<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Our upgrade was done in Oct 2012,
version 5.8<br>
Does anyone know if it also has this problem?<br>
Judith Kornblatt<br>
Concordia University<br>
Montreal<br>
<br>
On 1/25/2013 9:29 AM, Ghirlando, Rodolfo (NIH/NIDDK) [E] wrote:<br>
</div>
<blockquote
cite="mid:C52D03BAE259874C86BD6C5179458291149BD98E45@NIHMLBX08.nih.gov"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 11 (filtered
medium)">
<o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place">
<o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PostalCode">
<o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="State">
<o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City">
<o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="Street">
<o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="address">
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Batang;
panose-1:2 3 6 0 0 1 1 1 1 1;}
@font-face
{font-family:"\@Batang";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:Arial;
color:windowtext;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="Section1">
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Dear friends and colleagues,<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">It has come to our (Joy
Zhao, Peter Schuck, Grzegorz Piszczek, Chad
Brautigam and myself) attention
that sedimentation coefficients based on SV
data collected using the
ProteomeLab XLA/I version 6 acquisition
software are up to 10% larger than
expected (depending on the rotor speed).<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">We have traced this to a
smaller than expected elapsed time stamp in
the file header. A correction for
this has been implemented in SEDFIT based in
part on the Windows OS file
creation time stamp. This version has been
released, as indicated in the
forwarded email from the SEDFIT-L list below,
and we will report more details
on this shortly.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">In addition Beckman Coulter has
been advised of this issue.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Sincerely,<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Rodolfo Ghirlando<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">FORWARDED MESSAGE<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Dear Colleagues,<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">This is to let you know of a
critical SEDFIT update with version 14.0c,
which you can download from <a
moz-do-not-send="true"
href="https://sedfitsedphat.nibib.nih.gov/software/Shared%20Documents/sedfit140c.zip">https://sedfitsedphat.nibib.nih.gov/software/Shared%20Documents/sedfit140c.zip</a><o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">It has a very important new
feature for the analysis of sedimentation
velocity: it automatically compares
the elapsed times reported in the data file
headers with the time differences
obtained from the file creation timestamps
generated by the Windows operating
system on the PC.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Why would we need this? In
the course of a joint study between our lab
and the labs of Rodolfo Ghirlando,
Greg Piszczek and Chad Brautigam, we have
recently discovered that data files
can have elapsed time entries less than the
differences from the operating
system timestamp, by as much as 10%.
Obviously, if the elapsed time entry is
10% too low then this leads to s-values that
are 10% too high!<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">We have double checked data
from many different instruments, and
correlated this discrepancy in elapsed
times with the ProteomeLab data acquisition
software version 6. No time
differences, or only trivial ones, were
observed for instruments running
earlier versions of the data acquisition
software. In some runs the overall
difference amounts to hours at the end of the
run, and I believe that the
operating system timestamp is correct. We will
distribute more detailed
information shortly, but want to give you
already a heads-up in the meantime
with this note: If you are running version 6
you may want to examine the data
files, and/or time the data acquisition
process yourself, to verify.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">We have discussed this
matter with our Beckman service engineer and
it appears as though the company
is now addressing this issue.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">The new SEDFIT release can
fix this problem for the data analysis. First,
it automatically checks and
creates a report if a systematic and
significant discrepancy exists between
differences in the file time-stamp and
differences in the header elapsed time.
If there appears to be a problem (i.e.
apparent dilation factor greater than a
user-defined threshold, initially defaulted to
1.005 or 0.5%), SEDFIT will
create a report and then offer to write data
files (under different names, of
course) with time entries based on a dilation
factor extracted from the file
timestamps. Subsequent analysis of these
time-corrected data files should
eliminate the problem, as it did perfectly for
the data in our study. Such
time-corrected scan files should also be the
ones loaded into SEDPHAT, which
will get its own update shortly.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Please let me know if you
have any questions, or if any problems occur
with the new version.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Best wishes and good luck,<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Peter<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Peter Schuck, PhD<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Chief, Dynamics of
Macromolecular Assembly Section Laboratory of
Cellular Imaging and
Macromolecular Biophysics National Institute
of Biomedical Imaging and
Bioengineering, NIH<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><st1:street
w:st="on"><st1:address w:st="on"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;
font-family:"Courier New"">13
South Drive</span></font></st1:address></st1:street><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">Bldg 13, Rm 3N17<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><st1:place
w:st="on"><st1:city w:st="on"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;
font-family:"Courier New"">Bethesda</span></font></st1:city><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">, <st1:state w:st="on">MD</st1:state>
<st1:postalcode w:st="on">20892</st1:postalcode></span></font></st1:place><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">phone: (301) 435-1950<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">fax: (301) 480-1242<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New"">email: <a class="moz-txt-link-abbreviated" href="mailto:schuckp@mail.nih.gov">schuckp@mail.nih.gov</a> <o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font
face="Courier New" size="2"><span
style="font-size:10.0pt;font-family:"Courier
New""><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
RASMB mailing list
<a class="moz-txt-link-abbreviated" href="mailto:RASMB@list.rasmb.org">RASMB@list.rasmb.org</a>
<a class="moz-txt-link-freetext" href="http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org">http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org</a>
</pre>
</o:smarttagtype></o:smarttagtype></o:smarttagtype></o:smarttagtype></o:smarttagtype></o:smarttagtype></blockquote>
<br>
</body>
</html>