<div dir="ltr">Hi Pavel,<div><br></div><div>It turns out I do have some special positions. Waters sit near a 2 fold axis. I have given them 0.5 occupancy. No error comes up but they simply get kicked out of the electron density. Maybe I should turn off rigid body refinement since I don't need it? Below is a link to a screen shot.</div>
<div><br></div><div><a href="https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png">https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png</a><br></div><div><br></div><div>-Yarrow</div><div><br></div></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Yarrow,<br>
<br>
oh good! I'm glad you solved the problem -:)<br>
<br>
All the best,<br>
Pavel<div><div class="h5"><br>
<br>
<div>On 6/18/14, 8:02 AM, Yarrow Madrona
wrote:<br>
</div>
<blockquote type="cite">Hi Pavel,
<div><br>
</div>
<div>Thanks for your quick response. It turns out that after I
reprocessed a data set in a higher symetry space group I forgot
to use a reference mtz so the orientation was completely off. I
just re-ran phaser and everything worked fine. I didn't run
rigid body refinement after phaser.</div>
<div><br>
</div>
<div>The original error message didn't list the atoms and I am not
sure how it could have any atoms on special positions with the
solution being completely wrong. Probably nothing to worry
about.</div>
<div>
<br>
</div>
<div>-Yarrow<br>
<br>
On Tuesday, June 17, 2014, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Yarrow,<br>
<br>
ok, I wish that error message (that I put a while ago, in 2009
to be precise) lists those atoms... Can you send me the file
so I can tell you what these atoms are?<br>
<br>
In general, if at rigid-body refinement stage you have atoms
at special positions it is unlikely to be right.<br>
<br>
Pavel<br>
<br>
On 6/17/14, 12:56 PM, Yarrow Madrona wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I am trying to do rigid body refinement, however I get an
error in phenix telling me that there are atoms at special
positions.<br>
<br>
I am not sure how to determine which atoms are at special
positions so that I can exclude them from rigid body
refinement. Can someone help me with this? Thank you.<br>
<br>
-Yarrow<br>
</blockquote>
<br>
</blockquote>
</div>
</blockquote>
<br>
</div></div></div>
</blockquote></div><br></div>