Ask about PRIMUS, GNOM, AutoRG, BODIES, PEAK, SASPLOT

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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AL
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Ask about PRIMUS, GNOM, AutoRG, BODIES, PEAK, SASPLOT

#1 Post by AL » 2007.08.20 12:09

If you have questions about ATSAS data processing tools such as PRIMUS, GNOM, AUTORG, BODIES, PEAK, SASPLOT etc. you may ask them here. Please indicate the version of the program. Supply information from the log file if relevant. If you want to provide some files - please attach them to your post.
Last edited by AL on 2010.11.18 20:59, edited 3 times in total.

Anne
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Data analysis evaluation

#2 Post by Anne » 2008.04.24 16:33

Hello,
I am new in the SAXS field. I obtained SAXS data of my protein in water solution and I used primus, gnom and dammin to analyze it. I have lot of questions to understand the result:
-Primus/guinier gave me a Rg of 10.8nm. With Gnom, I didn’t manage to reach the same value (I had 10.2nm maximum). Why? Which one I should believe?
-Gnom tells “Total estimate : 0.510 which is A REASONABLE solution”. What does that mean? What is the scale (I have also seen excellent, good and suspicious)
-Then I used Dammin on the Gnom result. It gave this shape:

see attach

Are the little handles meaningful? How can I have a better representation?
-I would like to have the form factor of my protein. Can I use Crysol, as it is written that it is adapted to known atomic structures (which is not the case of my protein? As the balls are not atoms, can I enlarge the size of the “atoms” (in point 17b), and to which size?

Thank you for your help

Anne
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Rg, volume, MM, P(R)...

#3 Post by AL » 2008.06.30 17:24

Hi Anne,

my advice would be to check the Rg value with AUTORG. May be you get an Rg value higher than expected because your sample is aggregated or forms oligomers. For globular proteins Rmax should be around 3*Rg.

Also please check if the molecular mass and the excluded volume are close to what you expect. You will find the "Overall excluded volume" value in the pdb file generated by DAMMIN or DAMMIF. The volume in cubic angstroms should be roughly twice the molecular mass in daltons (which you can calculate from the primary sequence).

Concerning GNOM I would pay more attention to the shape of the p(r) function than to the "total estimate". Also if you are going to run DAMMIN/DAMMIF on the GNOM output please make sure you cut the higher angles (at least > 2 nm-1). It will make your ab initio model less detailed, probably the little handles will disappear.

You might find interesting Roessle's reply concerning representation of DAMMIN results.

CRYSOL is a program that calculates theoretical scattering from a known pdb structure or checks how good your experimental data fits a known pdb structure. E.g. you can check how good 'nonAgg-1.pdb' fits your 'measured.dat'.
If you want to obtain the general shape of your particle without knowing any other information - use one of the ab initio programs. It is better to start with DAMMIF.

Please post further questions as a new topic in the Data Processing subforum.
Cheers,
Al

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