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Hi Alexandra,<br>
<br>
<blockquote
cite="mid:CAN_Pk50jBo5YXtOW61X+TgR_zi+328A_eqWnCrXci5iQapZsSw@mail.gmail.com"
type="cite">
<div dir="ltr"><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.</span></div>
</blockquote>
<br>
the map artifacts may be Fourier truncation ripples: see pages 8-14
here<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/presentations/faq.pdf">https://www.phenix-online.org/presentations/faq.pdf</a><br>
<br>
<blockquote
cite="mid:CAN_Pk50jBo5YXtOW61X+TgR_zi+328A_eqWnCrXci5iQapZsSw@mail.gmail.com"
type="cite">
<div dir="ltr"><span
style="font-family:"Arial","sans-serif"">
I read this message <a moz-do-not-send="true"
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 class="MsoNormal" style="margin-bottom:0.0001pt"><span
style="font-family:"Arial","sans-serif""></span><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>
</div>
</blockquote>
<br>
This is not a bad idea.<br>
<br>
<blockquote
cite="mid:CAN_Pk50jBo5YXtOW61X+TgR_zi+328A_eqWnCrXci5iQapZsSw@mail.gmail.com"
type="cite">
<div dir="ltr">
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span
style="font-family:"Arial","sans-serif"">�</span><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>
</div>
</blockquote>
<br>
This should be fine. Selections above are for individual ADPs.<br>
<br>
<blockquote
cite="mid:CAN_Pk50jBo5YXtOW61X+TgR_zi+328A_eqWnCrXci5iQapZsSw@mail.gmail.com"
type="cite">
<div dir="ltr">
<p class="MsoNormal" style="margin-bottom:0.0001pt">
</p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span
style="font-family:"Arial","sans-serif"">�</span><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: <br>
</span></p>
<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>
</div>
</blockquote>
<br>
Hm.. this sounds like a problem. Could you please send me input
files so that I can reproduce this problem and either fix it at our
end or explain what's done wrong.<br>
<br>
Pavel<br>
<br>
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