The site provides a simplified and convenient way for performing ab-initio low-resolution shape reconstructions of monodisperse non-interacting biological molecules (proteins, nucleic acids) in dilute solutions from SAXS or SANS data, where the hydration layer contribution to the scattering is taken into account. All you need to provide is the ASCII data of your solution scattering experiment, the parameters related to the contrast of the biomolecules, and the instrumental resolution (for SANS). Optionally you may provide an estimation of the maximum diameter of the particle (Dmax) and you may also limit the momentum transfer range (Qmax) that will be fitted. Scroll at the end of the page for details and hints related to data input.

avatar

The initial Indirect Fourier Transform (IFT) of the data is performed using the method of Bayesian estimation of hyperparameters, see:

Hansen J.Appl. Cryst (2000) 33, 1415

Shape reconstruction is performed with the program DENFERT v 2.3 described in the following two publications:

Koutsioubas & Perez J. Appl. Cryst. (2013) 46, 1884 and Koutsioubas et al. J. Appl. Cryst. (2016) 49, 690

If you need to control more parameters of the reconstruction procedure, please use the binary version of the program on your local machine. A complete manual with examples for the use of the program can be found here.

Note that you need to register as a user of the webserver by sending an email to denfertweb@gmail.com with the subject “denfert registration” and optionally including your name and affiliation in the message body. You will receive a verification message after a while.

Parameter Input (X-rays)

Important! your address shoud be registered (see above)

only alphanumeric characters (keep it simple)

paste ASCII scattering data (exclude any negative intensity values!)

momentum transfer (Q) in (1/Angstrom) (1/nm) units

(optional) maximum momentum transfer Qmax (in the same units (1/Angstrom or 1/nm) as for Q)
(optional) maximum diameter Dmax (in the same inverse units (Angstrom or nm) as for Q)
particle electron density (e/Angstrom^3): (default value for proteins)
solvent electron density (e/Angstrom^3): (default value for H2O)

large beads (faster reconstruction) small beads (slower reconstruction)

Parameter Input (neutrons)

Important! your address shoud be registered (see above)

only alphanumeric characters (keep it simple)

paste ASCII scattering data (exclude any negative intensity values!)

momentum transfer (Q) in (1/Angstrom) (1/nm) units

beam wavelength (Angstrom):
wavelength spread (%):
divergence (radians):
(Default values represent typical collimation settings at a neutron diffractometer)

(optional) maximum momentum transfer Qmax (in the same units (1/Angstrom or 1/nm) as for Q)
(optional) maximum diameter Dmax (in the same inverse units (Angstrom or nm) as for Q)
particle scattering length density (10^-6/Angstrom^2): (default value for proteins)
solvent scattering length density (10^-6/Angstrom^2): (default value for H2O)

large beads (faster reconstruction) small beads (slower reconstruction)

Hints about data input and the shape reconstruction procedure

  • The main body of the pasted ASCII data should be in a three column format (Q, intensity, intensity error bar) like in the following example:
    4.138455E-02          5.904029      1.555333E-01  
    4.371607E-02          5.652469      1.527037E-01  
    4.604759E-02          5.533381      1.521723E-01  
    4.837912E-02          5.547052      1.474577E-01 
    5.071064E-02          5.296281      1.436712E-01

  • Avoid any zero or negative values for Q, intensity and intensity error bar in the input file. Also exclude any high-Q flat plateaus that are obviously background dominated.

  • Any existing comment lines in the ASCII data file will be ignored.

  • Consider to remove from the ASCII data file any early experimental points that might not follow the Guinier law.

  • Units can be either in Angstrom or nm and this info needs to be specified in the radio buttons. If input experimental data are in Angstrom then the optional Dmax,Qmax values should be given in Angstrom and 1/Ansgtrom units respectively. If input experimental data are in nm then the optional Dmax,Qmax values should be given in nm and 1/nm units respectively.

  • Default sld and electron densities are those of proteins. In the case of nucleic acids, these values need to be adjusted by the user.

  • Default sld (neutron case) is that of deuterated water. If you work with a mixed H2O/D2O solvent you need to adjust this value.

  • Instrument resolution info has to be provided only for SANS reconstructions. Default values represent usual settings at a SANS diffractometer.

  • In most cases, the automatic IFT will be able to provide a reliable estimation of Dmax. If that is not the case, then the user should give an estimation of Dmax, and perform the calculations again.

  • Shape reconstruction may take from a few minutes up to several hours. A report of the results will be emailed to the specified address.

  • It is advised to run multiple reconstructions for the same dataset, in order to estimate solution stability. Please do not submit more than 4 shape reconstructions, simultaneously. In case of high server load, your reconstructions will be placed in a waiting list.