xpatpred
NAME
xpatpred - predict Patterson peaks from a list of sites.
USAGE
xpatpred solutionfile
DESCRIPTION
xpatpred allows you to enter and edit a set of sites and
output these in a form displayable by xcontur. The sites
can be written out in a solution file and refined using
xheavy. Different origin choices can be selected allowing a
rapid way to try all possible origins and visually choose
the correct one.
Crystal
The symmetry operators need to be present in the cry-
stal data file in the symm record.
Solution File
The solution file can be loaded or saved. The solution
file is a unique format to XtalView that is reminiscent
of the pdb file in that each record starts with a key
word. The solution files can be shared with xheavy in
order to refine the heavy atom sites. When a solution
is written out any origin choice is added to it and
when it is read back in, the origin is reset to 0,0,0.
Coordinates are fractional in solution files.
Prediction File
This file is a list of labels that can be read into
xcontur with the load labels option under files. The
labels are in fractional coordinates in u,v,w. The
label indicates which sites it is derived from in its
name. (i.e. pt1-pt1 is a self-vector of the site pt1
and pt1-pt3 is a cross-vector between pt1 and pt3).
The labels are transformed so that they are between 0
and 1. They are generated by looping through all sym-
metry operators in a pairwise fashion. It is not
guaranteed that all possible symmetry-related labels
will be generated so if a peak is not labeled a sym-
metry related one should be checked.
Site List
The sites are listed in a scrolling list. Clicking on
a site selects it and places its values in the fields
below where it can be edited. Insert takes the
information in the individual fields and places it in
the scrolling list at the end. Replace replaces the
currently highlighted line with the data in the fields.
Be careful to first select a line to be replaced and
then edit it (if you forget you can insert a new line
and then delete the line it was supposed to replace.)
Delete removes the highlighted line--the data is lost
forever (Solutions can be saved often, however.) Each
line contains the atom label, x, y, z, origin choice,
atom-type, occupancy and B-value. Their are 8 origin
choices of adding 0.5 or not to x,y,z. B-value and
occupancy are not directly used in this program.
Label, x, y, z, B-value, occupancy,
These are text fields that can be used to change or
enter data. To replace data in the scrolling list,
select the line, edit it, and then replace it.
Origin
This is a pull down list of 8 choices. Select the line
to be changed, then select the origin, and then replace
the line. To see the effect in xcontur, write out the
prediction and reread it in xcontur. Usually this is
used to find the relative origin of a second choice
while holding the first constant. Self-vectors will be
unaffected by an origin choice but the cross-vectors
are dependent upon the relative origin choice. With
two sites, only 4 of the choices will make a difference
(the other two are hand choices and are not detectable
with a Patterson map). With three or more sites all 8
choices may make a different pattern of cross-peaks.
Not all the origin choices are valid in every space
group. The possible origins are listed in the Interna-
tional Tables for Crystallography. The origin choices
given are valid for orthorhombic space groups. How-
ever, if an incorrect origin is chosen it will either
make no difference (e.g. adding 0.5 to y in monoclinic
makes no difference) or it will cause the self vector
not to match, and so, will be detectable. Other origin
choices will have to be entered by hand unless they are
added to a future version.
VERSION
Release 3.2 of XtalView
SEE ALSO
xtalview(1), xcontur(1), xheavy(1)