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Hi,<br>
<br>
I'm not sure I see what happens... Could you please send me the PDB
file and the command you run. You don't need to send me the data - I
can always simulate it. <br>
<br>
Normally, to do what you want you don't need to provide any selections.
Atoms in alternate conformations are detected automatically based on
altloc identifiers in PDB, the corresponding constrains are built
automatically and the constrained occupancy refinement happens by
default. <br>
<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
On 11/4/2008 3:46 AM, Anastassis Perrakis wrote:
<blockquote cite="mid:76EC8144-225C-4F73-8121-62440DAE5A69@nki.nl"
type="cite">Hi there -
<div><br>
</div>
<div><br>
</div>
<div>I was pleased to read in the manual:</div>
<div><br>
</div>
<div><span class="Apple-style-span"
style="font-family: Times; font-size: 16px;">
<ul class="simple" style="margin-bottom: 1em;">
<li>if no selections are provided (<tt class="docutils literal"
style="background-color: rgb(127, 255, 127);"><span class="pre"
style="white-space: pre;">refine.occupancies.individual=None</span></tt> and <tt
class="docutils literal" style="background-color: rgb(127, 255, 127);"><span
class="pre" style="white-space: pre;">refine.occupancies.group=None</span></tt>)
then phenix.refine by default will refine individual occupancies for
atoms that have partial occupancy values in input PDB file (except
zeros) and it will perform group constrained occupancy refinement for
all atoms in alternative conformations. Occupancies of all other atoms
will be fixed.</li>
<li>If selections are provided (<tt class="docutils literal"
style="background-color: rgb(127, 255, 127);"><span class="pre"
style="white-space: pre;">refine.occupancies.individual=atom_selection</span></tt> or <tt
class="docutils literal" style="background-color: rgb(127, 255, 127);"><span
class="pre" style="white-space: pre;">refine.occupancies.group=atom_selection</span></tt>)
then the selected atoms will be added to the list of atoms defined
above (atoms with partial occupancies or those in alternative
conformations). See this document for examples of atom_selection syntax.</li>
</ul>
</span></div>
<div><br>
</div>
<div>However, I want to refine my MET residues in double
conformations, one as MET (AMET) and the other one as MSE (BMSE) with
each 0.5 occupancy to start with. When I try that I get:</div>
<div><br>
</div>
<div>
<div>==</div>
<div> ----------Initial model statistics (before
refinement)---------- </div>
<div>...</div>
<div>|-Occupancies
statistics------------------------------------------------------|</div>
<div>Sorry: There are atoms with negative occupancies. Check input
PDB file.</div>
<div><br>
</div>
<div>===</div>
<div><br>
</div>
<div>The PDB file has 0.5 and 1.0 occupancies only.</div>
<div><br>
</div>
<div>I am also using:</div>
<div><br>
</div>
<div>==</div>
<div><br>
</div>
<div>
<div>refinement.refine.strategy=tls+individual_sites+individual_adp+group_anomalous</div>
<div>refinement.refine.adp.tls="chain A"</div>
<div>refinement.refine.adp.tls="chain B"</div>
<div>refinement.main.number_of_macro_cycles=4</div>
<div>refinement.simulated_annealing.start_temperature=5000</div>
<div>refinement.refine.adp.individual.anisotropic =" chain C"</div>
<div>refinement.input.xray_data.labels=I_Mystery(+),SIGI_Mystery(+),I_Mystery(-),SIGI_Mystery(-),merged</div>
<div>refinement.refine.anomalous_scatterers {</div>
<div> group {</div>
<div> selection = "name ZN "</div>
<div> f_prime = -0.3</div>
<div> f_double_prime = 2.5</div>
<div> refine = *f_prime *f_double_prime</div>
<div> }</div>
<div> group {</div>
<div> selection = "name SE "</div>
<div> f_prime = -5.2</div>
<div> f_double_prime = 3.8 </div>
<div> refine = *f_prime *f_double_prime</div>
<div> }</div>
<div>}</div>
<div><br>
</div>
<div>==</div>
<div><br>
</div>
<div><br>
</div>
<div>Any hints on how to proceed ? Should I define groups for the
occupancy refinement explicitely and not rely to automatic assignment?</div>
<div>And if so how? How do people treat this partial Se-Met issue ?
We solved the structure with SeSAD ... if I out MSE I get pretty large
negative density peaks on the Se ... if I put MET I get positive peaks
;-) And there are good reasons to believe in partial Se-substitution in
this case.</div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div><br>
</div>
<div>Tassos</div>
</div>
</div>
<pre wrap="">
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</blockquote>
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