CRYSOL is a program for evaluating the solution scattering from
macromolecules with known atomic structure and possibly fitting it to experimental
scattering curves from Small-Angle X-ray Scattering (SAXS). As an input one
can either use a coordinate file in PDB or mmCIF file format, with an X-ray
or NMR structure of a protein or a protein-DNA(RNA) complex. In addition, and
contrary to previous versions, as of v3.1 CRYSOL also processes dummy atom and
dummy residue models correctly.
The program uses multipole expansion of the scattering amplitudes to
calculate the spherically averaged scattering pattern and takes into account
different representations of the hydration shell. Given SAXS experimental data,
CRYSOL can fit the theoretical scattering curve by minimizing the discrepancy
(chi-square value) between the calculated scattering and the experimental data.
This fitting is done by varying three parameters:
(i) average displaced solvent volume per atomic group
(ii) contrast of the hydration shell
(iii) relative background
To determine the number of implicit hydrogens, CRYSOL requires components.cif,
the Chemical Component Dictionary
maintained by the EBI. If not found, an error is reported:
error: ATSAS resource files not found. Check installation and ATSAS environment variable.
At least one atomic coordinates file with extension .cif,
.pdb or .ent, in either PDB or mmCIF format, and one
or more optional experimental data files with extension .dat.
The experimental data file format may be described as follows: The first line
is always treated as a title. The following lines should contain momentum transfer,
non-zero intensity and standard deviation, separated by whitespace.
Use explicit hydrogens provided in the atomic structure file; default: use
implicit hydrogen groups determined by looking up the number of hydrogens in
See also option implicit-hydrogen.
Maximum order of harmonics; default: 20, minimum: 1, maximum: 100.
This defines the resolution of the calculated curve.
The default value should be sufficient in most of the cases. For large or
extended particles higher orders could improve the results, at the cost of
an increased run time. This value must be increased whenever the maximum
scattering angle is increased (smax).
Order of Fibonacci grid; default: 17, minimum: 10, maximum: 18
The order of Fibonacci grid defines the number of points describing the
surface of the macromolecule. Higher grid orders give a more accurate
surface representation, but more CPU expensive.
Only used if option shell=directional (the default).
All output files start with prefix and
If no prefix is provided, output file names
are generated based on the base name of the inputs. For example: "6lyz.cif" generates
6lyz.log, 6lyz.int, 6lyz.abs and "6lyz.cif lyzexp.dat" creates 6lyz_lyzexp.log
and 6lyz_lyzexp.fit in addition. With prefix, the two .log files are merged into one.
The first line is a title. Five columns contain: (1) experimental scattering vector in inverse angstroms, (2) theoretical intensity in solution, (3) in vacuo, (4) the solvent scattering and (5) the border layer scattering.