I have .dat files from scatter that contain the Dmax of a protein and now I want to generate ab initio models. however I dont know how to generate .out files that are needed byy DAMMIF programs on ATSAS online software. please help!
Download and install the ATSAS suite to your computer using the following link:
http://www.embl-hamburg.de/biosaxs/download.html
Select the Academic ATSAS download (if you're an academic)
Once installed open the primusqt software. If you are using windows 7 the easiest way is to use the start search bar. Once you have opened the software select file>open and open your .dat file. The .dat file should be of data which has been buffer subtracted. You should see a Log(I) vs s curve.
In the bottom right hand area of the window is one of three tab called analysis, select this.
Once selected you should see 3 tabs named Radius of Gyration, Distance Distribution and Porod Volume. It is good to check Guinier analysis by selecting Radius of Gyration to identify aggregation of sample. Next select the Distance Distribution tab, here you want to identify the Dmax, the software can automatically do this however it is not always correct therefore manual intervention is suggested. You want to alter the Dmax until the P(r) vs r reaches the baseline (x-axis) without too sharp an incline or dipping to a negative P(r) value. Also make sure the curve fits well the raw data as seen in the log(I) vs s graph. See this link for a more detailed explanation http://www.bioisis.net/tutorial/15
Once you are happy select save and you can save it as a .out file which you can use for dammin, dammif, gasbor modelling using the ATSAS online server here http://www.embl-hamburg.de/biosaxs/atsas-online/ or perform locally using the ATSAS suite.
For good explanations of Guinier plots and P(r) distribution as well as other analysis you can perform on SAXS data which I have found useful check out this website: http://www.bioisis.net/tutorial
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