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authorThomas White <taw@bitwiz.org.uk>2010-12-08 17:41:28 -0700
committerThomas White <taw@physics.org>2012-02-22 15:27:09 +0100
commit6759b56838606bca2ecc3e1182d6ecad252348d6 (patch)
treee5f24802f314b54e1991de4e1e40d9e8da44f71f /src/get_hkl.c
parent57f325c7d13f60ba0c5f71921209e0f8d4f850bf (diff)
get_hkl: Use beam parameters file
Diffstat (limited to 'src/get_hkl.c')
-rw-r--r--src/get_hkl.c54
1 files changed, 50 insertions, 4 deletions
diff --git a/src/get_hkl.c b/src/get_hkl.c
index ba5106ec..cddb54b8 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -51,7 +51,8 @@ static void show_help(const char *s)
" --no-phases Do not try to use phases in the input file.\n"
" --multiplicity Multiply intensities by the number of\n"
" equivalent reflections.\n"
-" -b, --beam=<file> Get beam parameters from file (used for sigmas).\n"
+" -b, --beam=<file> Get beam parameters from file (used for sigmas).\n"
+" --max-res=<d> Calculate structure factors out to d=<d> nm.\n"
);
}
@@ -267,6 +268,11 @@ int main(int argc, char *argv[])
ReflItemList *input_items;
ReflItemList *write_items;
UnitCell *cell = NULL;
+ char *beamfile = NULL;
+ char *rval;
+ struct beam_params *beam; /* Beam parameters for SF calculation */
+ int have_max_res = 0;
+ double max_res = 0.0;
/* Long options */
const struct option longopts[] = {
@@ -282,11 +288,13 @@ int main(int argc, char *argv[])
{"pdb", 1, NULL, 'p'},
{"no-phases", 0, &config_nophase, 1},
{"multiplicity", 0, &config_multi, 1},
+ {"beam", 1, NULL, 'b'},
+ {"max-res", 1, NULL, 2},
{0, 0, NULL, 0}
};
/* Short options */
- while ((c = getopt_long(argc, argv, "ht:o:i:p:w:y:e:",
+ while ((c = getopt_long(argc, argv, "ht:o:i:p:w:y:e:b:",
longopts, NULL)) != -1) {
switch (c) {
@@ -322,6 +330,20 @@ int main(int argc, char *argv[])
expand = strdup(optarg);
break;
+ case 'b' :
+ beamfile = strdup(optarg);
+ break;
+
+ case 2 :
+ max_res = strtod(optarg, &rval);
+ if ( *rval != '\0' ) {
+ ERROR("Invalid maximum resolution.\n");
+ return 1;
+ }
+ max_res = 1.0 / (max_res * 1.0e-9);
+ have_max_res = 1;
+ break;
+
case 0 :
break;
@@ -350,10 +372,33 @@ int main(int argc, char *argv[])
}
esds = new_list_sigma();
if ( input == NULL ) {
+
+ if ( beamfile == NULL ) {
+ ERROR("To calculate structure factors, you must"
+ " provide a beam parameters file (use -b)\n");
+ return 1;
+ }
+
+ beam = get_beam_parameters(beamfile);
+ if ( beam == NULL ) {
+ ERROR("Failed to read beam parameters from '%s'\n", beamfile);
+ return 1;
+ }
+ free(beamfile);
+
+ if ( !have_max_res ) {
+ STATUS("You didn't specify the maximum resolution to"
+ " calculate structure factors. I'll go to"
+ " d = 0.5 nm.\n");
+ max_res = 1.0/0.5e-9;
+ }
+
input_items = new_items();
- ideal_ref = get_reflections(mol, eV_to_J(1790.0), 1/(0.05e-9),
- phases, input_items);
+ ideal_ref = get_reflections(mol, eV_to_J(beam->photon_energy),
+ max_res, phases, input_items);
+
} else {
+
ideal_ref = new_list_intensity();
input_items = read_reflections(input, ideal_ref, phases,
NULL, esds);
@@ -363,6 +408,7 @@ int main(int argc, char *argv[])
" have symmetry %s\n", mero);
return 1;
}
+
}
if ( config_poisson ) poisson_reflections(ideal_ref, input_items);