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Hi Carsten,<br>
<br>
for the refinement of b-factors there is no difference between two
options. We use the sphere b-factors restraints which are calculated
based on interatomic distances and the information about alternative
conformations is not used at that point.<br>
<br>
However if you refine the coordinates, the difference is significant:
if you refine it as two separate residues then they will "see" each
other for non-bonded interactions term calculation and hence will be
pushed apart.<br>
<br>
Please let me know if you still have questions!<br>
Pavel.<br>
<br>
<br>
Schubert, Carsten [PRDUS] wrote:
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<title>Question about restraints in individual B-factor refinement</title>
<p><font size="2">Hi,</font>
</p>
<p><font size="2">I have a question about the handling of restraints
in the individual B-factor refinement routine.</font>
</p>
<p><font size="2">What I'd like to do is to refine a ligand, which
can be present in 2 or more different conformations/orientations in its
binding site. I'd like to use B-factor refinement on the various
instances of the ligand, which one is the most relevant one, assuming
that the most relevant conformation/orientation is associated with the
lowest B-factor (Validity of that assumption set aside ...)</font></p>
<p><font size="2">My question is now is there any difference in the
restraints applied to the b-factors in the scenarios where A) the
ligand is modeled as alternate conformations i.e.</font></p>
<p><font size="2">ATOM 2724 C01AINH I 1 27.808 26.376
23.301 0.50 27.77 I C</font>
<br>
<font size="2">ATOM 2733 C01BINH I 1 30.898 22.496
17.340 0.50 22.15 I C</font>
<br>
<font size="2">...</font>
</p>
<p><font size="2">vs. scenario B) where the same ligand is modeled as
2 different residues</font>
<br>
<font size="2">ATOM 2724 C01 INH I 1 27.808 26.376
23.301 0.50 27.77 I C</font>
<br>
<font size="2">ATOM 2733 C01 INH I 2 30.898 22.496
17.340 0.50 22.15 I C</font>
<br>
<font size="2">....</font>
</p>
<p><font size="2">Basically, what I am trying to achieve is to
uncouple the B-factor refinement of each individual instance of the
ligand from its other instance(s). Are there any hidden pitfalls
between these 2 scenarios I should be aware of?</font></p>
<br>
<p><font size="2">Many thanks for any input.</font>
</p>
<br>
<p><font size="2">Cheers</font>
</p>
<p> <font size="2">Carsten</font>
</p>
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