<b>Verzonden:</b> woensdag 25 juni 2014 18:22<br>
<b>Aan:</b> Elke De Zitter; phenixbb@phenix-online.org<br>
<b>Onderwerp:</b> Re: [phenixbb] Anisotropic B-factor restraints<br>
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<div>Hi Elke,<br>
<br>
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.<br>
<br>
Alternatively, you can make ADP restraints weight, wu, larger than the default (1.0), which is equivalent.<br>
<br>
Let me know if you have any questions or need help with this!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/25/14, 7:18 AM, Elke De Zitter wrote:<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt"><font face="Arial" size="2">Dear Pavel</font>
<div><font face="Arial" size="2"><br>
</font></div>
<div><font face="Arial" size="2">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?</font></div>
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<div><font face="Arial" size="2">Kind regards</font></div>
<div><font face="Arial" size="2">Elke</font><br>
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Elke De Zitter</p>
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PhD student, KU Leuven</p>
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Biochemistry, Molecular and Structural Biology</p>
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<div id="divRpF4014" style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>Van:</b> Pavel Afonine [<a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>]<br>
<b>Verzonden:</b> dinsdag 24 juni 2014 14:31<br>
<b>Aan:</b> Elke De Zitter; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org" target="_blank">
phenixbb@phenix-online.org</a><br>
<b>Onderwerp:</b> Re: [phenixbb] Anisotropic B-factor restraints<br>
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<div>Hi Elke,<br>
<br>
phenix.refine uses similarity restraints on anisotropic ADPs as described here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf" target="_blank">http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/24/14, 5:03 AM, Elke De Zitter wrote:<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Dear All
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<div>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)?</div>
<div><br>
</div>
<div>Thanks</div>
<div>Elke<br>
<div><br>
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Elke De Zitter</p>
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PhD student, KU Leuven</p>
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Biochemistry, Molecular and Structural Biology</p>
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