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Hi Yarrow,<br>
<br>
if you are at the water picking stage then it's almost certain you
don't need to do rigid-body refinement. Normally, you do rigid-body
refinement once at the very beginning if you believe it's necessary.
Regarding that water. What happens if you run refinement without
rigid-body and with automatic water update (that will
add/remove/refine waters)?<br>
<br>
Here is how phenix.refine treats atoms on special positions. It it
"sees" an atom close to special position (within some tolerance,
which is 0.5 or 1A, I forgot exact number) it moves that atoms
exactly onto special position, and then keep it there throughout
refinement. So if you see that water moves, then I guess it is close
to s.p. but not enough. Or perhaps there is something else is going
on..<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/18/14, 12:06 PM, Yarrow Madrona
wrote:<br>
</div>
<blockquote
cite="mid:CAMHjG6bKUvb3r5Xu_F3JaQ2dNq4usOO6KehCoN+gp11UjF8kjg@mail.gmail.com"
type="cite">
<div dir="ltr"><span
style="font-family:arial,sans-serif;font-size:15.555556297302246px">Hi
Pavel,</span>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px">
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
style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px"><a
moz-do-not-send="true"
href="https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png"
target="_blank">https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png</a></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 moz-do-not-send="true"
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
moz-do-not-send="true"
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>
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