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Hi Yarrow,<br>
<br>
I guess it this point it's easiest of you send me files and I try
various things myself. Then I send you what I get and also post
summary. Of course all files will be handled confidentially! I may
not be able to look into this right away but I wil do my best to
look by tonight.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/18/14, 1:25 PM, Yarrow Madrona
wrote:<br>
</div>
<blockquote
cite="mid:CAMHjG6bDmFCgLfE4HPk5dtL7dNcfJZv1QfwdoBxEaVMrnum5rw@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Pavel,
<div><br>
</div>
<div>The waters move away when I do as you suggested. I am
providing a screen shot: </div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="https://www.dropbox.com/s/lv1vvq8kcr8rion/special_positions_2.png">https://www.dropbox.com/s/lv1vvq8kcr8rion/special_positions_2.png</a></div>
<div><br>
</div>
<div>I'm not sure what is going on but there is definitely a 2
fold symmetry near these waters.</div>
<div><br>
</div>
<div>-Yarrow</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Jun 18, 2014 at 1:01 PM, 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>
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..<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span>
<div class=""><br>
<br>
<div>On 6/18/14, 12:06 PM, Yarrow Madrona wrote:<br>
</div>
<blockquote 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><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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