hercules
NAME
hercules - searches for heavy atom sites. This is a brute
force application of Patterson correlation methods. It is
slow, but extremely robust.
USAGE
hercules control-file print-file
DESCRIPTION
control-file
The control-file describes what you want done. The input
data descriptions are listed below. The first five lines
are string values for file names and the crystal name, and
the rest of the lines in the file contain numeric data.
1. fin file with (merged native and derivative data)
2. solution file (NONE for the first round, then
solution file output from xheavy or xpatpred for
the second round)
3. correlations file (output)
4. correlation map file (output in xcontur/xfit for-
mat)
5. crystal (crystal name)
6. grid (should be 1/4 to 1/6 resolution in
Angstroms)
7. resmax, resmin (resolution limits on diffraction
data)
8. xmin, xmax (in fractions of unit cell, x asym-
metric unit)
9. ymin, ymax (in fractions of unit cell, y asym-
metric unit)
10. zmin, zmax (in fractions of unit cell, z asym-
metric unit)
11. occupancy (see description)
print-file
The print-file will contain some of the output from the pro-
gram. Other output goes into the correlations and correla-
tion map files.
DISCUSSION
If you put "NONE" in the heavy solution file name spot (line
2), then atom data is read from the control-file. Other-
wise, it is read from the file specified in that field
(which may be results from a previous run). The atom data
in the solution file is in the same format as that used by
xheavy.
For example, to use hercules to search for an initial site,
enter "NONE" for the solution file (line 2), run hercules,
and select the highest hit. You can put this initial site
into a solution file using xpatpred. Then, to search for a
second site, enter the new solution file in line 2 instead
of "NONE" and run hercules again.
To guess an occupancy for the second site relative to the
first, examine the Patterson map. It's not very sensitive
to the occupancy, so numbers like 1, .75, .5, or .25 are
sufficient.
Use xpatpred to display the predicted Patterson positions.
To do this, enter the site and then write out a prediction
file. Read this file into xcontur as a labels file. The
vectors are put into the volume as 0-1, 0-1, 0-1, so they
won't show up on negative sections. For multiple site solu-
tions, pay particular attention to the cross-peaks.
The search volume should be the asymmetric volume of the
Patterson map. The input format only allows for rectangular
asymmetric units. This may cause some redundant computation
in high symmetry space groups. For single sites there will
be extra symmetry due to the fact that both hands and all
origin shifts are valid interpretations of the Patterson
map. For a second site there is a two-fold ambiguity due to
the hand choice. You can reduce the search volume accord-
ingly. If not, note that there will be several equivalent
hits (They will all give identical predictions with
xpatpred).
The solution can then be read directly into xheavy for
refinement. If you want to use the PHASES package from
Furey, then xheavy can rewrite the solution into a file
that's more or less ready to use depending on the PHASES
version you use.
Hercules writes an fsfour style map that may be examined
with xcontur. To get the coordinates in xcontur, click on
the peaks. Sites are added to the solution file as they are
found and the program is rerun. The peaks can be entered
into xpatpred and displayed on the Patterson map to verify
their correctness.
Hercules only takes a .fin file, not a .df file. You can
split off part of the data in a .df file to from a .fin file
with awk. If you do this, you can extract the first entry
in the .df file with the command:
awk '{print $1,$2,$3,$4,$5,$6,$7}' < file.df > file.fin
You can extract the second entry with the command:
awk '{print $1,$2,$3,$8,$9,$10,$11}' < file.df > file.fin
(For information about .fin and .df file formats, see
Chapter 3 of the XtalView user guide.)
You can view the results of a hercules run with a command
such as:
sort -nr +3 test.list | head -20 > top20.hits
This command produces a sorted list of the top 20 hits.
EXAMPLES
Example control-file
The following is an example control-file.
NONE
ex.list
ex.map
cvccp
2.5
1000.0, 6.0
0.0 0.5
0.0 0.3
0.0 0.05
1.0
On an SGI workstation, you may need to enclose each of the
first five lines in double quotes to make your file look
like this:
"ccpniau1.fin"
"NONE"
"ex.list"
"ex.map"
"cvccp"
2.5
1000.0, 6.0
0.0 0.5
0.0 0.3
0.0 0.5
1.0
NOTES
Runs can take several hours and are proportional to the
number of sites that are input.
VERSION
Release 3.2 of XtalView
SEE ALSO
xtalview(1), xhercules(1)