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<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2>RASMBers, I am re-posting this thread from the SEDFIT user's list (which
concerns AUC hardware issues rather than SEDFIT itself) to RASMB at
Walt Stafford's suggestion.</FONT></SPAN></DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2>John</FONT></SPAN></DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2>-----------------------------</FONT></SPAN></DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2>Mathew,</FONT></SPAN></DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff size=2>The
issue of whether rotor stretching affects radial calibration is is a very common
source of confusion. Remember, the optical components that measure the radial
positions for both optical systems are permanently mounted on the base
plate of the instrument. Thus the rotor stretching does not affect the
measurement accuracy (yes, the sample actually moves out to higher radii when
the rotor stretches, and hence experiences higher forces, but the optics
correctly measure that fact). </FONT></SPAN></DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff size=2>The
radial calibration is based on the accurate machining of the rotor and the
precision edges in the counterbalance. Based on that machining the edges will be
exactly 5.85 and 7.15 cm from the center of the rotor, <U>but only when the
rotor has not stretched</U>. If you calibrate on a stretched rotor, and assign
those positions as still being at 5.85 and 7.15 cm, the calibration will be
wrong.</FONT></SPAN></DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=497384315-10052006><FONT face=Arial color=#0000ff
size=2>John</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>
sedfit-bounces@bilbo.bio.purdue.edu
[mailto:sedfit-bounces@bilbo.bio.purdue.edu] <B>On Behalf Of </B>Parker,
Matthew<BR><B>Sent:</B> Wednesday, May 10, 2006 7:51 AM<BR><B>To:</B> Sedfit
User's Group Mailing List<BR><B>Subject:</B> RE: [Sedfit] radial
calibration<BR><BR></FONT></DIV>
<DIV class=Section1>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">John,<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">
Now that you mention it, I have a question about the radial calibration
procedure. I understand the reason for doing the calibration at 3000 rpm,
where there is minimal rotor stretching, but my question is: wouldn’t the
calibration be more accurate if it were done at the speed at which the data is
collected, where the calibration would presumably correct for the rotor
stretching that occurs? I am sure that the answer is “no,” but I am curious
about exactly why that is.<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">
Thanks,<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">
Matt<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<DIV>
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face="Times New Roman" size=3><SPAN style="FONT-SIZE: 12pt">
<HR tabIndex=-1 align=center width="100%" SIZE=2>
</SPAN></FONT></DIV>
<P class=MsoNormal><B><FONT face=Tahoma size=2><SPAN
style="FONT-WEIGHT: bold; FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">From:</SPAN></FONT></B><FONT
face=Tahoma size=2><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">
sedfit-bounces@bilbo.bio.purdue.edu
[mailto:sedfit-bounces@bilbo.bio.purdue.edu] <B><SPAN
style="FONT-WEIGHT: bold">On Behalf Of </SPAN></B>John Philo<BR><B><SPAN
style="FONT-WEIGHT: bold">Sent:</SPAN></B> Wednesday, May 10, 2006 10:38
AM<BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> 'Sedfit User's Group
Mailing List'<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> RE:
[Sedfit] radial calibration</SPAN></FONT><o:p></o:p></P></DIV>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"><o:p> </o:p></SPAN></FONT></P>
<DIV>
<P class=MsoNormal><st1:City w:st="on"><st1:place w:st="on"><FONT face=Arial
color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">Marina</SPAN></FONT></st1:place></st1:City><FONT
face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">, it is possible to
do runs without the counterbalance, but for <U>interference</U> scans only.
The counterbalance must be present for absorbance scans in order to calibrate
the timing of the lamp pulses (the 'delay' setting). <U>Sometimes</U> the
absorbance scans will actually run okay with a sample cell in the
counterbalance position, but often this fails totally or gives noisy scans
because the delay setting is not quite
right.</SPAN></FONT><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P></DIV>
<DIV>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">I am surprised though
that the error message you get is about radial calibration---I would expect it
to fail on the delay calibration. It sounds like you may have turned on the
'calibrate radius before first scan' option. You generally do <U>not</U> want
to use this option. That option is dangerous because you may
inadvertently do the calibration at high rotor speed (when the rotor has
stretched) and this will cause the calibration to be wrong. Basically the
radial calibration only needs to be done if the optical components permanently
mounted on the instrument have been serviced (and normally your service
technician would do this).</SPAN></FONT><o:p></o:p></P></DIV>
<DIV>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P></DIV>
<DIV>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">John</SPAN></FONT><o:p></o:p></P></DIV>
<BLOCKQUOTE style="MARGIN-TOP: 5pt; MARGIN-BOTTOM: 5pt; MARGIN-RIGHT: 0in">
<P class=MsoNormal style="MARGIN-BOTTOM: 12pt"><FONT face=Tahoma
size=2><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">-----Original
<st1:PersonName w:st="on">Me</st1:PersonName>ssage-----<BR><B><SPAN
style="FONT-WEIGHT: bold">From:</SPAN></B>
sedfit-bounces@bilbo.bio.purdue.edu
[mailto:sedfit-bounces@bilbo.bio.purdue.edu] <B><SPAN
style="FONT-WEIGHT: bold">On Behalf Of </SPAN></B>Fasolini, Marina
[Nervianoms]<BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B>
Wednesday, May 10, 2006 3:39 AM<BR><B><SPAN
style="FONT-WEIGHT: bold">To:</SPAN></B>
sedfit@bilbo.bio.purdue.edu<BR><B><SPAN
style="FONT-WEIGHT: bold">Subject:</SPAN></B> [Sedfit] radial
calibration</SPAN></FONT><o:p></o:p></P>
<P><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><!-- Converted from text/rtf format -->I'm
running a velocity experiment without the couterbalance cell, because I've
understood that it is possible, but during the run I have always an error
message for the radial calibration.</SPAN></FONT><o:p></o:p></P>
<P><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Is it correct?</SPAN></FONT>
<o:p></o:p></P>
<P><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">MARINA FASOLINI</SPAN></FONT>
<BR><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Structural
Chemistry</SPAN></FONT> <BR><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Nerviano <st1:PersonName
w:st="on">Me</st1:PersonName>dical Sciences</SPAN></FONT> <BR><FONT
face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Viale Pasteur 10</SPAN></FONT>
<BR><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">20014 Nerviano
(MI)</SPAN></FONT> <BR><st1:place w:st="on"><st1:country-region
w:st="on"><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">ITALY</SPAN></FONT></st1:country-region></st1:place>
<BR><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">tel. +39 0331
581462</SPAN></FONT> <BR><FONT face=Verdana size=2><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">fax. +39 0331
581360</SPAN></FONT> <BR><U><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">marina.fasolini@nervianoms.com</SPAN></FONT></U>
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