<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Alex,<br>
<br>
if packing/contacts make sense that may be something (even
unexpected) from crystallization cocktail. <br>
<br>
I guess Autobuild needs to know what to look for and build,
otherwise given the resolution there may be impractically too many
choices. And if you knew what it is then building it by hand in this
case is easier.<br>
<br>
If you have no idea what it is then perhaps it's better to leave
this density blob alone rather than stick into it something that you
are not confident about.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/18/16 13:56, Alex Lee wrote:<br>
</div>
<blockquote
cite="mid:CANEq62a5zfdtu4H6nLv5eTG6J3Yt-WKBhyivTOu3SUF2et+uhw@mail.gmail.com"
type="cite">
<div dir="ltr">Dear Phenixbb members,
<div><br>
</div>
<div>I have a protein (90aa length) structure with 2.3A
resolution and space group P21 refined to Rfree/R to around
0.27 / 0.20. There are 3 protein dimers in one asym unit. For
two dimers (chain A, B, C, D), I can see clearly continuous
electron density from residue 10 to residue 89. However for
the third dimer (chain E and F), I can only see clearly
continuous density between residue 10 to residue 72 and lost
tracing of the main chain.� I did see a large electron density
blob close to the third dimer. (<span
style="color:rgb(33,33,33);font-family:Roboto,RobotoDraft,Helvetica,Arial,sans-serif;font-size:13px;line-height:20px"><a
moz-do-not-send="true"
href="https://goo.gl/photos/R1SaHPKS6VLfcesb7"><a class="moz-txt-link-freetext" href="https://goo.gl/photos/R1SaHPKS6VLfcesb7">https://goo.gl/photos/R1SaHPKS6VLfcesb7</a></a>
; G</span><span
style="font-size:13px;color:rgb(33,33,33);font-family:Roboto,RobotoDraft,Helvetica,Arial,sans-serif;line-height:20px">reen
is positive density at 3 sigma and blue is FWT PHWT at
2sigma and 1sigma�</span><font color="#212121" face="Roboto,
RobotoDraft, Helvetica, Arial, sans-serif"><span
style="line-height:20px">). I do not know how to explain
this blob. It seems to me that this blob is unlikely
protein fragments (some parts of the blob is so chunky).
Even if it's true that it's certain protein fragment
between residue 73 to residue 89 of chain E or chain F,
then the position of this fragment is totally different
from the position of its fragment�counterparts�in chain
A,B, C,D. I assume NCS copies (in this case maybe 3
copies) should have the same morphology as to each other.
�</span></font></div>
<div><br>
</div>
<div>It also seems to me that this density is not from my
crystal growth or harvest conditions, which has: Bis-Tris;
PEG3350; PEG400 and NaCl.�</div>
<div><br>
</div>
<div>I do not know if Phenix Autobuild could build this
automatically for me, but I'll try this later.</div>
<div><br>
</div>
<div>Thanks in advance for any input on this.</div>
<div><br>
</div>
<div>The density link is:�<span
style="color:rgb(33,33,33);font-family:Roboto,RobotoDraft,Helvetica,Arial,sans-serif;font-size:13px;line-height:20px"><a
moz-do-not-send="true"
href="https://goo.gl/photos/R1SaHPKS6VLfcesb7"><a class="moz-txt-link-freetext" href="https://goo.gl/photos/R1SaHPKS6VLfcesb7">https://goo.gl/photos/R1SaHPKS6VLfcesb7</a></a></span></div>
<div><span
style="color:rgb(33,33,33);font-family:Roboto,RobotoDraft,Helvetica,Arial,sans-serif;font-size:13px;line-height:20px"><br>
</span></div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
</body>
</html>