<div dir="ltr">Alexandra<div><br></div><div>The restraints refining to a too short a distance is a real problem. The first thing to do is check in the .geo file to ensure that the restraints are being set correctly. It is a simple text file so it should be easy to read.</div><div><br></div><div>Feel free to send it to me driectly (with the .pdb file) if you want me to take a look.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709     Email : NWMoriarty@LBL.gov<br>Fax   : 510-486-5909       Web  : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div>
<br><div class="gmail_quote">On Thu, Jul 2, 2015 at 9:14 AM, Alexandra Marques <span dir="ltr">&lt;<a href="mailto:at.marques@fct.unl.pt" target="_blank">at.marques@fct.unl.pt</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">Hi,</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">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" target="_blank">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:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">Isotropic atoms: not element Mo</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">Anisotropic atoms: element Mo</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">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:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">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>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span> </span>refinement.geometry_restraints.edits {</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span> 
</span>bond {</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span>   
</span>action = *add</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span>   
</span>atom_selection_1 = name MO<span>   </span>and
chain A and resname 4MO and resseq 1</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span>   
</span>atom_selection_2 = name<span>  </span>O<span>   </span>and chain A and resname O and resseq 2</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span>   
</span>distance_ideal = 1.900000</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span>   
</span>sigma = 0.050</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><span> 
</span>}</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">}</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">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:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">Thank you very much,</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;">Alexandra</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"> </span></p>

</div>
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