WAXS in Solvent (WAXSiS) computes small- and wide-angle X-ray scattering curves based on explicit-solvent all-atom molecular dynamics simulations.

Jobs can be submitted by entering a PDB ID, uploading a PDB file (max 20 MB), or uploading trajectory files. PDB files may have 300 to 40000 heavy atoms.




Please select one of the above options.







Job will be submitted using default options.

Basic Options

Ligands

q Scattering Specify the maximum q scattering vector ( Å-1 )
Buffer Subtraction Select the buffer subtraction method:


Experimental Curve - Optional Fit an experimental SAXS / WAXS curve to the calculated curve.

No experimental curve

 Units:    
 Scattering Convention:    

Advanced Options

Output q Units Select the output q units:

   
Solvent Density Specify the solvent density ( e/nm-3 )
Selenomethionine Replace selenomethionine with methionine?



Envelope Distance Specify the envelope distance ( Å )
Convergence

 
Random Seed Use new random seed for initial velocities?








Running an Example Job

If you are using WAXSiS for the first time, you might want to try the following example to get started:

  • Download this Lysozyme experimental curve (courtesy of Bioisis)
  • Click the PDB ID button above and then pre-fill the example PDB ID: 1LYS
  • Under Review Options, upload the experimental curve file which you downloaded
  • Leave all other options as their default and submit the job

The job will run and generate results that look much like our example results data.

WAXSiS will try to automatically detect the crystallization agents. Click for more info.
This option is significantly slower and runs after other jobs. Click for more info.

 
 

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