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<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>Thank you,
Pavel. </FONT></FONT></FONT></DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT
size=3></FONT></FONT></FONT> </DIV>
<DIV>I am not clear about "model_based_outliers"; I searched phenix.refine
documentation </DIV>
<DIV>but did not find anything. Is it based on my structure model?</DIV>
<DIV>I will look at the paper you suggested. </DIV>
<DIV> </DIV>
<DIV>By the way, "main.<SPAN class=il>outliers_rejection</SPAN>=<WBR>False" can
also keep those model_based_outliers?</DIV>
<DIV><A
href="http://www.phenix-online.org/documentation/refinement.htm">http://www.phenix-online.org/documentation/refinement.htm</A> did
not mention this type</DIV>
<DIV>of outliers:</DIV>
<DIV>outliers_rejection= <SPAN style="COLOR: rgb(204,0,0)">True</SPAN> <FONT
size=3><SPAN style="COLOR: blue">Remove basic wilson outliers , extreme
wilson<BR>
outliers , and beamstop shadow outliers</SPAN><BR></FONT></DIV>
<DIV>Thanks</DIV>
<DIV> </DIV>
<DIV>Rongjin </DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT face="Courier New"
size=3></FONT> </DIV></FONT></FONT>
<DIV><FONT size=2><FONT face="Times New Roman"><FONT color=#666666>= = = = = = =
= <FONT color=#000000>On </FONT></FONT>2010-12-08 15:28:59 You
wrote <FONT color=#666666>= = = = = = = = </FONT></FONT></FONT></DIV>
<DIV><FONT face="Times New Roman" size=2>
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<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">Rongjin,<BR><BR>outliers
detection and rejection was inspired by this paper<BR>R.Read, Acta
Cryst. (1999). D55, 1759-1764.<BR><BR>and the paper by R.Agarwal's
(197?/198?) mentions this too.<BR><BR>You can always turn this off using
"main.<SPAN class=il>outliers_rejection</SPAN>=<WBR>False" if you
believe it's necessary.<BR><BR>It's probably the quality of your data
that causes the amount of outliers you
quote.<BR><BR>Pavel.<BR><BR>PS> FYI: I got your email sent off-list
and I always get the emails sent to phenixbb, so there is no need to
duplicate them. <BR><BR><BR>On 12/8/10 11:45 AM, <A
class=moz-txt-link-abbreviated
href="mailto:guanrj@foxmail.com">guanrj@foxmail.com</A> wrote:
<BLOCKQUOTE cite=mid:201012081445211878599@foxmail.com type="cite"><PRE wrap="">Hi All
I have a question regarding reflection outliers detection in phenix.refine:
in my input reflection file, there are 24432 reflections, but only 22769 of them
were used in refinement. I checked the log file and saw 1663 outliers.
(below if from the log)
basic_wilson_outliers = 14
extreme_wilson_outliers = 18
beamstop_shadow_outliers = 0
model_based_outliers = 1657
total = 1663
What is the "model_based_outliers"? What causes so many reflections rejected
and not used in the refinement?
Thanks
Rongjin
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