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<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">Hi,</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">I am refining a protein with a Mo in
the active site and which is bound to a cofactor and to a water molecule. After
each refinement step there is always a lot of positive and negative density
around the Mo and the cofactor molecules, although their occupancy refined to 1.
I read this message <a href="http://www.phenix-online.org/pipermail/phenixbb/2015-May/022031.html">http://www.phenix-online.org/pipermail/phenixbb/2015-May/022031.html</a>,
but I still have doubts about how to choose the refinement parameters. I know I
have to select the Mo atoms to be refined anisotropically. And the other atoms,
do I have to specifically select them to be refined isotropically?. For
instance:</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">Isotropic atoms: not element Mo</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">Anisotropic atoms: element Mo</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">I am asking that because I have been
using TLS for the protein atoms during refinement, so I am not sure if it is correct
to select the other atoms as isotropic or if I leave it in blank…</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">My other problem is with the metal
restraints. I am not sure about the ideal distance between the Mo and O atom
but based on homologous protein structures I choose the following:</span></p>
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<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style> </span>refinement.geometry_restraints.edits {</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style>
</span>bond {</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style>
</span>action = *add</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style>
</span>atom_selection_1 = name MO<span style> </span>and
chain A and resname 4MO and resseq 1</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style>
</span>atom_selection_2 = name<span style> </span>O<span style> </span>and chain A and resname O and resseq 2</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style>
</span>distance_ideal = 1.900000</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style>
</span>sigma = 0.050</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""><span style>
</span>}</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">}</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">However after the refinement this ideal
distance interval (1.95-1.85) is not respected; I have 4 active sites and in
some of them the Mo-O distance refines to 0.83 A although there is a lot of density
for the water molecule to be at 1.9 A. How to make the restrainst work? Am I
missing something?</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">Thank you very much,</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif"">Alexandra</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:"Arial","sans-serif""> </span></p>
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