FW: [RASMB] Origin software and vbar
Karen Fleming
Karen.Fleming at jhu.edu
Thu May 5 21:53:00 PDT 2005
Regarding favorite software packages.....We use NONLIN.
I'll make my yearly plea to please please please compile/update Nonlin
for Mac OSx. I don't find the speed constants, etc, too cumbersome, and
I think that the ability to separate the Ks as a test for the robustness
of a global fit can be a particularly powerful one. Even when the
Beckman software is working, it does not have this feature and so in my
mind it is not equivalent to the Nonlin program.
I know that there are programs out there with more bells and whistles,
which make the fitting process a bit less mysterious, but in fact, I
WANT my students to know what the equations are, to know what goes into
the fitting, to know what this buoyant molecular weight quantity is, and
to know how the components of it can affect the expected results.
-Karen F.
James Cole wrote:
> 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
> <mailto:jcorreia at biochem.umsmed.edu>
> homepage location: http://biochemistry.umc.edu/correia.html
> dept homepage location: http://biochemistry.umc.edu/
> -------------------------------------------------------------------
>
>
>
--
* * * * * * * * * * * * * * * * * * * * * * * * * * * *
Karen G. Fleming, Ph.D.
Assistant Professor
T. C. Jenkins Department of Biophysics
Johns Hopkins University
3400 North Charles Street
Baltimore, MD 21218
Karen.Fleming at jhu.edu
Voice: 410-516-7256
Fax: 410-516-4118
http://www.jhu.edu/~biophys/
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