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Hi Simon,<br>
<br>
yes, as Folmer suggested, you can use atom selections to define the
rigid body groups such that they do not include the atoms at special
positions. For example:<br>
<br>
phenix.refine model.pdb data.mtz rigid.params<br>
<br>
where the file rigid.params contains lines like these:<br>
<br>
<font face="Courier New, Courier, monospace">refinement.refine {<br>
sites {<br>
rigid_body = chain A and not (resseq 123 and (name XX or name ZZ))<br>
</font><font face="Courier New, Courier, monospace"> rigid_body = </font><font
face="Courier New, Courier, monospace">chain B and not (resseq 456 and
element Fe)</font><br>
<font face="Courier New, Courier, monospace"> rigid_body = </font><font
face="Courier New, Courier, monospace">chain Y or chain Z</font><br>
<font face="Courier New, Courier, monospace"> }<br>
}</font><br>
<br>
However, since the large-scale movements of the rigid groups are
expected during rigid body refinement, it may happen that they will
move away from fixed atoms (and therefore breaking the bonds), but may
be it is ok at the level of accuracy at rigid body refinement stage.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
<br>
On 8/13/09 7:14 AM, Simon Kolstoe wrote:
<blockquote cite="mid:01AFB709-270B-4690-8E96-0EED195ACBE7@ucl.ac.uk"
type="cite">
<pre wrap="">Dear Pavel et al.
Is there any way of defining a residue for rigid body refinement if a
couple of the atoms are sitting on a symmetry axis? i.e. can I define
the rigid body to be chain L but not the atoms that are giving the
problems? I keep on getting the error:
================== Extract refinement strategy and selections
=================
Some atoms selected for rigid body refinement are in special positions
(listed
below). Please remove these atoms from the rigid body selection and
run
refinement again.
"ATOM 4 C4 A12 L 2 .*. C "
Sorry:
Atoms at special positions are within rigid groups.
Thanks,
Simon
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