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Hi Timothy,<br>
<br>
the default values (coordinate_sigma = 0.05 , b_factor_weight = 10)
should be good in most cases. It depends what you call "looser".
Yes, you can make them looser by increasing coordinate_sigma (for
refinement of individual coordinates), and decreasing
b_factor_weight (for individual isotropic B-factor refinement). You
can do it specifically for selected atoms, since you can define as
many NCS related groups of atoms as you wish and each defined with
their individual weights:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/refinement.htm#anch24">http://phenix-online.org/documentation/refinement.htm#anch24</a><br>
<br>
refinement.ncs.restraint_group {<br>
reference = chain A resid 1:4<br>
selection = chain B and resid 1:3<br>
selection = chain C<br>
coordinate_sigma = 0.05<br>
b_factor_weight = 10<br>
}<br>
refinement.ncs.restraint_group {<br>
reference = chain E<br>
selection = chain F<br>
coordinate_sigma = 0.025<br>
b_factor_weight = 3<br>
}<br>
refinement.ncs.restraint_group {<br>
reference = chain Z and backbone<br>
selection = chain F and backbone<br>
}<br>
refinement.ncs.restraint_group {<br>
reference = chain Z and sidechain<br>
selection = chain F and sidechain<br>
selection = (chain I or chain K) and sidechain<br>
}<br>
<br>
Let me know if you have any questions.<br>
<br>
Pavel.<br>
<br>
<br>
On 12/7/10 7:31 PM, Timothy Springer wrote:
<blockquote
cite="mid:0FD52519-7E98-4623-9A43-9B0F59CFB004@idi.harvard.edu"
type="cite">Hi, I am using NCS restraints for 4 copies of a
molecule at 3.05 Å. We are using the standard weights:
<div>
<div> coordinate_sigma = 0.05</div>
<div> b_factor_weight = 10</div>
<div>and the 4 molecules look identical. What are suggested
values for looser restraints? One of my colleagues said that
varying them did not make a difference- ncs was still very
strict. Is there a way to make them less strict?</div>
<div>Thanks,</div>
<div>
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style="border-collapse: separate; color:
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class="Apple-style-span"
style="border-collapse: separate;
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<div style="font-family: Arial;">Timothy
A. Springer, Ph.D.
</div>
</span></span></span></span><br>
</div>
</span></div>
</span></div>
</span></div>
</span></span></div>
</div>
</blockquote>
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