phenix.refine does not work with the LINK lines in any way (long story).<div><br></div><div>Could you send me (off-list) the inputs?</div><div>I suspect something must be pushing the ZN the wrong way. It will be much easier for me to diagnose your problem if I have the inputs for phenix.refine.</div>
<div>If you don&#39;t want to share the data, I could probably do without, but the other files are essential.</div><div><br></div><div>Ralf</div><div><br><br><div class="gmail_quote">On Wed, Aug 31, 2011 at 10:05 AM, Zhang yu <span dir="ltr">&lt;<a href="mailto:phenixzyfish@gmail.com">phenixzyfish@gmail.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><font size="4">Dear all,</font><div><font size="4"><br></font></div><div><font size="4">I have been stuck in the problem for a while. I appreciate any suggestions.</font></div>

<div><font size="4"><br></font></div><div><font size="4"><span>I have two </span><span>zinc binding domain in my 3A structure which are Cys4 type.  The geometry is OK for one domain, but it is not refined properly in the other one.</span></font></div>

<div><span><font size="4"><br></font></span></div><div><span><font size="4">The problems during phenix refinement are</font></span></div>
<div><span><font size="4">1.  Zinc is always refined to position ~0.5A off from its correct position</font></span></div><div><font size="4">2. The refined bond lengths of four Cys-Zn are all below 2.3</font></div>
<div><font size="4">3. Sometimes, distances between SG atoms of nearby cysteines are too close, and coot just connect them as disulfate bond.</font></div><div><font size="4">4. Sometimes, I get the following message showing that all bond angles are outliers with &gt;8 sigmas, I listed part of the outliers.</font></div>

<div>        </div><div><div><font color="#3333ff">Top angle outliers (sorted by deviation):</font></div><div><font color="#3333ff">atoms                                 ideal       model  difference   deviation (sigma)</font></div>

<div><font color="#3333ff">----------------------------------------------------------------------------</font></div><div><font color="#3333ff"> SG  CYS D1204            57.894     104.470      46.576                9.32</font></div>

<div><font color="#3333ff">ZN    ZN D2001      </font></div><div><font color="#3333ff"> SG  CYS D1112      </font></div><div><font color="#3333ff"><br>
</font></div><div><font color="#3333ff">  SG  CYS D1201            50.842      92.496      41.654                8.33</font></div><div><font color="#3333ff">ZN    ZN D2001      </font></div>
<div><font color="#3333ff"> SG  CYS D1204      </font></div><div><font color="#3333ff"><br></font></div><div><font color="#3333ff"> SG  CYS D1204           126.952      92.496     -34.455               -6.89</font></div>

<div><font color="#3333ff">ZN    ZN D2001      </font></div><div><font color="#3333ff"> SG  CYS D1201      </font></div><div><font color="#3333ff"><br>
</font></div><div><font color="#3333ff"> SG  CYS D1201            52.183      86.105      33.922                6.78</font></div><div><font color="#3333ff">ZN    ZN D2001      </font></div>
<div><font color="#3333ff"> SG  CYS D1112      </font></div><div><font color="#3333ff"><br></font></div><div><font color="#3333ff"> SG  CYS D1194           152.275     119.729     -32.546               -6.51</font></div>

<div><font color="#3333ff">ZN    ZN D2001      </font></div><div><font color="#3333ff"> SG  CYS D1112      </font></div><div><font color="#3333ff"><br>
</font></div><div><font color="#3333ff"> SG  CYS D1112            89.273     119.729      30.456                6.09</font></div><div><font color="#3333ff">ZN    ZN D2001      </font></div>
<div><font color="#3333ff"> SG  CYS D1194      </font></div><div><font size="4"><br></font></div></div><div><font size="4">I also post my metal.edit file for refinement </font></div>
<div><font size="4"><br></font></div><div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font color="#3333ff">  bond {</font></div>
<div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name ZN   and chain D and resname ZN and resseq 2001</font></div>
<div><font color="#3333ff">    atom_selection_2 = name  SG  and chain D and resname CYS and resseq 1201</font></div><div><font color="#3333ff">    distance_ideal = 2.310000</font></div>
<div><font color="#3333ff">    sigma = 0.100</font></div><div><font color="#3333ff">  }</font></div><div><font color="#3333ff">}</font></div><div>
<font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font color="#3333ff">  bond {</font></div>
<div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name ZN   and chain D and resname ZN and resseq 2001</font></div>
<div><font color="#3333ff">    atom_selection_2 = name  SG  and chain D and resname CYS and resseq 1194</font></div><div><font color="#3333ff">    distance_ideal = 2.310000</font></div>
<div><font color="#3333ff">    sigma = 0.100</font></div><div><font color="#3333ff">  }</font></div><div><font color="#3333ff">}</font></div><div>
<font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font color="#3333ff">  bond {</font></div>
<div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name ZN   and chain D and resname ZN and resseq 2001</font></div>
<div><font color="#3333ff">    atom_selection_2 = name  SG  and chain D and resname CYS and resseq 1112</font></div><div><font color="#3333ff">    distance_ideal = 2.310000</font></div>
<div><font color="#3333ff">    sigma = 0.100</font></div><div><font color="#3333ff">  }</font></div><div><font color="#3333ff">}</font></div><div>
<font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font color="#3333ff">  bond {</font></div>
<div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name ZN   and chain D and resname ZN and resseq 2001</font></div>
<div><font color="#3333ff">    atom_selection_2 = name  SG  and chain D and resname CYS and resseq 1204</font></div><div><font color="#3333ff">    distance_ideal = 2.310000</font></div>
<div><font color="#3333ff">    sigma = 0.100</font></div><div><font color="#3333ff">  }</font></div><div><font color="#3333ff">}</font></div><div>
<font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div><div><font color="#3333ff">  angle {</font></div>
<div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name  SG  and chain D and resname CYS and resseq 1194</font></div>
<div><font color="#3333ff">    atom_selection_2 = name ZN   and chain D and resname ZN and resseq 2001</font></div><div><font color="#3333ff">    atom_selection_3 = name  SG  and chain D and resname CYS and resseq 1201</font></div>

<div><font color="#3333ff">    angle_ideal = 112.172178</font></div><div><font color="#3333ff">    sigma = 5</font></div><div><font color="#3333ff">  }</font></div>
<div><font color="#3333ff">}</font></div><div><font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font color="#3333ff">  angle {</font></div><div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name  SG  and chain D and resname CYS and resseq 1112</font></div>

<div><font color="#3333ff">    atom_selection_2 = name ZN   and chain D and resname ZN and resseq 2001</font></div><div><font color="#3333ff">    atom_selection_3 = name  SG  and chain D and resname CYS and resseq 1201</font></div>

<div><font color="#3333ff">    angle_ideal = 87.092184</font></div><div><font color="#3333ff">    sigma = 5</font></div><div><font color="#3333ff">  }</font></div>
<div><font color="#3333ff">}</font></div><div><font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font color="#3333ff">  angle {</font></div><div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name  SG  and chain D and resname CYS and resseq 1112</font></div>

<div><font color="#3333ff">    atom_selection_2 = name ZN   and chain D and resname ZN and resseq 2001</font></div><div><font color="#3333ff">    atom_selection_3 = name  SG  and chain D and resname CYS and resseq 1194</font></div>

<div><font color="#3333ff">    angle_ideal = 118.116518</font></div><div><font color="#3333ff">    sigma = 5</font></div><div><font color="#3333ff">  }</font></div>
<div><font color="#3333ff">}</font></div><div><font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font color="#3333ff">  angle {</font></div><div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name  SG  and chain D and resname CYS and resseq 1204</font></div>

<div><font color="#3333ff">    atom_selection_2 = name ZN   and chain D and resname ZN and resseq 2001</font></div><div><font color="#3333ff">    atom_selection_3 = name  SG  and chain D and resname CYS and resseq 1201</font></div>

<div><font color="#3333ff">    angle_ideal = 91.677138</font></div><div><font color="#3333ff">    sigma = 5</font></div><div><font color="#3333ff">  }</font></div>
<div><font color="#3333ff">}</font></div><div><font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font color="#3333ff">  angle {</font></div><div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name  SG  and chain D and resname CYS and resseq 1204</font></div>

<div><font color="#3333ff">    atom_selection_2 = name ZN   and chain D and resname ZN and resseq 2001</font></div><div><font color="#3333ff">    atom_selection_3 = name  SG  and chain D and resname CYS and resseq 1194</font></div>

<div><font color="#3333ff">    angle_ideal = 130.829256</font></div><div><font color="#3333ff">    sigma = 5</font></div><div><font color="#3333ff">  }</font></div>
<div><font color="#3333ff">}</font></div><div><font color="#3333ff"><br></font></div><div><font color="#3333ff">refinement.geometry_restraints.edits {</font></div>
<div><font color="#3333ff">  angle {</font></div><div><font color="#3333ff">    action = *add</font></div><div><font color="#3333ff">    atom_selection_1 = name  SG  and chain D and resname CYS and resseq 1204</font></div>

<div><font color="#3333ff">    atom_selection_2 = name ZN   and chain D and resname ZN and resseq 2001</font></div><div><font color="#3333ff">    atom_selection_3 = name  SG  and chain D and resname CYS and resseq 1112</font></div>

<div><font color="#3333ff">    angle_ideal = 104.886672</font></div><div><font color="#3333ff">    sigma = 5</font></div><div><font color="#3333ff">  }</font></div>
<div><font color="#3333ff">}</font></div><div><br></div><div><br></div><div><font size="4">Questions, </font></div><div><font size="4">1. Why the ideal bond angle are different in the metal.edit file and final model ? How does phenix determine the ideal bond_angle?</font></div>

<div><font size="4">    For example, in the metal.edit file</font></div><div><font color="#3333ff"><font size="4">  </font>atom_selection_1 = name  SG  and chain D and resname CYS and resseq 1204</font></div>
<div><font color="#3333ff">    atom_selection_2 = name ZN   and chain D and resname ZN and resseq 2001</font></div><div><font color="#3333ff">    atom_selection_3 = name  SG  and chain D and resname CYS and resseq 1112</font></div>

<div><font color="#3333ff"> The angle_ideal = 104.886672 </font></div><div><br></div><div><font size="4">But in the final model</font></div><div><font size="4"> </font></div>
<div><div><font color="#3333ff">atoms                                 ideal       model  difference   deviation (sigma)</font></div><div><font color="#3333ff">----------------------------------------------------------------------------</font></div>

<div><font color="#3333ff"> SG  CYS D1204            57.894     104.470      46.576                9.32</font></div><div><font color="#3333ff">ZN    ZN D2001      </font></div>
<div><font color="#3333ff"> SG  CYS D1112      </font></div></div><div style="font-size:large"><br></div></div><div style="font-size:large">2. Do I need to put the following LINK in the pdb header to run refinement?</div>

<div><font color="#3333ff">LINK        ZN    ZN D2001                 SG  CYS D1201     1555   1555  2.34  </font></div><div><font color="#3333ff">LINK        ZN    ZN D2001                 SG  CYS D1112     1555   1555  2.33  </font></div>

<div><font color="#3333ff">LINK        ZN    ZN D2001                 SG  CYS D1194     1555   1555  2.38  </font></div><div><font color="#3333ff">LINK        ZN    ZN D2001                 SG  CYS D1204     1555   1555  2.37</font></div>

<div><br></div><div><font size="4">3. After phenix refinement, the output pdb doesn&#39;t contain these LINK lines no matter what the inpout pdb is. Does phenix_refine use these restrains of LINK lines?</font></div>
<div><font size="4"><br></font></div><div><font size="4">Thanks.</font></div><div><font size="4"><br></font></div><font color="#888888"><div><font size="4">Yu Zhang</font></div>
<div><font size="4">Postdoc fellow</font></div><div><font size="4">Rutgers University</font></div>
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<br></blockquote></div><br></div>