<div dir="ltr">On Mon, Jun 23, 2014 at 9:35 PM, Egor Tchesnokov <span dir="ltr"><<a href="mailto:etchesnokov@chemistry.otago.ac.nz" target="_blank">etchesnokov@chemistry.otago.ac.nz</a>></span> wrote:<br><div class="gmail_extra">
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><div>Active site contains iron (FE2) coordinated by three histidines. </div>
<div>After Phaser the active site does not contain un-explained green density.</div>
<div>After Refinement blobs of various shapes appear in the vicinity and upto 3-4A of active site iron.</div>
<div>Refinement is done using occupancy and anomalous of iron options.</div>
<div>Buffers do not contain molecules that could fit in those blobs.</div></div></div></blockquote><div><br></div><div>Phaser resets all heteroatoms to zero occupancy unless you specifically request otherwise, and I don't think refinement will magically take care of that. If you're using the GUI, click the button labeled "Modify start model" in the middle configuration tab, choose occupancies, and enter 1 for the new occupancy. (The occupancy refinement will still take place.) Or you can just do this manually in PDBtools or the PDB editor.</div>
<div><br></div><div>-Nat</div></div></div></div>