xheavy
NAME
xheavy - refine heavy atom derivatives and calculate phases.
USAGE
xheavy [file.sol file.phs]
DESCRIPTION
xheavy is used to calculate Multiple Isomorphous Replacement
phases and to refine heavy atom solutions. The MIR phasing
is done in an iterative manner where SIR phases for each
derivative are first calculated. These are combined, new
errors are estimated based on the combined SIR phases, and
finally, new phases are output using the new E estimates.
The refinement method used is a recursive correlation
search. Each heavy atom is moved in turn on a finer and
finer grid until no improvement in the correlation between
the observed and calculated difference is found and then the
relative occupancies are refined. The B-values are not
currently refined. Residual maps and difference maps can be
calculated to locate more heavy atom sites.
There are two windows for xheavy; the main one and an edit
pop-up. On the main window is the Crystal field which is
the key to the file containing this crystal types parame-
ters. Unit Cell is used as a verification that you have the
information for the crystal loaded. Do not edit this here
but edit the crystal file instead with xtalmgr. Directory
is where the program looks for files. The Derivative File
is a solution file where the heavy atom parameters are
saved. You can Load and Save the solutions files. The
save button is a menu button that gives you the option of
saving a single derivative (the one that is highlighted in
list), all of them, or outputting all of them in a PHASIT (a
Bill Furey program from his PHASES package) format file.
Several derivatives can be put into a single solution by
loading their individual solution files and then saving all
of them in a new file. Output Phases is the name of a file
that will contain the output phases. Next is the list of
Derivatives where a single derivative can be selected by
clicking on and highlighting it. Below are three buttons
for manipulating the list. Use New to start a list from
scratch. Edit is used to enter/replace parameters and sites
for the selected derivative. Selecting it pops up the edit
window (see below) and saves the current data in a buffer.
Delete deletes the currently selected derivative.
With Method you can choose, in the order they are meant to
be used, either Correlation Refinement, Calculate Protein
Phases, Map coefficients or Clear Phases. Correlation
Refinement is unique to this program but has proved very
robust and successful. It is independent of scale factor so
that it is not necessary to start with a close approximation
of the occupancy as in least-squares methods. Since it is a
search method, it finds the global minimum (within the
search radius) and does not get stuck in a local minimum.
(For the true global minimum use xhercules which searches
the entire unit cell using the same correlation function).
Protein phases are calulated in a several step procedure.
First, the single isomorphous replacement phases are com-
puted for each derivative. These are then gathered together
to get a rough estimate of the protein phase. Fc is then
rescaled using the protein phase to account for the extra
scattering power of the heavy atom (i.e. the scale should be
greater than 1.0 - for a well-occupied derivative it is from
1.05 to 1.10). Better error coefficients are then calcu-
lated and these are used to rephase each derivative; then
the final protein phases are gathered from these. The
method is similiar to lack-of-closure error refinement
except that the only parameters changed are the errors and
the scales. The map coefficients should be calculated for a
selected derivative after the phases are calculated. The
map coefficients option creates a phase file for the
selected derivative with the coefficients: h, k, l, |FP-
FPH|, (FPH-FP) - FHcalc, aprotein. Use xfft with the
Fourier type Fo to make a heavy atom difference map or Fo-Fc
to make a residual map. These are used to look for new
sites. Finally we come to the Apply button which is used to
start one of the methods and Abort is used to stop it in the
middle if something goes wrong.
SOLUTION EDITOR
Solutions can be read from xpatpred or entered with the edi-
tor. The derivative picked on the list of derivatives is
edited when the Edit button is pushed. First the deriva-
tive title is entered. A fin or df file containing the
difference information must be specified in the DataFile.
Tell the program which one it is with File Type. Addition-
ally, you can specify which of the columns in the df file
contains the phasing pair. One of three phase types is
specified next: isomorphous, isomorphous anamolous (must use
a df file), and native anamolous. You can downweight this
derivative relative to other derivatives with the Weight
slider. There are two resolution limits between which data
is used. Sigma Cut is used to remove small weakly observed
reflections. If either of a pair of measurements is below
this value, the pair is not considered. Then comes a filter
for removing ridiculous differences by comparing the the
value EMBED Equation. If this is greater than the value in
filter, then the reflection is rejected. A value of 100 is
about right for most derivatives. Derivatives with large
differences can use a larger value of about 130. Below
this is the list of heavy atom Sites. They are edited with
the controls below. Start the list by first entering the
values you want and then select Insert. Insert will insert
at the end of the list if nothing is selected, otherwise it
inserts after the selection (however, never select a line in
the middle of entering values as it will overwrite what you
have just done!). To edit, first highlight the atom in the
list you want to change, edit the values and then select
Replace. To delete an atom, select it and then use Delete.
Next to the Atom type is a little pull-down menu button
(with the triangle) that lists all of the available atom
types. It is best to use the pull-down menu and select one
than type it in to avoid typing errors. The choice of atom
type is non-critical in the isomorphous and native anomalous
case as it mainly just changes the scale factor. It does
matter when using the isomorphous anomalous phasing calcula-
tions because it sets the ratio of f'' to f'. If your atom
does not exist, choose the closest one. See below for more
information about adding new scattering factors. When you
are done editing you can either push Apply to save the edits
or close the window. (Although this may be window manager
dependen apply is safer.) If you mess things up you can
recover to the last saved position with Reset.
Verbose output is given in the message window. Don't forget
that this can be saved using the MENU button in this window
to pull up the FILE submenu.
NOTES
This program is under active development. As mentioned, the
native anomalous phasing has yet to be implemented. The
function is there to remind the developer of his shortcom-
ings and to tease users. The program has been used to solve
several structures. In particular, the correlation refine-
ment works very well. To date, no one has trusted it as the
only source of phasing, however. So far everyone has used
the phasit output option to confirm the phases with that
program. Comparison of maps shows very little difference
between the phases calculated, but the calculation is so
important that no one was willing to rely on the newer pro-
gram. Also, PHASIT prints more statistics which the
developer promises to add in some future version. Right
now, one has to rely on Rcentric and figure of merit as
guide posts. Adding new scatterers is cumbersome because
the program must be recompiled. See the README file in
src/xheavy for the location of added elements.
VERSION
Release 3.2 of XtalView
SEE ALSO
xtalview(1)