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<DIV dir=ltr align=left><SPAN class=861534220-05052005><FONT size=2>This is a
really important discussion for the group. As someone developing a
new equilibrium package (it is called HeteroAnalysis, more info to
follow soon), I'd be very interesting in hearing from more of the RASMB members
regarding what packages they are using for analysis of equilibrium experiments,
what feature they like/dislike, and most importantly, what features they
wish were available. Regarding the general issue of software for
analysis of equilibrium and velocity AU data, we are very lucky to have a
broad range of packages with very different user interfaces, fitting models and
analysis algorithms along with miscellaneous bells and whistles. There
is inevitably a trade-off between ease of use and
flexibility, so that as packages evolve to do more sophisticated analyses
they become more difficult to use for the novice. In particular, it
becomes easier to make silly mistakes with more complicated analysis algorithms
using large data sets. So, if you just want to fit to simple models,
I think there's no problem using a simple package as long as it is works
correctly (i.e. , no bugs in the calculation of
molecular weights based on user input of of vbar).
</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=861534220-05052005><FONT
size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=861534220-05052005><FONT size=2>As the
keeper of the faith here at UCONN </FONT></SPAN><SPAN
class=861534220-05052005><FONT size=2>I do want to make a correction regarding
the use of NONLIN. Yes, the speed factors, concentration factors, and the
bizarre units of the equilibrium constants are a pain. In fact, these features
were one of the motivations for us to create a new package.
However, you can make NONLIN give answers in real molecular
weight rather than sigma by choosing the appropriate values for the speed
factors. If you set them equal to (1-vbar*rho)omega^2/RT then you get molecular
weight. Admitted, this is not the most convenient
thing. </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=861534220-05052005></SPAN><SPAN
class=861534220-05052005><FONT size=2>Jim</FONT></SPAN></DIV>
<DIV dir=ltr align=left><FONT size=1></FONT><FONT size=1></FONT><BR></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT size=2><B>From:</B> rasmb-admin@server1.bbri.org
[mailto:rasmb-admin@server1.bbri.org] <B>On Behalf Of </B>John
Philo<BR><B>Sent:</B> Wednesday, May 04, 2005 9:16 PM<BR><B>To:</B>
rasmb@server1.bbri.org<BR><B>Subject:</B> RE: [RASMB] Origin software and
vbar<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV><SPAN class=449012900-05052005><FONT size=2>No, Jack, the Beckman software
doesn't do heteroanalysis, which you should know if you have used it, but
neither does NONLIN for that matter. Hetero-association is only a "major issue"
if that is what you are working on, and clearly John <FONT size=2>McGeehan was
not.</FONT></FONT></SPAN></DIV>
<DIV><SPAN class=449012900-05052005><FONT size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=449012900-05052005><FONT size=2>I like fancy and
powerful software as much as anyone else, but I really don't see any
reason to criticize anyone for using software that they find easy
to use and adequate for their purposes, or to suggest that they need to be using
software that does many different things that aren't relevant to what they are
doing. The good news is that we have more and better software choices, and the
more choices we have then the less it is true that anyone should say there
is only one "right" approach. I'm glad you are enthusiastic about SEDANAL,
but I think the members of this community are plenty smart and can figure
out for themselves what works well for them.</FONT></SPAN></DIV>
<DIV><SPAN class=449012900-05052005><FONT size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=449012900-05052005><FONT size=2>John</FONT></SPAN></DIV>
<DIV><SPAN class=449012900-05052005><FONT size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=449012900-05052005><FONT size=2></FONT></SPAN> </DIV>
<DIV></DIV>
<DIV><FONT size=2>-----Original Message-----<BR><B>From:</B>
rasmb-admin@server1.bbri.org [mailto:rasmb-admin@server1.bbri.org] <B>On Behalf
Of </B>John Correia<BR><B>Sent:</B> Wednesday, May 04, 2005 2:47
PM<BR><B>To:</B> jphilo@mailway.com; rasmb@server1.bbri.org;
apl3@york.ac.uk<BR><B>Cc:</B> John.McGeehan@port.ac.uk<BR><B>Subject:</B> RE:
[RASMB] Origin software and vbar<BR><BR></DIV></FONT>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV><FONT size=2>That is why I asked John. SEDANAL & I believe
Jim's progam fit both velocity and equilibrium data to MW too! The major
issue is hetero-analysis - does the Beckman software do hetero?</FONT></DIV>
<DIV><FONT size=2></FONT><FONT size=2></FONT><FONT
size=2></FONT><BR><BR>>>> "John Philo" <jphilo@mailway.com>
05/04/05 04:19PM >>><BR></DIV><FONT size=1>
<DIV>
<DIV><SPAN class=502370221-04052005><FONT size=2>Sorry Jack, but I have
to disagree with you. First, you are talking about velocity analysis, not
equilibrium. The Beckman software is by far the most user-friendly equilibrium
analysis package I have seen. Its algorithms are equivalent to those
in NONLIN, but you don't have to fight with obscure speed factors etc.,
and it actually gives you answers in real molecular weight (at least when it
works correctly), which NONLIN never does. Yes, there are more
sophisticated things that can be done, but if you don't need them, why
struggle? </FONT></SPAN></DIV>
<DIV><SPAN class=502370221-04052005><FONT size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=502370221-04052005><FONT size=2>Second, what is wrong with
simple? Isn't it particularly important for new users to achieve some quick
success so they are encouraged to do more, including learning these 'powerful
and elegant' approaches?</FONT></SPAN></DIV>
<DIV><SPAN class=502370221-04052005><FONT size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=502370221-04052005><FONT
size=2>John</FONT></SPAN></DIV></DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
size=2>-----Original Message-----<BR><B>From:</B>
rasmb-admin@server1.bbri.org [mailto:rasmb-admin@server1.bbri.org] <B>On
Behalf Of </B>John Correia<BR><B>Sent:</B> Wednesday, May 04, 2005 11:34
AM<BR><B>To:</B> rasmb@server1.bbri.org; apl3@york.ac.uk<BR><B>Cc:</B>
John.McGeehan@port.ac.uk<BR><B>Subject:</B> Re: [RASMB] Origin software and
vbar<BR><BR></FONT></DIV>
<DIV><FONT size=2>This may seem to be an odd question, but why are you using
the Beckman Origin software? Depending upon your guru (Schuck &
sedfit or Stafford & SEDANAL or Demeler & Ultrascan
or ... ) there are incredible packages being developed out there -
& they all work when applied to appropriate systems - we use a
combination of c(s) g(s) to establish a hypothesis, maybe some weight
average fitting to explore energetics, and then global direct
boundary fitting to hetero models with SEDANAL as the final step! I
realize Beckman is trying to make it uniform & simple, but with the
versatility, power and elegance of these new analysis methods, why would you
settle for simple?</FONT></DIV>
<DIV> </DIV>
<DIV><FONT
size=2>-------------------------------------------------------------------<BR> Dr.
John J. "Jack" Correia<BR> Department of
Biochemistry<BR> University of Mississippi Medical Center<BR> 2500
North State Street<BR> Jackson, MS 39216<BR> (601)
984-1522
<BR> fax (601)
984-1501
<BR> email address: <A
href="mailto:jcorreia@biochem.umsmed.edu">jcorreia@biochem.umsmed.edu</A>
<BR> homepage location: <A
href="http://biochemistry.umc.edu/correia.html">http://biochemistry.umc.edu/correia.html</A><BR> dept
homepage location: <A
href="http://biochemistry.umc.edu/">http://biochemistry.umc.edu/</A><BR>-------------------------------------------------------------------<BR> <BR> <BR></FONT></DIV></BLOCKQUOTE></BLOCKQUOTE></FONT></BODY></HTML>