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Ensemble fit - Purpose

Your email adress - More info....

Job title - More info....

  • PDB or PQR files (mandatory)
    More info....

  • Model1.pdb
    Model2.pdb
    Model3.pdb
    Model4.pdb
    Model5.pdb
    Model6.pdb
    Model7.pdb
    Model8.pdb
    Model9.pdb
    Model10.pdb

  • Which solvation method do you want to use?
    More info....



  • Experimental data file (mandatory)
    More info.... -Example file-


  • All set?



    Options

  • Max. q value / q step (Å-1) - More info....
        

  • Unit of q (in the experimental profile)
              

  • Bulk solvent electronic density:
      (e.Å-3)

  • Perform fit to experimental data?
    - C1 and C2 will be adjusted by the program.
      (this can take a while, please make sure you do not use too many models...)
    - Please set your own values for C1 and C2:

    • User-defined weight for the excluded volume
      (C1 parameter, see here for explanations)

        The default value is 1.

    • User-defined weight for the hydration shell
      (C2 parameter, see here for explanations)

        The default value is 1.

  • Do you provide your own solvent maps?
    More info....









  • User-defined residue type file? - More info....

  • User-defined atom type file? - More info....

  • Refinement parameters - More info....
      Simulated annealing parameters
      Initial temp. / Final temp. / Number of iterations


      Additional refinement parameters
      Maximum number of iterations per S.A. step

      Convergence criterium

      Damping parameter


    Output

      Once your job has finished, you will be redirected to the result's page.
      An example is available here.
      This is the result's page you would get with the example files proposed above (with user-defined values for C1 and C2 of 1).


    More informations on how to use AquaSAXS and the meaning of the above mentioned options can be found on the Flowchart page.



  •   Marc Delarue http://lorentz.dynstr.pasteur.fr
    Page last modified 18:07 November 12, 2013.