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SAXS AXES Server, Version 7f
Fitting Small-Angle X-Ray Scattering Curves to
the Atomic Coordinates for Proteins/RNA/DNA.
axesLogo AXES: Analysis of X-ray Scattering in Explicit Solvent

Contacts:
Alex Grishaev AlexanderG@intra.niddk.nih.gov
Ad Bax bax@nih.gov
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[ About Axes ]

PDB File for SAXS Prediction
PDB File: The file containing the macromolecular coordinates in PDB format, 20000 atoms max. Both ATOM and HETATM entries will be processed. In the absence of experimental data, AXES will simply return the predicted scattering curve only. Example: saxs.pdb

Note: if you have a previously-created AXES prediction, you can use it here as an alternative to PDB Input. In this case, the Advanced SAXS Prediction Options below will be ignored. Example: Fqpred.dat
Optional Experimental Sample and Buffer Scattering Data for Fitting
SAXS Buffer: The optional input file containing the SAXS buffer scattering curve. The file should contain three columns: q, Intensity (Arbitrary units), and the Uncertainty in Intensity. The units for q can be inverse-Angstroms or inverse-nm, as selected below. This file is optional, but recommended for the fitting options. If no SAXS Buffer Data is given, any SAXS Sample Data given below will be treated as already buffer-subtracted. For best results with AXES, it is recommended to supply both Buffer and Sample data. Example: saxs_buf.txt
SAXS Sample: The optional input file containing the SAXS sample scattering curve. The file format and q values within it should be the same as for the buffer scattering curve above. This file is optional, but required for the fitting options. Example: saxs_sam.txt
  q Units: Units for the q values in the experimental sample and buffer files.
Inverse-Angstroms
Inverse-nm

q Definition: Convention for defining the q values used in the sample and buffer files.
q Convention: 4psin(theta)/lambda
s Convention: 2sin(theta)/lambda

Replace Noise Estimate: if this option is enabled, AXES will replace existing noise estimates in the buffer and sample data with automatically determined values.

[ Hide Advanced Options ]

Advanced SAXS Prediction Options
nQsim: Number of simulated data points, 0 - 201. Simulation starts at q = 0.0 with a step of 0.01 A^-1. The scattering vector q is defined as 4psin(theta)/lambda, where 2*theta is the scattering angle, and lambda is the wavelength in A.
nFib: Order of the Fibonacci grid, 11-19. Determines the number of vectors used in the calculation, from order 11 = 145 vectors to order 19 = 6766 vectors.
nMod: Number of structure models to use from the PDB. Use 0 to include all structure models from the PDB in the calculation. Otherwise, the first nMod structures will be used.
nWfile: Number of water files to be used for averaging of the excluded and surface solvent contributions, 1-100. Small proteins require large numbers (50-100), large proteins require fewer.
rho0: Electron density of the solvent in electrons/A^3. Default value 0.334 is for pure water at 1 atm and 25 C. Typical range: 0.334 +/- 0.010.

Advanced Options for Fitting Experimental Scattering Data
resc_SAXS: Target value for the buffer rescaling constant; this should be equal to the volume fraction of the solvent in the sample. The likely range for this parameter is 0.98 to 0.9999.
sresc_SAXS: RMS uncertainty of the buffer rescaling constant above. The likely range for this uncertainty is 0.001 to 0.01.
rhoSur_Min: Minimum value for the fractional increase in the contrast of the surface solvent as compared to the bulk solvent.
rhoSur_Max: Maximum value for the fractional increase in the contrast of the surface solvent as compared to the bulk solvent. The suggested setting for protein data is 0.07 and 0.10 for oligonucleotides.

Fitting Region and Evaluation Region
qMin_Fit: Minimum value of the scattering vector to be fitted. The units and q or s convention for these values should correspond to those used in the experimental sample and buffer data files. Use keyword qmin to set the qMin_Fit parameter to the smallest q value in the experimental data.
qMax_Fit: Maximum value of the scattering vector to be fitted. The units and q or s convention for these values should correspond to those used in the experimental sample and buffer data files. Use keyword qmax to set the qMax_Fit parameter to the largest q value in the experimental data.
qMin_Eval: By default, AXES will report a chi statistic for the specified fit region. Use the qMin_Eval parameter to specify the lower limit for an additional chi statistic report over a different range of q. The units and q or s convention for these limits should correspond to those used in the experimental sample and buffer data files. Use keyword qmin to set the qMin_Eval parameter to the smallest q value in the experimental data. Keyword none will suppress the additional chi report.
qMax_Eval: By default, AXES will report a chi statistic for the specified fit region. Use the qMax_Eval parameters to specify the upper limit for an additional chi statistic report over a different range of q. The units and q or s convention for these limits should correspond to those used in the experimental sample and buffer data files. Use keyword qmax to set the qMax_Eval parameter to the largest q value in the experimental data. Keyword none will suppress the additional chi report.

[ Hide Advanced Options ]


Note: AXES calculations will generally be completed within several minutes. However, when the server is under heavy use, calculations may take several hours or more to complete.

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last update: Apr 2 2012