diff options
| -rwxr-xr-x | scripts/eV-to-A | 10 | ||||
| -rwxr-xr-x | scripts/gen-sfs-ano | 38 | ||||
| -rw-r--r-- | src/get_hkl.c | 61 | ||||
| -rw-r--r-- | src/render_hkl.c | 44 |
4 files changed, 115 insertions, 38 deletions
diff --git a/scripts/eV-to-A b/scripts/eV-to-A new file mode 100755 index 00000000..941e422b --- /dev/null +++ b/scripts/eV-to-A @@ -0,0 +1,10 @@ +#!/usr/bin/perl + +my $eV = $ARGV[0]; + +printf("%5.2f eV\n", $eV); + +my $J = $eV*1.6021773e-19; +my $lambda = (6.62606896e-34 * 299792458)/$J; + +printf("%5.2f eV = %5.5f A\n", $eV, $lambda*1e10); diff --git a/scripts/gen-sfs-ano b/scripts/gen-sfs-ano index be4598d6..522e0a6d 100755 --- a/scripts/gen-sfs-ano +++ b/scripts/gen-sfs-ano @@ -2,16 +2,27 @@ PDB=$1 SYMM=$2 -WAVEL=$3 -RESOLUTION=$4 +PG=$3 +WAVEL=$4 +RESOLUTION=$5 + +function show_help() +{ + echo -n "Syntax: $0 <PDB file> <space group> <point group>" + echo "<wavelength in Angstroms> [<resolution>]" + echo + echo "The space group and point group must be consistent, it's just" + echo "that I don't know how to convert the space group to a point" + echo "group." +} if [ "x$PDB" = "x" ]; then - echo "Syntax: $0 <PDB file> <space group> <wavelength in Angstroms> [<resolution>]" + show_help exit fi if [ "x$SYMM" = "x" ]; then - echo "Syntax: $0 <PDB file> <space group> <wavelength in Anstroms> [<resolution>]" + show_help exit fi @@ -25,17 +36,17 @@ ano_sfall.com ${PDB} ${RESOLUTION}A wave=${WAVEL} if [ $? -ne 0 ]; then exit 1; fi echo "Converting structure factors to text..." -mtz2various hklin ideal_ano.mtz hklout ${PDB}-temp.hkl >> gen-sfs.html <<EOF +mtz2various hklin ideal_ano.mtz hklout ${PDB}-temp1.hkl >> gen-sfs.html <<EOF LABIN H=H K=K L=L DUM1=Fplus DUM2=Fminus OUTPUT USER '(3I4,2F9.1)' EOF if [ $? -ne 0 ]; then exit 1; fi rm -f ${PDB}.mtz -perl < ${PDB}-temp.hkl > ${PDB}.hkl << WIBBLE +perl > ${PDB}-temp2.hkl << WIBBLE use strict; my \$line; -open(FILE, "${PDB}-temp.hkl"); +open(FILE, "${PDB}-temp1.hkl"); printf(" h k l I phase sigma(I) 1/d(nm^-1) ". "counts fs/px ss/px\\n"); @@ -51,13 +62,10 @@ while ( \$line = <FILE> ) { my \$iminus = \$5*\$5; printf("%3i %3i %3i %10.2f - 0.0 %s %7i %6.1f %6.1f\n", - \$h, \$k, \$l, \$iplus, 0.0, - " -", 1, 0.0, 0.0); + \$h, \$k, \$l, \$iplus, " -", 1, 0.0, 0.0); printf("%3i %3i %3i %10.2f - 0.0 %s %7i %6.1f %6.1f\n", - -\$h, -\$k, -\$l, \$iminus, 0.0, - " -", 1, 0.0, 0.0); - + -\$h, -\$k, -\$l, \$iminus, " -", 1, 0.0, 0.0); } else { printf(STDERR "Couldn't understand line '%s'\n", \$line); @@ -67,6 +75,8 @@ while ( \$line = <FILE> ) { close(FILE); printf("End of reflections\n"); WIBBLE -exit -rm -f ${PDB}-temp.hkl +get_hkl -i ${PDB}-temp2.hkl -o ${PDB}.hkl -p ${PDB} -y ${PG} --trim-centrics + +rm -f ${PDB}-temp1.hkl +rm -f ${PDB}-temp2.hkl diff --git a/src/get_hkl.c b/src/get_hkl.c index cb0446d8..e5e1a180 100644 --- a/src/get_hkl.c +++ b/src/get_hkl.c @@ -51,6 +51,11 @@ static void show_help(const char *s) " point group.\n" " -e, --expand=<sym> Expand reflections to this point group.\n" "\n" +"Use this option with care, and only if you understand why it might sometimes\n" +" be necessary:\n" +" --trim-centrics Remove reflections which are duplicated in the\n" +" point group specified with the '-y' option.\n" +"\n" "You can restrict which reflections are written out:\n" " -t, --template=<filename> Only include reflections mentioned in file.\n" "\n" @@ -294,12 +299,49 @@ static RefList *expand_reflections(RefList *in, const SymOpList *target, } +static RefList *trim_centrics(RefList *in, const SymOpList *sym) +{ + Reflection *refl; + RefListIterator *iter; + RefList *out; + + out = reflist_new(); + + for ( refl = first_refl(in, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) + { + signed int h, k, l; + signed int ha, ka, la; + Reflection *new; + + get_indices(refl, &h, &k, &l); + + /* Put it into the asymmetric unit */ + get_asymm(sym, h, k, l, &ha, &ka, &la); + + new = find_refl(out, ha, ka, la); + if ( new != NULL ) { + STATUS("Trimmed %i %i %i\n", h, k, l); + continue; + } + + /* Add new reflection under asymmetric (unique) indices */ + new = add_refl(out, ha, ka, la); + copy_data(new, refl); + } + + return out; +} + + int main(int argc, char *argv[]) { int c; int config_noise = 0; int config_poisson = 0; int config_multi = 0; + int config_trimc = 0; char *holo_str = NULL; char *mero_str = NULL; char *expand_str = NULL; @@ -328,6 +370,7 @@ int main(int argc, char *argv[]) {"multiplicity", 0, &config_multi, 1}, {"beam", 1, NULL, 'b'}, {"pdb", 1, NULL, 'p'}, + {"trim-centrics", 0, &config_trimc, 1}, {0, 0, NULL, 0} }; @@ -430,7 +473,10 @@ int main(int argc, char *argv[]) return 1; } free(input_file); - if ( check_list_symmetry(input, mero) ) { + + STATUS("%i reflections in input.\n", num_reflections(input)); + + if ( !config_trimc && check_list_symmetry(input, mero) ) { ERROR("The input reflection list does not appear to" " have symmetry %s\n", symmetry_name(mero)); return 1; @@ -478,6 +524,19 @@ int main(int argc, char *argv[]) } + if ( config_trimc ) { + + RefList *new; + + STATUS("Trimming duplicate reflections in %s\n", + symmetry_name(mero)); + new = trim_centrics(input, mero); + reflist_free(input); + input = new; + STATUS("%i output reflections\n", num_reflections(input)); + + } + if ( config_multi ) { Reflection *refl; diff --git a/src/render_hkl.c b/src/render_hkl.c index b37cc00b..4c37c005 100644 --- a/src/render_hkl.c +++ b/src/render_hkl.c @@ -559,9 +559,9 @@ int main(int argc, char *argv[]) UnitCell *cell; RefList *list; char *infile; - int config_zoneaxis = 0; int config_sqrt = 0; int config_colkey = 0; + int config_zawhinge = 0; unsigned int nproc = 1; char *pdb = NULL; int r = 0; @@ -583,7 +583,7 @@ int main(int argc, char *argv[]) /* Long options */ const struct option longopts[] = { {"help", 0, NULL, 'h'}, - {"zone-axis", 0, &config_zoneaxis, 1}, + {"zone-axis", 0, &config_zawhinge, 1}, {"output", 1, NULL, 'o'}, {"pdb", 1, NULL, 'p'}, {"boost", 1, NULL, 'b'}, @@ -667,7 +667,7 @@ int main(int argc, char *argv[]) } - if ( config_zoneaxis ) { + if ( config_zawhinge ) { ERROR("Friendly warning: The --zone-axis option isn't needed" " any longer (I ignored it for you).\n"); } @@ -733,28 +733,26 @@ int main(int argc, char *argv[]) return render_key(colscale, scale_top); } - if ( config_zoneaxis ) { - if ( (( down == NULL ) && ( right != NULL )) - || (( down != NULL ) && ( right == NULL )) ) { - ERROR("Either specify both 'down' and 'right'," - " or neither.\n"); + if ( (( down == NULL ) && ( right != NULL )) + || (( down != NULL ) && ( right == NULL )) ) { + ERROR("Either specify both 'down' and 'right'," + " or neither.\n"); + return 1; + } + if ( down != NULL ) { + int r; + r = sscanf(down, "%i,%i,%i", &dh, &dk, &dl); + if ( r != 3 ) { + ERROR("Invalid format for 'down'\n"); return 1; } - if ( down != NULL ) { - int r; - r = sscanf(down, "%i,%i,%i", &dh, &dk, &dl); - if ( r != 3 ) { - ERROR("Invalid format for 'down'\n"); - return 1; - } - } - if ( right != NULL ) { - int r; - r = sscanf(right, "%i,%i,%i", &rh, &rk, &rl); - if ( r != 3 ) { - ERROR("Invalid format for 'right'\n"); - return 1; - } + } + if ( right != NULL ) { + int r; + r = sscanf(right, "%i,%i,%i", &rh, &rk, &rl); + if ( r != 3 ) { + ERROR("Invalid format for 'right'\n"); + return 1; } } |