CRYSOL3 is a tool based on and complementary to CRYSOL.
It is a program for evaluating the solution scattering from
macromolecules with known atomic structure and fitting it to experimental
scattering curves from Small-Angle X-ray Scattering (SAXS). As an input one
can use a
PDB file with an X-ray or NMR structure of a protein or a protein-DNA(RNA)complex.
The program is different from CRYSOL in the way how the hydration shell
and its scattering are evaluated. Instead of representation the shell as envelope function
CRYSOL3 "incrusts" the surfaces and interiors (were possible) of atomic structure
with the dummy water beads like raisins in a muffin. This way of the shell representation
is more suitable for macromolecules with complex non-globular shapes and/or with cavities.
Based on the location, the beads are split into three types:
(i) Outer (convex) surface
(ii) Concave surface
(iii) Small internal cavities
The third type of the beads can in fact account for two cases
where water is actually present in a cavity or, the other way around,
the area is actually remains inaccessible to water and additional excluded volume
should be taken into consideration (by the negative contrast of these kind of beads).
Given SAXS experimental data, CRYSOL3 can fit the theoretical
scattering curve by minimizing the discrepancy (chi-square value).
Fitting is done by varying the contrasts of the three bead types,
whereby all other parameters (e.g. everage radius of atomic group or the total volume)
are taken by default. The default parameters of the contrasts for the three types
of water beads are 1, 1, 0 in relative units (where 1 corresponds
to dro = 0.03 e/A3),
i.e. the outer and inner surfaces are hydrated similarly and the internal cavities are not
contributing. The limits during the fitting are -10 to 2, where negative
value corresponds to the space in fact inaccessible to water and therefore indirectly
contributing to the total excluded volume (that's why the absolute value of the lower limit
is higher then the upper one).
It is possible to provide one or multiple arguments to CRYSOL.
Regular expressions, e.g. *.pdb or exp*.dat are supported
and should be surrounded by double quotes (e.g. "m*.pdb" or "a??.dat").
Experimental data. The first line is always treated as a title. The
following lines should contain momentum transfer, non-zero intensity and
standard deviation in a free format (separated by blanks or commas). If
standard deviations are not present, the errors are estimated automatically
with the help of a polynomial smoothing procedure.
Maximum order of harmonics (min = 1, max = 50). Defines the resolution of
the calculated curve. Default value should be sufficient in most of the cases.
For large particles high orders could improve the results, but more CPU time is
required. Fractional values are not allowed.
Solvent density (e/Å3). Default value is the electron density of
pure water. Solvents with high salt concentration may have a somewhat higher
electron density. User can adjust the value accordingly.
Constant subtraction. This operation accounts for possible
systematic errors due to mismatched buffers in the experimental
data. Constant is a sum of intensities over high-angle part
of the experimental data divided by number of experimental points in
this part. By default, lower and upper limit for constant subtraction is
-0.5 and 0.5 respectively. Limit is a multiplier for the constant subtraction.
Limits can be manually adjusted when minimization with new limits
is selected. Constant subtraction may improve the fit. No value is required
If the optional arguments are omitted, settings available through
command-line arguments and options may also be configured interactively as
shown in the table below.
CRYSOL3 offers two modes: with and without fitting.
The table below shows a list of questions for fitting mode.
The hydrogen atoms are automatically taken into account as a part of
atomic group. It means that any ATOM/HETATM line in the input
PDB file,
which has a string 'H' in the 13 or 14th column will be discarded. If hydrogens
generated by third party program are explicitly taken into account, they must conform with
PDB conventions or simply have "H" in the 14th column, whereas 13th, 15th and 16th column
should be empty
Experimental data. The first line is always treated as a title.
The following lines should contain momentum transfer, non-zero intensity
and standard deviation in a free format (separated by blanks).
If no data file name is provided, CRYSOL3 will run in prediction mode,
i.e. without the fitting.
The option accounts for a background constant (e.g. due to slightly mismatched buffer)
in the experimental data. The question is only asked in the fitting mode.
15, if s-max < 0.5 50, if s-max > 1.0 20 otherwise
Maximum order of harmonics (min = 5, max = 50). Defines the resolution
of the calculated curve. Default value should be sufficient in most of the cases.
For large particles high orders could improve the results, but more CPU time is required. Fractional values are not allowed.
Solvent density (e/Å3). Default value is the electron density of
pure water. Solvents with high salt concentration may have a somewhat higher
electron density. User can adjust the value accordingly.
The first line is a title. Seven columns contain:
(1) experimental scattering vector in inverse Angstroems
(2) resulting intensity in solution (3) atomic scattering
in vacuo (4) scattering from excluded volume
(5) convex border layer (6) concave border layer (7) waters in internal cavities
The following lines of output will be typically generated in the prediction mode
Brookhaven file name ................... < .pdb >: 6lyz
Use explicit hydrogens ................. < no >:
Enter data file, CR for none ........... < .dat >:
Maximum s value ........................ < 0.5000 >:
Number of points ....................... < 101 >:
Maximum order of harmonics ............. < 20 >:
Electron density of the solvent, e/A**3 < 0.3340 >:
Generating waters ...
Classifying waters ...
Computing atomic amplitudes ...
Computing shell amplitudes ...
Writing the files ...
The following lines of output will be typically generated in the fitting mode
Brookhaven file name ................... < .pdb >: 6lyz
Use explicit hydrogens ................. < no >:
Enter data file, CR for none ........... < .dat >: lyz_014
Angular units in the input file:
4*pi*sin(theta)/lambda [1/angstrom] (1)
4*pi*sin(theta)/lambda [1/nm] (2)
2 * sin(theta)/lambda [1/angstrom] (3)
2 * sin(theta)/lambda [1/nm] (4) ..... < 1 >: 2
Adjust constant ........................ < yes >:
Maximum s value ........................ < 0.5000 >:
Number of points ....................... < 101 >:
Maximum order of harmonics ............. < 20 >:
Electron density of the solvent, e/A**3 < 0.3340 >:
Generating waters ...
Classifying waters ...
Computing atomic amplitudes ...
Computing shell amplitudes ...
Fitting experimental data ...
Writing the files ...