[RASMB] Compare MW obtained from Segal vs. MW obtained from Beckman Origi n

[Chin, Christopher]

Dear Ariel,

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I am a big fan of your Segal program because of the user-friendly feature.
The dynamic fitting pictures that change in front of your eyes for you to
select the best fitting radius region to use is a great time saver in data
analysis.  In the Beckman Origin program, editing equilibrium curve in the
dark by guessing is no fun.  I have to edit several radius regions, one by
one, in order to obtain the best variance value so I can have confident in
the result. 

 

I do a lot of calculation for Ka at various GuHCl concentrations in order to
estimate the free energy of subunit dissociation using Beckman's origin
program.  I constantly worry that I am not getting the best apparent
molecular weight to use for Ka calculation.  Lately I have combined Segal
and Origin program, meaning that I apply Segal program to get what I think
is the best fitting radius region, I then reapply this same radius region to
edit the subset from the Beckman Origin program (since your program can not
be used to calculate Ka), thinking that with this combine approach I can
surely get the best reliable MW to use for an accurate Ka. 

 

However, to my surprise, I do not get the same molecular weight even if I
use exactly the same radius boundary values.  Of the 4 set of edited subset
data I tested, the discrepancy various from 4 to 14 %.  Do you know where is
this discrepancy coming from? Is Beckman fitting equation different than the
equation you used for Segal program?  Is 4-14% discrepancy acceptable?  I
think I can live with 5-6% discrepancy. I am including the raw data
00008.ra1 for anyone who is interested in looking into this.  I have not
included NONLIN in this comparison.

 

Summary:  4 set of the edit data from raw data 00008.ra1

 


Edit Equilibrium curve

Boundary radius region used

MW obtained from Origin / variance

MW obtained from Segal / correlation

 


Discrepancy@ %



Edit 1

6.913-7.148

67 KD / 17.1

59 KD / 0.999458

12


Edit 2

6.942-7.139

66KD / 18.3

60 KD / 0.999504

9


Edit 3

6.920-7.139

65 KD / 17.8

56 KD / 0.999322

14


Edit 4

6.897-7.118

56 KD / 13.1

54 KD / 0.999435

4

@ ( MW obtained from Origin  -  MW obtained from Segal) / MW obtained from
Origin  

 

 

 

With best regards,

 

Chris

 

-------------------------------------------------------------------------- 
Christopher Chin 
Manager, XLA-Analytical Ultracentrifugation facility 
Sealy Center for Structural Biology 
HBC&G, 5.134 MRB.UTMB, Galveston,Tx 77555-1055 
cchin at utmb.edu, 409-772-1693, efax 708-585-1920 
--------------------------------------------------------------------------- 


 
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