FW: [RASMB] Origin software and vbar

James Cole jimcole at snet.net
Thu May 5 20:44:00 PDT 2005


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). 
 
As the keeper of the faith here at UCONN  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. 
Jim


  _____  

From: rasmb-admin at server1.bbri.org [mailto:rasmb-admin at server1.bbri.org] On
Behalf Of John Philo
Sent: Wednesday, May 04, 2005 9:16 PM
To: rasmb at server1.bbri.org
Subject: RE: [RASMB] Origin software and vbar


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 McGeehan was not.
 
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.
 
John
 
 
-----Original Message-----
From: rasmb-admin at server1.bbri.org [mailto:rasmb-admin at server1.bbri.org] On
Behalf Of John Correia
Sent: Wednesday, May 04, 2005 2:47 PM
To: jphilo at mailway.com; rasmb at server1.bbri.org; apl3 at york.ac.uk
Cc: John.McGeehan at port.ac.uk
Subject: RE: [RASMB] Origin software and vbar



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?


>>> "John Philo" <jphilo at mailway.com> 05/04/05 04:19PM >>>


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? 
 
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?
 
John

-----Original Message-----
From: rasmb-admin at server1.bbri.org [mailto:rasmb-admin at server1.bbri.org] On
Behalf Of John Correia
Sent: Wednesday, May 04, 2005 11:34 AM
To: rasmb at server1.bbri.org; apl3 at york.ac.uk
Cc: John.McGeehan at port.ac.uk
Subject: Re: [RASMB] Origin software and vbar


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?
 
-------------------------------------------------------------------
 Dr. John J. "Jack" Correia
 Department of Biochemistry
 University of Mississippi Medical Center
 2500 North State Street
 Jackson, MS  39216
 (601) 984-1522                                 
 fax (601) 984-1501                             
 email address: jcorreia at biochem.umsmed.edu     
 homepage location: http://biochemistry.umc.edu/correia.html
 dept homepage location:    http://biochemistry.umc.edu/
-------------------------------------------------------------------
 
 


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://list.rasmb.org/pipermail/rasmb-rasmb.org/attachments/20050505/dcb1fd91/attachment.htm>


More information about the RASMB mailing list