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<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff
size=2>Samantha,</FONT></SPAN></DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff size=2>It is
very common with the <EM>c(s)</EM> method to see what you are calling a
'half-peak' at the left end, but this is often a 'false' peak. Basically it
arises because the data do not go out to long enough times to provide any real
information about the very small sedimentation coefficients, because they never
pull significantly away from the meniscus. If you are analyzing data taken at
30K rpm, you probably really can't 'see' any species below 0.5 S (if that). If
you allow the fitter to play with parameters that have no real influence on the
data, it is virtually guaranteed that it will come up with some nonsense trying
to fit what is really noise in the data.</FONT></SPAN></DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff size=2>So you
probably want to start the distribution at a higher s value, but doing that
doesn't always get rid of your half-peak. Once you realize it is false, just
ignore it. If you need a graph with that peak gone, just copy and paste the
distribution table into another graphing program and delete those low
sedimentation coefficient points.</FONT></SPAN></DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff size=2>It is
of course possible with interference data that you are actually detecting some
sedimentation of buffer components, but that is much less likely at 30K. As Walt
Stafford often points out, even if you use a dialysate the buffer sedimentation
will not perfectly cancel unless the reference meniscus is matched to the sample
meniscus.</FONT></SPAN></DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=575363719-23012004><FONT face=Arial color=#0000ff size=2>John
Philo</FONT></SPAN></DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
rasmb-admin@rasmb-email.bbri.org [mailto:rasmb-admin@rasmb-email.bbri.org]
<B>On Behalf Of </B>Jones, Samantha<BR><B>Sent:</B> Friday, January 23, 2004
9:20 AM<BR><B>To:</B> rasmb@rasmb-email.bbri.org<BR><B>Subject:</B> [RASMB]
Low s value peaks<BR><BR></FONT></DIV>
<DIV><SPAN class=459145716-23012004><FONT face=Arial size=2>Hello
all</FONT></SPAN></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004>I have been
trying to analyse some interference data on Sedfit and have been repeatedly
seeing a</SPAN> <SPAN class=459145716-23012004>large 'half' peak at very
low s values on my s value distributions.</SPAN></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004>On the
continuous c(s) distributions after fitting to range of 0.1s to 10s the
distribution line starts at c(s) values of 1.5 to 0.5 on 0 on the x axis,
dropping to 0 on the y axis by 0.1s value. This is still the case after
changing the parameters to 0.01s to 10s. </SPAN></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004>The buffer
used at first was 10mM NaAcetate, 0.2% Azide and 2mM DTT pH 4. At first I
thought it could be the DTT but I saw the same thing using a sample in a
buffer 10mM Tris 10mM Na Acetate, 0.2% Azide no DTT pH 8.
</SPAN></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004>I have seen
this spinning at 30K and 50K for about 16hours.</SPAN></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN
class=459145716-23012004></SPAN></FONT></FONT> </DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004>Could Azide
be the problem? I don't expect either sample to be contaminated, however
anything of this size would have been missed by the SDS-PAGE gel run on both
samples.</SPAN></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN
class=459145716-23012004></SPAN></FONT></FONT> </DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004>Thank
you</SPAN></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN
class=459145716-23012004></SPAN></FONT></FONT> </DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004>Samantha
Jones</SPAN></FONT></FONT></DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=459145716-23012004><!-- Converted from text/rtf format -->
<P><SPAN lang=en-gb><I><FONT face="Palatino Linotype" size=2>Samantha
Jones</FONT></I></SPAN> <BR><SPAN lang=en-gb><I><FONT face="Palatino Linotype"
size=2>MRC Prion Unit</FONT></I></SPAN> <BR><SPAN lang=en-gb><I><FONT
face="Palatino Linotype" size=2>St Marys Hospital</FONT></I></SPAN> <BR><SPAN
lang=en-gb><I><FONT face="Palatino Linotype" size=2>Norfolk
Place</FONT></I></SPAN> <BR><SPAN lang=en-gb><I><FONT face="Palatino Linotype"
size=2>London</FONT></I></SPAN> <BR><SPAN lang=en-gb><I><FONT
face="Palatino Linotype" size=2>W2 1PG</FONT></I></SPAN>
</P></SPAN></FONT></FONT></DIV></BLOCKQUOTE></BODY></HTML>