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Man page of XGEN
XGEN
Section: XGEN Commands (1)
Updated: April 2005
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NAME
XGEN  refine1
DESCRIPTION
"refine1" provides for a lineoriented 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 oneletter command designator
followed, in some cases, by one or more command arguments.
Commands:
The command designators, together with their associated arguments (shown
here in italics), are:
 a

Nonlinear refinement with specified weightfactors 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.
 c

Choose an autoindexing 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
sampletodetector distance to 12.65 cm.
 e

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
thirdbest 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").
 g

Read in the parameters from the file whose environment
variable is UPARAMS.
 h

This does a detector remapping based on a polynomial fit of
the errors in detector (X,Y) positions of the form
dX = u_{0} + u_{1}*X + u_{2}*Y +
u_{3}*X*X + u_{4}*X*Y + u_{5}*Y*Y,
dY = v_{0} + v_{1}*X + v_{2}*Y +
v_{3}*X*X + v_{4}*X*Y + v_{5}*Y*Y,
These twelve parameters (u_{0}u_{5} and
v_{0}v_{5}) are determined by
leastsquares fit to the dX and dY values.
 i [axerr angerr angle q]

Autoindex. The user can specify

the fractional error in axis lengths and axis angles, and the
minimum angle between the differencevector basis vectors.
Ordinarily the autoindexing operation is followed by a
twodimensional optimizationa determination of the minimal
residual as a function of the X and Ycenter offsets. If the
user specifies a fourth argument to the command, then the
twodimensional 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 Xcenter value.
 k

Do a linear leastsquares refinement of the active

parameters based on a minimization of the scanningangle residual.
This particular style of refinement is lightly tested and may be
faulty.
 l [a]

Do a linear leastsquares 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.
 m

Recreate the pixeltocentimeter 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.
 n

An internal command; don't use it.
 o

Print out the reflections under refinement, including the
observed and predicted values of X, Y, and omega and the
noninteger value of (h,k,l).
 p

Alter the management of reflections in icerings.
By default icering reflections are treated the same as any other
reflections. "P" with no arguments toggles that behavior, i.e.
if icering reflections are currently treated as normal,
then invoking "P" will cause icering reflections to be excluded.
If icering 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
icerings, and P OFF unconditionally turns it off.
The list of resolution ranges associated with icerings 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
icerings at even higher resolution than 2.21 Angstroms; if those prove
to be a problem during refinement, we recommend setting up your own file.
 q

Quit the program without writing the parameters out.
 r

Rockingcurve refinement: the only parameters under
refinement are gamma0, gamma1, and gamma2.
 s

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).
 u

Update the parameters and print the (X,Y,omega,index)

statistics based on that update.
 v

List the available commands.
 w

Write out the current parameters but do not exit.
 x

Linear refinement based on a minimization of the "X"
residual. This option has not been carefully tested.
 y

Linear refinement based on a minimization of the "Y"

residual. This option has not been carefully tested.
 z

Linear refinement based on a minimization of the "Z"

residual. This option has not been carefully tested.
 0

Nonlinear refinement based entirely on minimizing the
scatteringangle residual.
 9

Nonlinear refinement based entirely on minimizing the
integerness residual.
 18

Nonlinear refinement as a weighted mixture of indexing
and scanningangle refinement; 1 involves primarily scanningangle
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 pseudogoniostat 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 righthanded (X,Y,Z) system with
the others.

* plateD: the sampletodetector distance in cm.

* Xcen: the X offset of the mainbeam from the detector center at

2theta = 0, in centimeters.

* Ycen: the Y offset of the mainbeam 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: 226230 (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 rockingcurve
refinements and during autoindexing. 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 lowestresolution
and largestresolution 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
P2_{1}2_{1}2_{1} is spacegroup 19,
and P6_{1} 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
fouraxis 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 Xradiation wavelength in Angstroms

(0.1nm).

* 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).
Examples

A refine1 script to autoindex and refine a data set is
given in the refall documentation.
REPORTING BUGS
Report bugs to Andy Howard at howard@iit.edu or 3125675881.
COPYRIGHT
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
Index
 NAME

 DESCRIPTION

 REPORTING BUGS

 COPYRIGHT

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