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Dear Busters,<br>
Is there any way to introduce Ramachandran restraints for the
refinement in cases of (very) low resolution?<br>
And side chain rotamer restrictions to infavor
energetically-favorable conformations? <br>
Thanks,<br>
Xavier<br>
<br>
El 03/02/2012 18:40, Oliver Smart escribió:
<blockquote
cite="mid:alpine.DEB.2.00.1202031725550.10557@hypatia.globalphasing.com"
type="cite">
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On Fri, 3 Feb 2012, Dale Tronrud wrote:
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I agree with Peitro. I don't know of a reason why an atom must be exactly
on the symmetry axis. Often the density on the axis is not spherical so either
you have anisotropic B's (for a small deviation) or the atom has to shift a
bit off center.
If a bad contact restraint is pushing the atom away, then the EXCLUDE
statement should do the trick.
Dale Tronrud
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<pre wrap="">
It can be a reasonable choice to model an atom or ion on a special
position with a single atom that lies exactly on axis or position.
I think that SHELX allows this to be done with constraints. I would
like to allow BUSTER users to choose this with the distance restraints
(next release).
If the atom is allowed to drift from axis then it is a bit like allowing
two alternates on a "normal" water. It is a perfectly reasonable modelling
choice. But additional refinement parameters are introduced by allowing
the atom to move off axis. In my limited experience density on symmetry
axes is difficult to interpret and can have artefacts.
The special position handling in BUSTER is not yet completely sorted. The
current state-of-play is described:
<a class="moz-txt-link-freetext" href="http://www.globalphasing.com/buster/manual/gelly/manual/gelly7.html">http://www.globalphasing.com/buster/manual/gelly/manual/gelly7.html</a>
The distance cut-off used does mean that drift can suddenly mean fully
non-bonded terms appear and the atom flys away from the axis.
Regards
Oliver
| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK |
| <a class="moz-txt-link-freetext" href="http://www.globalphasing.com/people/osmart/">http://www.globalphasing.com/people/osmart/</a> |
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</pre>
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<br>
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