How can I decide Dmax correctly?

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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Anna
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How can I decide Dmax correctly?

#1 Post by Anna » 2018.04.29 11:27

Hi,

I am now performing distance distribution analysis using primusqt.
I have some troubles:

1. I managed to obtain the plot which seems to have smooth shape and reasonable Rg compared with the one I obtained from Guinier analysis (Rg = 63.99) (Fig. 1). However, If I unchecked rmax = 0, the value of p(r) at rmax was far from 0 (Fig. 2).

2. I then increased the value of Dmax to make the value of p(r) at rmax come closer to 0. I could get the smooth graph, but in this case, the message "Warning: Dmax*smin greater than pi" appeared and moreover, Rg (72.49) did not fit with the Rg obtained from Guinier analysis (63.99) (Fig. 3).

I want to use this pr function for ab initio modeling by DAMMIN.
I've learned from previous posts that it is not good to use the input file with the warning message for ab initio modeling.
Also, I've read that dmax value would largely affect the result of bead modeling, so I was worrying that I might get wrong bead models if I used pr function which I have shown in Fig. 1.
How can I obtain accurate dmax value in this case?
Thank you so much.
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Figure 1.png
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Anna
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Re: How can I decide Dmax correctly?

#2 Post by Anna » 2018.04.29 11:35

I'm sorry, this is Figure 3.
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aemiele
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Re: How can I decide Dmax correctly?

#3 Post by aemiele » 2018.06.07 17:33

Dear Anna,
you have very low intensity scattering (negative Log scale), is this curve coming from SEC-SAXS?
If yes, try to better select the range for integration.
Your data between 0.018 and 0.02 curve negatively, this will affect both Rg and Dmax. Therefore, unless you have a good structure to guide you, I would not trust too much the envelope from DAMMIN-DAMMIF.

HTH
best regards
Adriana

Anna
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Re: How can I decide Dmax correctly?

#4 Post by Anna » 2018.06.15 12:32

Dear Adriana,

Thank you for your advice.
The curves are not from SEC-SAXS, but are from normal SAXS.
Unfortunately, I do not have a crystal structure of the protein I used for this SAXS measurement, so I think I should try the measurement again.
Is there any way to increase the scattering intensity other than increasing the concentration?
I would appreciate it if you could give me advice again.

Yours sincerely,
Anna

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AL
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Validate your MW, try DARA, DATCLASS

#5 Post by AL » 2018.06.18 11:21

Fig. 3 looks like your Dmax is about 265 A. Indeed your smin = 0.013 A-1, so formally you cannot correctly estimate Dmax > 242 A.
If Dmax = 265 A fits your expectations (for the MW computed from the sequence) make sure 'Rmax=0' is checked, save and give DAMMIN/DAMMIF a try.

Before starting any modelling make sure the MW estimated from the SAXS data fits the expected MW.
If you don't know how to estimate Dmax you may submit your data to DARA and check what the Dmax values of proteins with similar scattering patterns are. You may also use the command line tool DATCLASS to estimate MW and Dmax.

Anna
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Re: How can I decide Dmax correctly?

#6 Post by Anna » 2018.06.29 06:52

Dear AL,

Thank you for your kind response, and I apologize for this late reply.
Dmax = 265 A is reasonable, so I will try DAMMIN with this Dmax.
Thank you also for the information of DARA and DATCLASS.
I will try both of them before using DAMMIN.

Best reagards,
Anna

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