How can I determine the data's Dmax with the ATSAS(2.8)?

Interactive and automated data processing tools (PRIMUS, GNOM, AUTORG).
Scattering from simple bodies (BODIES), peak analysis (PEAK), data plotting (SASPLOT) etc.
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change
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How can I determine the data's Dmax with the ATSAS(2.8)?

#1 Post by change » 2017.03.10 14:39

How can I determine the data's Dmax accurately with the ATSAS(2.8)? In which gnom has no interactive mode to view the p(r) function variation while I changing the value of Dmax.

Can we trust the results of autorg and datgnom ?

Is the Dmax value important for the beads model building?

my sparse dat is attached. e.g. :
$ autorg D12_30.dat

Rg = 42.3 +/- 0.071 (0%)
I(0) = 0.619 +/- 1.9e-06
Points 3 to 11 (9 total)
Quality: 98%

$ datgnom D12_30.dat -rg 42.3

dmax: 88.019999999999996 Total: 0.50162419268791925
Guinier: 32.605462766563470 Gnom: 32.601649569447140

$ datgnom4 D12_30.dat -rg 42.3
Random seed is: 5359158339160948368
Dmax = 148.04999999999998 Total = 0.40844761368760735
Guinier = 42.299999999999997 Gnom = 44.129151718796884

what is the difference between datgnom and datgnom4, which result should be trusted?
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Alex
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Re: How can I determine the data's Dmax with the ATSAS(2.8)?

#2 Post by Alex » 2017.03.13 16:25

How can I determine the data's Dmax accurately with the ATSAS(2.8)? In which gnom has no interactive mode to view the p(r) function variation while I changing the value of Dmax.
Is not there an interactive mode for determining Dmax in Primus?
Is the Dmax value important for the beads model building?
Yes, it is. From my experience Dmax determination can be tricky for extended and/or flexible proteins,
in the latter case, bead modeling can be not so meaningful. For extended proteins, like say coiled-coils one expects long trailing tails in P or R function and one has to provide additional constrains when
doing bead modeling (e.g., by specifying that object is prolate).
what is the difference between datgnom and datgnom4, which result should be trusted?
I had the similar question recently:
viewtopic.php?f=4&t=3411

Alex

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AL
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Re: determine the data's Dmax

#3 Post by AL » 2017.03.15 11:48

change wrote:How can I determine the data's Dmax accurately with the ATSAS(2.8)? In which gnom has no interactive mode to view the p(r) function variation while I changing the value of Dmax.
As Alex mentioned, there is an interactive mode. Open your experimental data in PRIMUS (primusqt on Windows), go to the "Analysis" tab (bottom of the right panel), click "Distance Distribution". Change Dmax, see how the p(r) and its fit to the data are changing.
change wrote:Can we trust the results of autorg and datgnom ?
In most cases AUTORG will choose an acceptable Guinier range. You can check it visually in PRIMUS ("Analysis" tab, "Radius of Gyration").
DATGNOM automatically suggests a Dmax value based on Guinier Rg. It works fine on decent data with correct error estimates. But you better make sure that the resulting p(r) fits the experimental data and the decay at p(Dmax) looks natural.
change wrote:Is the Dmax value important for the beads model building?
Yes!
change wrote:what is the difference between datgnom and datgnom4, which result should be trusted?
datgnom (v.5) works better on globular particles. datgnom4 suggests a more realistic Dmax for elongated particles. We are working on a version that would work best in the majority of cases.

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