[RASMB] s20w calculation ... more

Sat Aug 10 03:41:09 PDT 2013

SEDANAL does the conversion to s(20,w)  only in DCDT and the only if the v-vbar and density and viscosity ratio have been entered into the database though the Preprocessor. All other values of s* are the raw value. I.e. s(t,b). The equation used is the standard equation used by Svedberg in "The Ultracentrifuge" and hasn't changed since then.

In the Fitter the correct value of density increment must be entered to get the correct molar mass. So in the fitter only the buoyancy correction is made since the correction from s*(t,b) to s(20,w) and from D(t,b) to D(20,w) is the same and cancels out. The values used by the fitter are the raw values, i.e. the actual values that pertain to solution conditions being fitted.

Sent from my iPad Mini

On Aug 9, 2013, at 5:25 PM, "Laue, Thomas" <Tom.Laue at unh.edu> wrote:

> Hi-
> Sorry to be late replying... I am out of town... and sorry there is a problem with Sednterp.
> I've forwarded this thread to the gang to see what the problem might be. 
> One thing they might try is to see if the desktop and web version give the same error. The calculations are identical, but the rendering engines are different.
> Again, sorry for any trouble.
> Tom
> From: rasmb-bounces at list.rasmb.org [rasmb-bounces at list.rasmb.org] on behalf of David Hayes [drdavidbhayes at yahoo.com]
> Sent: Friday, August 09, 2013 5:04 PM
> To: rasmb at rasmb.org
> Subject: Re: [RASMB] s20w calculation
> 
> Hi John,
> 
> I sent some off list response with extra information and opinion I am not sure about and don't want to be on list.
> I am also waiting for Walter or Peter Sherwood to answer about SEDANAL questions, but I suspect that you are thinking SEDANAL is doing s20w corrections that it really is not, but I don't know if that is the problem.
> 
> Everyone should know that the Web SEDNTERP and the desktop beta share the exact same calculation source code, so if they are the same version, they better agree on everything, feature for feature, bug for bug.
> 
> But also, basically trust the by hand calculations as was posted previously, ask the programmers which numbers are s20w and which are not, and thank you for posting the problems so the developers of SEDNTERP can work out the bugs.  Due to John Philo's incredible and meticulous work, SEDNTERP 1.2 was incredibly reliable and calculated things to 5 decimal places reliably and exactly the same as the published equations.  the new version of SEDNTERP will take a lot of sweat to get to that level of excellence.
> 
> David Hayes
> 
> From: John Sumida <jpsumida at u.washington.edu>
> To: drdavidbhayes at yahoo.com 
> Cc: rasmb at rasmb.org 
> Sent: Friday, August 9, 2013 1:44 PM
> Subject: Re: [RASMB] s20w calculation
> 
> Hi David,
>  
> Thanks for taking the time to respond. I’m attempting to respond to your post. Apologies if I’m committing some type of etiquette violation in responding to the group, but as you requested some clarification as to my process I thought to respond publicly.
>  
> To answer your questions.
>  
> I’ve been trying to understand why this particular polymer material produces a large s20w value when another material with different surface charge properties produces an s20w of 7.9s and sediments very differently.
>  
> So the back calculation, going from s20w to s*, was me playing with the data to see if I could go from the 17.3 s20w back to s* which I would have hoped – as you point out – would not have been much different from 17.3s.
>  
> My initial calculation using the s20w correction equation  (equation 19) was comforting in that the calculated s* was 16.4s.  I used SEDFIT to perform the same calculation just to check that all was in order – and as I stated SEDFIT returned the 16.4s value as had the calculation and the analysis in SEDANAL.  Note that vbar and solvent parameters had been entered in into the experiment file and gOfs files had been generated by running DCDT.  So I believe the s values returned in SEDNAL are s20w values.
>  
> The problem arose when I used the Experiment page in SEDNTERP (version 20120828 BETA). Using the calculated value of s*, SEDNTERP did not return the same value for s20w that SEDANAL output.
>  
> I also attempted the same operation using the web version of SEDNTERP which resulted in the same result, namely calculating an s20w of 27.8s when the experimentally observed s20w was17.3s.
>  
> I had not thought to turn off the s20w calculation (in order to do so do I just remove vbar from the experiment info?) and attempt to fit for s*.  Will try that next.
>  
> Best regards,
>  
> John Sumida, Ph.D.
> Analytical Biopharmacy Core Facility
> University of Washington
> Molecular Engineering & Sciences Institute, G22
> 3946 West Stevens Way NE
> Seattle WA 98195-1653
> 
> 
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> RASMB at list.rasmb.org
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