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Hi Renato,<br>
<br>
could you please send me files that are sufficient to reproduce
this? <br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/11/17 10:06, Renato Ferras wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAC2Wzsg9AcOkXXw+f0dCFqP2VNr1P_XbyqVCiKGu=Zh8wOgxHA@mail.gmail.com">
<div dir="ltr">Dear all,<br>
<br>
I am refining a protein structure at 1.74 A resolution with
phenix.refine (version 1.10.1_2155) and I have noticed that some
side chains don't remain in the electronic density even after
careful hand adjustment in which they are almost perfect. It
seems pretty clear where the side chain should (must) be
located, moreover it is consistent with two rotamers (either
rotamer tp60 - #4 in coot - or rotamer tp-100 - #9 in coot -,
which are approx. at 180 deg for chi3). In spite of that, after
reciprocal space refinement, I observe that the end of side
chain rotates chi3 angle and both N and O gets far from where
they started (there is this difference in the chi3 angle).<br>
My concerns are about the proper interpretation of geometrical
restraints listed in .geo file, specially what the ideal value
is, how weights are applied to ideal value and why phenix
doesn't reach convergence in reciprocal space refinement. Below
are the values from .geo for the referred Gln:<br>
<br>
<span class="gmail-im">dihedral pdb=" CB GLN B 21 "<br>
pdb=" CG GLN B 21 "<br>
pdb=" CD GLN B 21 "<br>
pdb=" OE1 GLN B 21 "<br>
ideal model delta sinusoidal sigma weight
residual<br>
0.00 23.41 -23.41 2 3.00e+01
1.11e-03 8.42e-01<br>
<br>
</span><br>
is there a description for us to interpret what these numbers
are? To my understanding, the ideal values are established as
being either 0 or 180 degrees (yet sinusoidal 2). I cannot say
about how heavy the weights are on these (in fact, I left my
refinement to optimize weights), but anyway, if I understand
correctly, the ideal value (for chi3) should be rotamer
dependent. Taking Gln as an example, I see several rotamers do
have values close to either 0 or 180 degree, but what about
rotamers 4 and 9? I might imagine a similar situation for
residues like Asn and His, though I have not searched deep for
these yet.<br>
Thanks,<br>
<br>
<br>
Renato<span class="gmail-im"></span></div>
<br>
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