DAMMIN - Fit Differs from GNOM

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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Spencer
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DAMMIN - Fit Differs from GNOM

#1 Post by Spencer » 2007.09.07 23:03

Hello,

I am trying to have DAMMIN do a fit to my GNOM .out file. However, in GNOM, the fit corresponds with my data points but in DAMMIN the fit (in green) does not correspond with my data points. If I look at the GNOM file in Excel, I can see that the GNOM fit corresponds with my data points, so I do not think I am doing anything wrong in GNOM. Currently, while trying to figure out this problem, I am taking the default values in DAMMIN. Should I be doing something else? I am using DAMMIN53qw on a laptop running Windows XP and using the interface (not command line) to run the program.

SaxsMax
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#2 Post by SaxsMax » 2007.09.10 17:50

Hi,

Are you looking at the *.fir or *.fit file?
In *.fit a constant is usually subtracted from the data to ensure
the s^-4 decay (Porod behavior)

What is the Final SQRT(Chi) against raw data
(can be seen in the *.log or *.fir files)?

Also the programs PRIMUS/SASPLOT can be used for visualizing the fit
which should be more convenient than Excel

Spencer
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#3 Post by Spencer » 2007.09.10 19:11

My final sqrt(Chi) is 1.493

I was looking at my .fit file from DAMMIN. The .fit does not match the fit from GNOM. I'm trying to figure out what constant has been applied but I'm not sure where to look in the .fit file. Can you give me a pointer? My log file doesn't show a final Chi after constant subtraction.

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#4 Post by SaxsMax » 2007.10.01 18:11

In the log file it should be written something like
"A constant was subtracted .............................. : 8.780e-2"

To see the fit to the original unsubtracted data you need to plot the *.fir file

rithi
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there is no .fir file

#5 Post by rithi » 2008.08.17 00:49

I tried using DAMMIN from my .out from GNOM, it runs. I can get .fit file and .log file but no .fir

The fit in the DAMMIN interface is not the same as I got from GNOM

Pls. help

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#6 Post by SaxsMax » 2008.09.03 11:54

Could you post several last lines from the log file?
I have an impression that Dammin did not terminate properly

tk
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fit to exp data in dammin

#7 Post by tk » 2009.07.30 00:50

could you explain why the green line does not fit the experimental points in
dammin, should it??? higher res. seems to differ for me for various samples.
what could be wrong??
thanks.

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AL
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green line?

#8 Post by AL » 2009.07.30 14:59

could you explain why the green line does not fit the experimental points in dammin, should it?
Dammin produces a *.fit and a *.fir file. The *.fir file shows the fit to experimental data. Do you mean this file?
If Dammin finished and this fit looks bad it means the resulting shape does not fit the experimental data, for example because you defined a symmetry that is not present in your particle.

tk
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#9 Post by tk » 2009.07.30 22:00

what i find confusing is that during the dammin run the model (red line in dammin interface, i assume) is being fitter to a green line (apparently a modified/substrated version of raw data?) and also the "raw"(experimental data) curve is shown, but that is different from the green line --- i guess this is suppose to be?? but no fit to that is shown. if model is being fitted in the dammin run to both, why is that not shown? In any case what exactly is being done is not very clearly explained. so i was talking about the plots shown not the files (while i realise, after reading this chain of discussion, i should look at the files). still isnt totally clear to me how the fit is done to two different data apparently?? probably can find a reference for that.
thanks.

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