Content-type: text/html Man page of X-GEN


Section: X-GEN Commands (1)
Updated: April 2005
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X-GEN - refine1  


"refine1" provides for a line-oriented interactive refinement of crystal and detector parameters. The current definitions of the run parameter file, the calibration mapping, and the border definition are invoked upon mapping.

When you invoke refine1 a brief help menu and a prompt appear. The user can specify a variety of sample properties, operational designations, and refinement commands. The user specifies the command or property by entering a one-letter command designator followed, in some cases, by one or more command arguments.


The command designators, together with their associated arguments (shown here in italics), are:

Nonlinear refinement with specified weight-factors for integerness and for RMS errors in X, Y, and omega.
b [q]
Perform a Bravais lattice determination. If an
argument (e.g. q) is specified, then the program will prompt the user for acceptance of the Bravais lattice with the best figure of merit; otherwise, it simply informs the user of the choices.
Choose an auto-indexing solution.
d param val ...
Specify one or more parameters by value.
For example,
d a 46.5 beta 107.5 plated 12.65
would set a to 46.5 Angstroms, beta to 107.5 degrees, and the sample-to-detector distance to 12.65 cm.
Write out the current parameter values and exit.
f [q]
Perform a Bravais determination and pick the solution
specified by the letter given as q. Thus if after the Bravais determination the user prefers the Bravais lattice that gives the third-best figure of merit, then the correct specification would be f c. If the user specifies "f -50", then the symmetry imposed will be that of the most recently specified spacegroup (e.g., from a "d spacegroup 96" command). If the user specifies "f -51", then the symmetry imposed will be that of a recently specified crystal system (e.g. "d system 3").
Read in the parameters from the file whose environment variable is UPARAMS.
This does a detector remapping based on a polynomial fit of the errors in detector (X,Y) positions of the form
dX = u0 + u1*X + u2*Y + u3*X*X + u4*X*Y + u5*Y*Y,
dY = v0 + v1*X + v2*Y + v3*X*X + v4*X*Y + v5*Y*Y,
These twelve parameters (u0-u5 and v0-v5) are determined by least-squares fit to the dX and dY values.
i [axerr angerr angle q]
Auto-index. The user can specify
the fractional error in axis lengths and axis angles, and the minimum angle between the difference-vector basis vectors. Ordinarily the auto-indexing operation is followed by a two-dimensional optimization--a determination of the minimal residual as a function of the X and Y-center offsets. If the user specifies a fourth argument to the command, then the two-dimensional optimization is omitted.
j param y/n ...
Turn on or off the refinement of one or
more parameters. Thus "j beta n xcen y" would turn off the refinement of beta and turn on the refinement of the X-center value.
Do a linear least-squares refinement of the active
parameters based on a minimization of the scanning-angle residual. This particular style of refinement is lightly tested and may be faulty.
l [a]
Do a linear least-squares refinement of the active
parameters based on a minimization of the integerness residual. This is a carefully tested option. Note that linear refinements can prove to be unstable if the unit cell lengths and the detector parameters are both active.
Recreate the pixel-to-centimeter mapping. The technique is straightforward: the signed error in X and Y in several hundred "neighborhoods" across the detector face is determined, and the nominal position of the fiducial point at the center of each neighborhood is moved in (X,Y) by that amount.
An internal command; don't use it.
Print out the reflections under refinement, including the observed and predicted values of X, Y, and omega and the non-integer value of (h,k,l).
Alter the management of reflections in ice-rings. By default ice-ring reflections are treated the same as any other reflections. "P" with no arguments toggles that behavior, i.e. if ice-ring reflections are currently treated as normal, then invoking "P" will cause ice-ring reflections to be excluded. If ice-ring reflections are currently being excluded, then invoking "P" will cause them to be treated normally. If P is invoked with arguments, they change this from a toggle to a selector, viz. P ON unconditionally turns on exclusion of ice-rings, and P OFF unconditionally turns it off. The list of resolution ranges associated with ice-rings is read from the file with environment variable name ICERING. If that file is absent, the excluded ranges are set to be (3.97 to 3.60 Å), (3.48 to 3.40Å), (2.70 to 2.63Å), and (2.28 to 2.21Å). There are prominent ice-rings at even higher resolution than 2.21 Angstroms; if those prove to be a problem during refinement, we recommend setting up your own file.
Quit the program without writing the parameters out.
Rocking-curve refinement: the only parameters under refinement are gamma0, gamma1, and gamma2.
Perform an indexing of a crystal based on an explicit indexing of three or more reflections.
t [x]
Transform the unit cell into a different orientation.
"t q" prints out the specific transformations allowed; other values (e.g. "t c") perform specific transformations, e.g. permuting (a, b, c) into (b, c, a).
Update the parameters and print the (X,Y,omega,index)
statistics based on that update.
List the available commands.
Write out the current parameters but do not exit.
Linear refinement based on a minimization of the "X" residual. This option has not been carefully tested.
Linear refinement based on a minimization of the "Y"
residual. This option has not been carefully tested.
Linear refinement based on a minimization of the "Z"
residual. This option has not been carefully tested.
Nonlinear refinement based entirely on minimizing the scattering-angle residual.
Nonlinear refinement based entirely on minimizing the integerness residual.
Nonlinear refinement as a weighted mixture of indexing and scanning-angle refinement; 1 involves primarily scanning-angle refinement, 8 involves primarily indexing. The weight with which the index residual enters into the total residual is specified by the numerical value parameter; the weight associated with the omega error residual is 1 - (index weight). Thus if we use a command value u, 0 <= u <= 9, then
wx = 0, wh = 0.11 * u, wp = 1 - wh .

Refinable or adjustable parameters:

The specific parameters whose values can be adjusted with a "d" command, or whose refinement can be turned on or off with the "j" command, are:

* a, b, c:
The unit cell lengths a, b, and c in Angstroms.
In space groups where cell lengths are tied to one another, the output will reflect those ties: thus in tetragonal spacegroups, even if the user enters values of a and b that are not equal, the program will force b to equal a.
* alpha, beta, gamma:
The unit cell angles alpha, beta, and gamma
in degrees. The software will force values of the cell angles appropriate to the crystal system: thus in hexagonal spacegroups it will force alpha = beta = 90, gamma = 120. In rhombohedral spacegroups indexed rhombohedrally, gamma is taken to be the independent angle, so the software sets beta to gamma and alpha to gamma.
* omega, chi, phi: The pseudo-goniostat Euler angles omega, chi, and
phi in degrees. These angles specify the rotation from the goniostat's true (omega = chi = phi = 0) position to one at which a will lie along X and b mostly along Y, where X is the direction pointing from the crystal toward the source, Z is the rotation axis, and Y is forms a right-handed (X,Y,Z) system with the others.
* plateD: the sample-to-detector distance in cm.
* Xcen: the X offset of the main-beam from the detector center at
2theta = 0, in centimeters.
* Ycen: the Y offset of the main-beam from the detector center at
2theta = 0, in centimeters.
* tilt: the angle between the detector's nominal vertical axis and
the crystal goniostat's omega direction, in degrees. This value is typically close to zero, but with a detector turned on its side it could be +/- 90.
* swing: the angle between the direct beam direction and the
normal to the detector face. The sign of this angle is typically opposite to that of the 2theta angle defined in the data acquisition software of on most goniostats.
* gamma0, gamma1, gamma2: Three parameters characterizing the
dependence of the rocking width of the reflections on their (X,Y) position. The first two parameters are specified in frames; the third in degrees. The definitions of these parameters are given in Harrison et al, Methods in Enzymology 114: 226-230 (1985), except that what they call gamma(y) is called gamma0 here; their gamma(z) is gamma1; and their gamma(1) is gamma2 here.
* xerror, yerror, zerror: These define the maximum errors
allowed in reflection index, detector X, detector Y, and scanning angle. Any reflection violating these criteria will be excluded from refinement. These errors are ignored for rocking-curve refinements and during auto-indexing. For linear refinements on index, the index errors are examined individually. For nonlinear refinements and linear refinements on scanning angle, all the error limits must be satisfied in order for a reflection to be included in the residual calculations.
* resmin, resmax: These define the minimum resolution (maximum D
spacing) and maximum resolution (minimum D spacing) for reflections used in refinement. The default values of these parameters will be taken somewhat outside the lowest-resolution and largest-resolution reflections encountered in the CENTROIDS file, so that small changes in detector parameters will not cause any reflections to drop off the refinable list. Thus if the data extend from 24 to 1.8 Angstroms, the program will set the limits to about 29 and 1.6.
* isys: This defines the crystal system as an integer between 1 and 7.
1 is triclinic, 2 is monoclinic, 3 is orthorhombic, 4 is tetragonal, 5 is cubic, 6 is trigonal or hexagonal, and 7 is rhombohedral indexed rhombohedrally. Rhombohedral spacegroups may be specified as being in either a rhombohedral (7) or a hexagonal (6) system, depending on how you wish to index the crystal.
* spacegroup: This defines the spacegroup as an integer between 1
and 230. The number is the International Tables numerical designation for the spacegroup; thus P212121 is spacegroup 19, and P61 is spacegroup 169. Rhombohedral spacegroups may be specified either with rhombohedral or hexagonal crystal systems; the International Tables number given in this slot will be unaffected.
* stepsize: This is the stepsize between images, in degrees. The
sign convention is opposite to that found on most three- and four-axis goniostats, so if the data acquisition program is set up to step by +0.25 degrees per frame, the value specified here should often be -0.25.
* lambda: This defines the X-radiation wavelength in Angstroms
* startomega, startchi, startphi: These define the position,
in degrees, of the goniostat as of frame zero of the current data run. Thus if frame 1 was collected at (omega, chi, phi) = (40.0, 45.0, 180.0) and the stepsize is -0.2 degrees, the start values should be (40.2, 45.0, 180.0).


A refine1 script to auto-index and refine a data set is given in the refall documentation.


Report bugs to Andy Howard at or 312-567-5881.  


Copyright © 2002, Illinois Institute of Technology. See the file 'LICENSE' for information on usage and redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES




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Time: 02:08:09 GMT, October 03, 2005