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Hi Tony,<br>
<br>
could you please send me the PDB file or its part that contains all
residues (atoms) in question, tell occupancies of which atoms should
be refined and how, and I will send you back working example as soon
as I can.<br>
<br>
What you are trying to do is definitely possible to do in
phenix.refine. <br>
<br>
Please send files off list (to may email directly).<br>
<br>
Thanks,<br>
Pavel<br>
<br>
On 9/19/11 8:02 AM, Antony Oliver wrote:
<blockquote
cite="mid:52D1A1FD-5809-4724-89DA-88EC32DCF3A6@sussex.ac.uk"
type="cite">
<div>Dear all,</div>
<div><br>
</div>
<div>Apologies if this has been covered already in a previous post
� but I can't find a suitable response in the archive.</div>
<div><br>
</div>
<div>We have the following situation...</div>
<div><br>
</div>
<div>We have soaked a ligand into an apo-crystal, collected
diffraction data, and solved the structure.</div>
<div><br>
</div>
<div>What is apparent from the electron density, �is that the
ligand isn't in the crystal at full occupancy, it's roughly
about 70-80%. �</div>
<div>However, as the ligand binds, it causes a small conformation
change in the active site of the protein, altering the position
of around 4 amino acids.</div>
<div><br>
</div>
<div>What I want to do, and can't quite get phenix.refine to do is
the following...</div>
<div><br>
</div>
<div>Refine the occupancy of the ligand (chain C resname LIG) with
the "A" conformation of the active site residues (which should
be the same, as they are mutually dependent) � and then refine
the occupancy of the "B" conformation of the active site
residues ���which should all theoretically add up to a total of
1.</div>
<div><br>
</div>
<div>Could anyone help me with how the occupancies /
constrained_group parameters should be set up in this case?</div>
<div><br>
</div>
<div>With thanks,</div>
<div><br>
</div>
<div>Tony.</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div><span class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family: Helvetica;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; font-size: medium;">
<div>
<div style="word-wrap: break-word;">
---</div>
<div style="word-wrap: break-word;">
Dr Antony W Oliver
<div>Senior Research Fellow</div>
<div>CR-UK�DNA Repair Enzymes Group</div>
<div>Genome Damage and Stability Centre</div>
<div>Science Park Road</div>
<div>University of Sussex</div>
<div>Falmer, Brighton, BN1 9RQ</div>
<div><br>
</div>
<div>email:�<a moz-do-not-send="true"
href="mailto:antony.oliver@sussex.ac.uk">antony.oliver@sussex.ac.uk</a></div>
<div>tel (office): +44 (0)1273 678349</div>
<div>tel (lab): +44 (0)1273 677512</div>
</div>
</div>
</span></div>
<br>
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</blockquote>
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