Fast SAXS Profile Computation with Debye Formula

This section will contain answers to the most common questions received about FoXS.
For any information, suggestion and question, please feel FREE to email

Question 1

I get an error message about my input from the server. What is wrong with my input?

Answer:

Possible Input Errors:

  • PDB code: make sure you enter valid PDB code, i.e. the molecule with this code exists in PDB.
  • Chain ID: make sure that the chains you specified exist in the PDB file.
  • Uploaded file: should be in PDB format only!

  • IMPORTANT! please use standard PDB atom naming in the files you upload!

Question 2

I compare crystal structure to the experimental SAXS profile, however the fit between the theoretical profile and the experimental one is not good. What can be wrong?

Answer:

There can be several reasons for a bad fit:

  • Missing residues/atoms in PDB file compared to the sample the data was collected with can contribute to a bad fit. SAXS profile is equivalent to electron distance distribution, so missing atoms contribute to distances that are not accounted for in a theoretical profile. It is recommended to add all the missing loops, linkers, N-/C-termini, His tags, metal ions. The content of the structure should be as close as possible to the content of the sample used to collect the SAXS data. It is preferrable to have inaccurate loop conformation, rather than a missing loop!
  • Molecules in solution can have a different conformation compared to crystal structure. Please note that X-ray and SAXS data collection are performed under different condition, which may result in different conformations. This can happen very often with multi domain proteins.
  • Molecules in solution can have multiple conformations. SAXS provides information about rotational as well as conformational average. Since many molecules in solution exist as an ensemble of various conformations, SAXS profile will be an ensemble averaged profile.

Question 3

My structure includes non-protein atoms, such as mercury, gold or selenium. Are they accounted for in FoXS?

Answer:

FoXS includes form factors for the following elements:
H, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, Se, Br, I, Ir, Pt, Au, Hg
If your element is not in this list, please let us know and we will add it.
IMPORTANT! please verify that the element name is specified in the element field of PDB format (columns 77-78)