diff -r -u 20110907/ccp4-6.2.0/configure 20110921/ccp4-6.2.0/configure --- 20110907/ccp4-6.2.0/configure 2011-05-05 16:07:55.000000000 +0100 +++ 20110921/ccp4-6.2.0/configure 2011-09-08 15:01:01.000000000 +0100 @@ -4428,14 +4428,14 @@ xopts="${xopts} --with-ccp4=${prefix}" if test "$non_shared" = yes; then #this is a bit of a cheat/fudge but that's life! - xopts="${xopts} cmaplocal_LDFLAGS=-static cmakereference_LDFLAGS=-static caniso_LDFLAGS=-static cecalc_LDFLAGS=-static cfft_LDFLAGS=-static chltofom_LDFLAGS=-static cinvfft_LDFLAGS=-static convert2mtz_LDFLAGS=-static cpatterson_LDFLAGS=-static cphasecombine_LDFLAGS=-static cphasematch_LDFLAGS=-static csfcalc_LDFLAGS=-static csigmaa_LDFLAGS=-static csymmatch_LDFLAGS=-static ctruncate_LDFLAGS=-static cpirate_LDFLAGS=-static cbuccaneer_LDFLAGS=-static csequins_LDFLAGS=-static cparrot_LDFLAGS=-static cmodeltoseq_LDFLAGS=-static cnsfrommodel_LDFLAGS=-static" + xopts="${xopts} cmaplocal_LDFLAGS=-static cmakereference_LDFLAGS=-static caniso_LDFLAGS=-static cecalc_LDFLAGS=-static cfft_LDFLAGS=-static chltofom_LDFLAGS=-static cinvfft_LDFLAGS=-static convert2mtz_LDFLAGS=-static cpatterson_LDFLAGS=-static cphasecombine_LDFLAGS=-static cphasematch_LDFLAGS=-static csfcalc_LDFLAGS=-static csigmaa_LDFLAGS=-static csymmatch_LDFLAGS=-static ctruncate_LDFLAGS=-static cpirate_LDFLAGS=-static cbuccaneer_LDFLAGS=-static csequins_LDFLAGS=-static cparrot_LDFLAGS=-static cmodeltoseq_LDFLAGS=-static cncsfrommodel_LDFLAGS=-static" fi if test "$static_libgcc" = yes; then #this is a bit of a cheat/fudge but that's life! if test "$shared_lib" = yes ; then - xopts="${xopts} cmaplocal_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cmakereference_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' caniso_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cecalc_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cfft_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' chltofom_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cinvfft_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' convert2mtz_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cpatterson_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cphasecombine_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cphasematch_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csfcalc_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csigmaa_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csymmatch_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' ctruncate_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cpirate_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cbuccaneer_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csequins_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cparrot_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cmodeltoseq_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cnsfrommodel_LDFLAGS='-Wl,-rpath\\\$\$ORIGIN/../lib -z origin -static-libgcc'" + xopts="${xopts} cmaplocal_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cmakereference_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' caniso_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cecalc_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cfft_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' chltofom_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cinvfft_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' convert2mtz_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cpatterson_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cphasecombine_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cphasematch_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csfcalc_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csigmaa_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csymmatch_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' ctruncate_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cpirate_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cbuccaneer_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' csequins_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cparrot_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cmodeltoseq_LDFLAGS='-Wl,-rpath,\\\$\$ORIGIN/../lib -z origin -static-libgcc' cncsfrommodel_LDFLAGS='-Wl,-rpath\\\$\$ORIGIN/../lib -z origin -static-libgcc'" else - xopts="${xopts} cmaplocal_LDFLAGS=-static-libgcc cmakereference_LDFLAGS=-static-libgcc caniso_LDFLAGS=-static-libgcc cecalc_LDFLAGS=-static-libgcc cfft_LDFLAGS=-static-libgcc chltofom_LDFLAGS=-static-libgcc cinvfft_LDFLAGS=-static-libgcc convert2mtz_LDFLAGS=-static-libgcc cpatterson_LDFLAGS=-static-libgcc cphasecombine_LDFLAGS=-static-libgcc cphasematch_LDFLAGS=-static-libgcc csfcalc_LDFLAGS=-static-libgcc csigmaa_LDFLAGS=-static-libgcc csymmatch_LDFLAGS=-static-libgcc ctruncate_LDFLAGS=-static-libgcc cpirate_LDFLAGS=-static-libgcc cbuccaneer_LDFLAGS=-static-libgcc csequins_LDFLAGS=-static-libgcc cparrot_LDFLAGS=-static-libgcc cmodeltoseq_LDFLAGS=-static-libgcc cnsfrommodel_LDFLAGS=-static-libgcc" + xopts="${xopts} cmaplocal_LDFLAGS=-static-libgcc cmakereference_LDFLAGS=-static-libgcc caniso_LDFLAGS=-static-libgcc cecalc_LDFLAGS=-static-libgcc cfft_LDFLAGS=-static-libgcc chltofom_LDFLAGS=-static-libgcc cinvfft_LDFLAGS=-static-libgcc convert2mtz_LDFLAGS=-static-libgcc cpatterson_LDFLAGS=-static-libgcc cphasecombine_LDFLAGS=-static-libgcc cphasematch_LDFLAGS=-static-libgcc csfcalc_LDFLAGS=-static-libgcc csigmaa_LDFLAGS=-static-libgcc csymmatch_LDFLAGS=-static-libgcc ctruncate_LDFLAGS=-static-libgcc cpirate_LDFLAGS=-static-libgcc cbuccaneer_LDFLAGS=-static-libgcc csequins_LDFLAGS=-static-libgcc cparrot_LDFLAGS=-static-libgcc cmodeltoseq_LDFLAGS=-static-libgcc cncsfrommodel_LDFLAGS=-static-libgcc" fi fi if test -z "$onlylibs" ; then diff -r -u 20110907/ccp4-6.2.0/share/BALBES/Package/bin_py/UtilitiesClasses.py 20110921/ccp4-6.2.0/share/BALBES/Package/bin_py/UtilitiesClasses.py --- 20110907/ccp4-6.2.0/share/BALBES/Package/bin_py/UtilitiesClasses.py 2010-12-16 16:05:04.000000000 +0000 +++ 20110921/ccp4-6.2.0/share/BALBES/Package/bin_py/UtilitiesClasses.py 2011-09-09 12:55:30.000000000 +0100 @@ -63,7 +63,13 @@ # use local disk at the node for # (1) scratch dir (molrep, refmac both write frequently to scratch) # (2) maybe database searching and MR template model building (that needs local database) ? - self['local'] = os.environ['TMPDIR'] + try: + self['local'] = os.environ['CCP4_SCR'] + except: + try: + self['local'] = os.environ['TMPDIR'] + except: + self['local'] = '/tmp' self['local_pdb_path'] = "/data2/fei/Database_BALBES/All_pdb/All" self['start_time'] = time.ctime(time.time() ) diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/Makefile.in 20110921/ccp4-6.2.0/src/clipper_progs/Makefile.in --- 20110907/ccp4-6.2.0/src/clipper_progs/Makefile.in 2010-11-18 13:11:38.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/Makefile.in 2011-09-08 15:02:56.000000000 +0100 @@ -162,7 +162,7 @@ cmakereference_LDFLAGS = @cmakereference_LDFLAGS@ cmaplocal_LDFLAGS = @cmaplocal_LDFLAGS@ cmodeltoseq_LDFLAGS = @cmodeltoseq_LDFLAGS@ -cnsfrommodel_LDFLAGS = @cnsfrommodel_LDFLAGS@ +cncsfrommodel_LDFLAGS = @cncsfrommodel_LDFLAGS@ convert2mtz_LDFLAGS = @convert2mtz_LDFLAGS@ cparrot_LDFLAGS = @cparrot_LDFLAGS@ cpatterson_LDFLAGS = @cpatterson_LDFLAGS@ diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/configure 20110921/ccp4-6.2.0/src/clipper_progs/configure --- 20110907/ccp4-6.2.0/src/clipper_progs/configure 2010-11-18 13:10:02.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/configure 2011-09-08 15:02:04.000000000 +0100 @@ -716,7 +716,7 @@ cmaplocal_LDFLAGS cmakereference_LDFLAGS cmodeltoseq_LDFLAGS -cnsfrommodel_LDFLAGS +cncsfrommodel_LDFLAGS csloop_LDFLAGS LIBOBJS LTLIBOBJS' @@ -7137,7 +7137,7 @@ cmaplocal_LDFLAGS!$cmaplocal_LDFLAGS$ac_delim cmakereference_LDFLAGS!$cmakereference_LDFLAGS$ac_delim cmodeltoseq_LDFLAGS!$cmodeltoseq_LDFLAGS$ac_delim -cnsfrommodel_LDFLAGS!$cnsfrommodel_LDFLAGS$ac_delim +cncsfrommodel_LDFLAGS!$cncsfrommodel_LDFLAGS$ac_delim csloop_LDFLAGS!$csloop_LDFLAGS$ac_delim LIBOBJS!$LIBOBJS$ac_delim LTLIBOBJS!$LTLIBOBJS$ac_delim diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/configure.ac 20110921/ccp4-6.2.0/src/clipper_progs/configure.ac --- 20110907/ccp4-6.2.0/src/clipper_progs/configure.ac 2010-11-18 13:08:29.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/configure.ac 2011-09-08 15:02:46.000000000 +0100 @@ -158,7 +158,7 @@ AC_SUBST(cmaplocal_LDFLAGS) AC_SUBST(cmakereference_LDFLAGS) AC_SUBST(cmodeltoseq_LDFLAGS) -AC_SUBST(cnsfrommodel_LDFLAGS) +AC_SUBST(cncsfrommodel_LDFLAGS) AC_SUBST(csloop_LDFLAGS) AC_CONFIG_FILES([Makefile diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/html/Makefile.in 20110921/ccp4-6.2.0/src/clipper_progs/html/Makefile.in --- 20110907/ccp4-6.2.0/src/clipper_progs/html/Makefile.in 2010-10-22 14:29:51.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/clipper_progs/html/Makefile.in 2011-09-08 15:03:08.000000000 +0100 @@ -146,7 +146,7 @@ cmakereference_LDFLAGS = @cmakereference_LDFLAGS@ cmaplocal_LDFLAGS = @cmaplocal_LDFLAGS@ cmodeltoseq_LDFLAGS = @cmodeltoseq_LDFLAGS@ -cnsfrommodel_LDFLAGS = @cnsfrommodel_LDFLAGS@ +cncsfrommodel_LDFLAGS = @cncsfrommodel_LDFLAGS@ convert2mtz_LDFLAGS = @convert2mtz_LDFLAGS@ cparrot_LDFLAGS = @cparrot_LDFLAGS@ cpatterson_LDFLAGS = @cpatterson_LDFLAGS@ diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/src/Makefile.in 20110921/ccp4-6.2.0/src/clipper_progs/src/Makefile.in --- 20110907/ccp4-6.2.0/src/clipper_progs/src/Makefile.in 2010-11-18 13:13:19.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/src/Makefile.in 2011-09-08 15:04:12.000000000 +0100 @@ -260,7 +260,7 @@ cmakereference_LDFLAGS = @cmakereference_LDFLAGS@ cmaplocal_LDFLAGS = @cmaplocal_LDFLAGS@ cmodeltoseq_LDFLAGS = @cmodeltoseq_LDFLAGS@ -cnsfrommodel_LDFLAGS = @cnsfrommodel_LDFLAGS@ +cncsfrommodel_LDFLAGS = @cncsfrommodel_LDFLAGS@ convert2mtz_LDFLAGS = @convert2mtz_LDFLAGS@ cparrot_LDFLAGS = @cparrot_LDFLAGS@ cpatterson_LDFLAGS = @cpatterson_LDFLAGS@ diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/src/buccaneer/Makefile.in 20110921/ccp4-6.2.0/src/clipper_progs/src/buccaneer/Makefile.in --- 20110907/ccp4-6.2.0/src/clipper_progs/src/buccaneer/Makefile.in 2010-11-18 13:13:22.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/src/buccaneer/Makefile.in 2011-09-08 15:03:22.000000000 +0100 @@ -177,7 +177,7 @@ cmakereference_LDFLAGS = @cmakereference_LDFLAGS@ cmaplocal_LDFLAGS = @cmaplocal_LDFLAGS@ cmodeltoseq_LDFLAGS = @cmodeltoseq_LDFLAGS@ -cnsfrommodel_LDFLAGS = @cnsfrommodel_LDFLAGS@ +cncsfrommodel_LDFLAGS = @cncsfrommodel_LDFLAGS@ convert2mtz_LDFLAGS = @convert2mtz_LDFLAGS@ cparrot_LDFLAGS = @cparrot_LDFLAGS@ cpatterson_LDFLAGS = @cpatterson_LDFLAGS@ diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/src/parrot/Makefile.in 20110921/ccp4-6.2.0/src/clipper_progs/src/parrot/Makefile.in --- 20110907/ccp4-6.2.0/src/clipper_progs/src/parrot/Makefile.in 2010-11-18 13:13:26.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/src/parrot/Makefile.in 2011-09-08 15:03:33.000000000 +0100 @@ -163,7 +163,7 @@ cmakereference_LDFLAGS = @cmakereference_LDFLAGS@ cmaplocal_LDFLAGS = @cmaplocal_LDFLAGS@ cmodeltoseq_LDFLAGS = @cmodeltoseq_LDFLAGS@ -cnsfrommodel_LDFLAGS = @cnsfrommodel_LDFLAGS@ +cncsfrommodel_LDFLAGS = @cncsfrommodel_LDFLAGS@ convert2mtz_LDFLAGS = @convert2mtz_LDFLAGS@ cparrot_LDFLAGS = @cparrot_LDFLAGS@ cpatterson_LDFLAGS = @cpatterson_LDFLAGS@ diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/src/pirate/Makefile.in 20110921/ccp4-6.2.0/src/clipper_progs/src/pirate/Makefile.in --- 20110907/ccp4-6.2.0/src/clipper_progs/src/pirate/Makefile.in 2010-11-18 13:13:28.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/src/pirate/Makefile.in 2011-09-08 15:03:46.000000000 +0100 @@ -168,7 +168,7 @@ cmakereference_LDFLAGS = @cmakereference_LDFLAGS@ cmaplocal_LDFLAGS = @cmaplocal_LDFLAGS@ cmodeltoseq_LDFLAGS = @cmodeltoseq_LDFLAGS@ -cnsfrommodel_LDFLAGS = @cnsfrommodel_LDFLAGS@ +cncsfrommodel_LDFLAGS = @cncsfrommodel_LDFLAGS@ convert2mtz_LDFLAGS = @convert2mtz_LDFLAGS@ cparrot_LDFLAGS = @cparrot_LDFLAGS@ cpatterson_LDFLAGS = @cpatterson_LDFLAGS@ diff -r -u 20110907/ccp4-6.2.0/src/clipper_progs/src/sloop/Makefile.in 20110921/ccp4-6.2.0/src/clipper_progs/src/sloop/Makefile.in --- 20110907/ccp4-6.2.0/src/clipper_progs/src/sloop/Makefile.in 2010-11-24 10:14:42.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/clipper_progs/src/sloop/Makefile.in 2011-09-08 15:04:01.000000000 +0100 @@ -170,7 +170,7 @@ cmakereference_LDFLAGS = @cmakereference_LDFLAGS@ cmaplocal_LDFLAGS = @cmaplocal_LDFLAGS@ cmodeltoseq_LDFLAGS = @cmodeltoseq_LDFLAGS@ -cnsfrommodel_LDFLAGS = @cnsfrommodel_LDFLAGS@ +cncsfrommodel_LDFLAGS = @cncsfrommodel_LDFLAGS@ convert2mtz_LDFLAGS = @convert2mtz_LDFLAGS@ cparrot_LDFLAGS = @cparrot_LDFLAGS@ cpatterson_LDFLAGS = @cpatterson_LDFLAGS@ diff -r -u 20110907/ccp4-6.2.0/src/pointless/ChangeLog 20110921/ccp4-6.2.0/src/pointless/ChangeLog --- 20110907/ccp4-6.2.0/src/pointless/ChangeLog 2011-05-16 16:00:09.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/ChangeLog 2011-09-06 17:49:04.000000000 +0100 @@ -1,5 +1,25 @@ Release notes +1.6.4 + - Reindexing merged files now deals properly with phase and ABCD columns, +eg for I2<->C2 or P2 21 21 <-> P21 21 2 conversions +Improved/fixed detection of new space group after reindexing + +1.6.3 + - Trap "*****" fields from format overflow in XDS headers, just to give a sensible error message + +1.6.2 + - XDS XSCALE now puts [U] = [I] to evade bug in Reindex, used in Xia2. Also restored the History record in the MTZ header (lost at some previous point) + +1.6.1 + - fixed serious bug present in all 1.5.x versions. If an MTZ file +input is in the highest point group of the higher symmetry group, +specifically 422, 622, R32 or 432, and the final output file is in the +same point group, then the symmetry operators were scrambled relative +to the ISYM flags on the observations, leading to wrong original hkl +being genereated in Scala/Aimless: this then affects the secondary beam +calculation and hence the absorption correction + 1.5.22 - WILDFILE option diff -r -u 20110907/ccp4-6.2.0/src/pointless/configure 20110921/ccp4-6.2.0/src/pointless/configure --- 20110907/ccp4-6.2.0/src/pointless/configure 2011-06-18 21:59:50.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/configure 2011-08-03 11:11:25.000000000 +0100 @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.61 for pointless 1.5.22. +# Generated by GNU Autoconf 2.61 for pointless 1.6.2. # # Report bugs to . # @@ -574,8 +574,8 @@ # Identity of this package. PACKAGE_NAME='pointless' PACKAGE_TARNAME='pointless' -PACKAGE_VERSION='1.5.22' -PACKAGE_STRING='pointless 1.5.22' +PACKAGE_VERSION='1.6.2' +PACKAGE_STRING='pointless 1.6.2' PACKAGE_BUGREPORT='pre@lmb-mrc.ac.uk' ac_unique_file="pointless.cpp" @@ -1223,7 +1223,7 @@ # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures pointless 1.5.22 to adapt to many kinds of systems. +\`configure' configures pointless 1.6.2 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1294,7 +1294,7 @@ if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of pointless 1.5.22:";; + short | recursive ) echo "Configuration of pointless 1.6.2:";; esac cat <<\_ACEOF @@ -1399,7 +1399,7 @@ test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -pointless configure 1.5.22 +pointless configure 1.6.2 generated by GNU Autoconf 2.61 Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, @@ -1413,7 +1413,7 @@ This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by pointless $as_me 1.5.22, which was +It was created by pointless $as_me 1.6.2, which was generated by GNU Autoconf 2.61. Invocation command line was $ $0 $@ @@ -2231,7 +2231,7 @@ # Define the identity of the package. PACKAGE=pointless - VERSION=1.5.22 + VERSION=1.6.2 cat >>confdefs.h <<_ACEOF @@ -5725,6 +5725,7 @@ include/ccp4 lib lib/src +lib/libccp4/ccp4 lib/ccif' for ac_dir in $ac_ccp4_dirs; do if test -r "$ccp4_prefix/$ac_dir/ccp4_errno.h"; then @@ -5856,7 +5857,7 @@ echo "$as_me: WARNING: assuming library $CCP4_LIBS headers $CCP4_CXXFLAGS" >&2;} have_ccp4=yes else - CCP4_CXXFLAGS="-I$ccp4_prefix/lib/src" + CCP4_CXXFLAGS="-I$ccp4_prefix/lib/src -I$ccp4_prefix/lib/libccp4/ccp4" CCP4_LIBS="-L$ccp4_prefix/lib/src -L$ccp4_prefix/lib -lccp4f -lccp4c -lccif -lmmdb" { echo "$as_me:$LINENO: WARNING: assuming library $CCP4_LIBS headers $CCP4_CXXFLAGS" >&5 echo "$as_me: WARNING: assuming library $CCP4_LIBS headers $CCP4_CXXFLAGS" >&2;} @@ -5938,8 +5939,6 @@ ac_CCTBX_LDOPTS="-lcctbx" fi - - # Check whether --enable-boost was given. if test "${enable_boost+set}" = set; then enableval=$enable_boost; @@ -7362,7 +7361,7 @@ # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by pointless $as_me 1.5.22, which was +This file was extended by pointless $as_me 1.6.2, which was generated by GNU Autoconf 2.61. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -7409,7 +7408,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF ac_cs_version="\\ -pointless config.status 1.5.22 +pointless config.status 1.5.1 configured by $0, generated by GNU Autoconf 2.61, with options \\"`echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\" diff -r -u 20110907/ccp4-6.2.0/src/pointless/configure.ac 20110921/ccp4-6.2.0/src/pointless/configure.ac --- 20110907/ccp4-6.2.0/src/pointless/configure.ac 2011-06-18 21:59:52.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/configure.ac 2011-09-07 12:12:30.000000000 +0100 @@ -2,13 +2,13 @@ # Process this file with autoconf to produce a configure script. dnl package-name version-number bugs-to: -AC_INIT(pointless, 1.5.22, pre@lmb-mrc.ac.uk) +AC_INIT(pointless, 1.6.2, pre@lmb-mrc.ac.uk) AC_CANONICAL_TARGET dnl package-name version-number, the gzip'd tar file is named dnl package-version.tar.gz. -AM_INIT_AUTOMAKE(pointless, 1.5.22) +AM_INIT_AUTOMAKE(pointless, 1.6.2) AC_CONFIG_SRCDIR([pointless.cpp]) @@ -51,7 +51,7 @@ AC_MSG_WARN([assuming library $CCP4_LIBS headers $CCP4_CXXFLAGS]) have_ccp4=yes else - CCP4_CXXFLAGS="-I$ccp4_prefix/lib/src" + CCP4_CXXFLAGS="-I$ccp4_prefix/lib/src -I$ccp4_prefix/lib/libccp4/ccp4" CCP4_LIBS="-L$ccp4_prefix/lib/src -L$ccp4_prefix/lib -lccp4f -lccp4c -lccif -lmmdb" AC_MSG_WARN([assuming library $CCP4_LIBS headers $CCP4_CXXFLAGS]) have_ccp4=yes diff -r -u 20110907/ccp4-6.2.0/src/pointless/controls.cpp 20110921/ccp4-6.2.0/src/pointless/controls.cpp --- 20110907/ccp4-6.2.0/src/pointless/controls.cpp 2011-05-09 10:24:49.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/controls.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -103,9 +103,15 @@ // Set up observation_part class (static method) with current flags // conditional on Ipr present or absent (col_Ipr == 0 absent) { - if (col_Ipr <= 0) SelectIcolFlag = 0; + if (col_Ipr <= 0) { + SelectIcolFlag = 0; + prfpresent = false; + } else { + prfpresent = true; // both profile-fitted and summation intensities + } int Iflag = SelectIcolFlag; SelectI::SetIcolFlag(Iflag, imid, IpowerComb); + SelectI::SetIprPresent(prfpresent); } //------------------------------------------------------------ std::string RejectFlags::formatReject2Policy() const @@ -196,7 +202,8 @@ ncycles = 10; converge = 0.3; iovsdmin = -3.0; - e2min = 1.0; + e2min = 0.8; + e2max = 5.0; } //------------------------------------------------------------ } diff -r -u 20110907/ccp4-6.2.0/src/pointless/controls.hh 20110921/ccp4-6.2.0/src/pointless/controls.hh --- 20110907/ccp4-6.2.0/src/pointless/controls.hh 2011-06-18 21:59:53.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/controls.hh 2011-09-06 17:49:04.000000000 +0100 @@ -122,7 +122,7 @@ // (a) profile-fitted or integrated intensity column { public: - col_controls() : SelectIcolFlag(-1), imid(-1.0) {} + col_controls() : prfpresent(false), SelectIcolFlag(0), IpowerComb(3), imid(-1.0) {} // Set column selection flags // see class observation_part (hkl_unmerge.hh) for implementation @@ -135,7 +135,17 @@ // conditional on Ipr present or absent (col_Ipr == 0 absent) void SetupColSelection(const int col_Ipr=1); + // Return selection flag + int IcolFlag() const {return SelectIcolFlag;} + + //! return true if Imid was set from command input + bool IsImidSet() const {return (imid > 0.1);} + + //! return true if file contains both profile-fitted and summation Is + bool BothIpresent() const {return prfpresent;} + private: + bool prfpresent; // true if file contains both profile-fitted and summation Is int SelectIcolFlag; int IpowerComb; double imid; @@ -151,10 +161,11 @@ AnalysisControls() : nresobins(10), nibins(10) {} AnalysisControls(const int& Nresobins, const int& Nibins, const double& Coneangle, const double& MinimumHalfdatasetCC, - const double& MinimumIoverSigma, const double& MinimumBatchIoverSigma) + const double& MinimumIoverSigma, const double& MinimumBatchIoverSigma, + const int& Nbatchsmooth=1) : nresobins(Nresobins), nibins(Nibins), coneangledegrees(Coneangle), minimumhalfdatasetcc(MinimumHalfdatasetCC), minimumioversigma(MinimumIoverSigma), - minimumbatchioversigma(MinimumBatchIoverSigma) + minimumbatchioversigma(MinimumBatchIoverSigma), nbatchsmooth(Nbatchsmooth) {} int NresoBins() const {return nresobins;} @@ -163,14 +174,17 @@ double MinimumHalfdatasetCC() const {return minimumhalfdatasetcc;} double MinimumIoverSigma() const {return minimumioversigma;} double MinimumBatchIoverSigma() const {return minimumbatchioversigma;} + int NbatchSmooth() const {return nbatchsmooth;} + void SetNbatchSmooth(const int& Nbatchsmooth) {nbatchsmooth = Nbatchsmooth;} private: - int nresobins; // number of resolution bins - int nibins; // number of intensity bins + int nresobins; // number of resolution bins + int nibins; // number of intensity bins double coneangledegrees; // cone angle double minimumhalfdatasetcc; double minimumioversigma; double minimumbatchioversigma; + int nbatchsmooth; // number of batches over which to smooth statistics }; //------------------------------------------------------------ class RejectFlags { @@ -248,6 +262,9 @@ float& E2min() {return e2min;} float E2min() const {return e2min;} + float& E2max() {return e2max;} + float E2max() const {return e2max;} + private: bool bfgs; // or Fox-Holmes if false int ncyc1; // number of 1st stage cycles @@ -255,6 +272,7 @@ float converge; // convergence limit (multiplier of sd) float iovsdmin; // /sd'() limit for 1st pass scaling float e2min; // |E^2| limit for 2nd pass scaling + float e2max; // |E^2| maximum limit for 2nd pass scaling }; //================================================================= class DatasetControl diff -r -u 20110907/ccp4-6.2.0/src/pointless/copymergedmtz.cpp 20110921/ccp4-6.2.0/src/pointless/copymergedmtz.cpp --- 20110907/ccp4-6.2.0/src/pointless/copymergedmtz.cpp 2011-05-09 10:24:50.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/copymergedmtz.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -33,7 +33,6 @@ const std::string& filename_out, const std::string& SpaceGroupName, const scala::ReindexOp& reindex, - const bool& reindexedTestData, const bool& reduce, const bool& verbose, phaser_io::Output& output) @@ -70,33 +69,26 @@ "\nReflections are not reduced to asymmetric unit\n"); } } - - char history[MTZRECORDLENGTH]; - char date[11]; - char time[9]; - CCP4::ccp4_utils_date(date); - CCP4::ccp4_utils_time(time); - std::string text = "POINTLESS, "+std::string(date)+" "+ - std::string(time)+ - " reindexed "+reindex.as_hkl(); - if (SpaceGroupName != "" && SpaceGroupName != "HKLIN") - {text += " Space group "+SpaceGroupName;} - strcpy(history, text.c_str()); - // int Nhist = MtzAddHistory(mtzin, &history, 1); + // New symmetry + std::string spacegroupname = SpaceGroupName; // local copy + bool sgnamegiven = true; + if (spacegroupname == "" || spacegroupname == "HKLIN") { + spacegroupname = std::string(mtzin->mtzsymm.spcgrpname); + sgnamegiven = false; // space group name not specified explicitly + //^ std::cout << "MTZ sgname: " << spacegroupname << "\n"; + } + + bool reindexed = !reindex.IsIdentity(); // true if reindex op is not h,k,l + bool translation = reindex.IsTranslation(); // true if translation component - // vectors of pointers to interesting columns - std::vector DanoCol; - // ... and pairs - std::vector PairCol; + scala::hkl_symmetry NewSymm= scala::hkl_symmetry(spacegroupname); - // Symmetry - scala::hkl_symmetry NewSymm= scala::hkl_symmetry(SpaceGroupName); - if (SpaceGroupName == "" || SpaceGroupName == "HKLIN") { + if (!sgnamegiven) { // space group name not given, so derive from MTZ name + reindex NewSymm.ChangeBasis(reindex); if (verbose) { output.logTabPrintf(1,LOGFILE, - "Reindexed space group : %s\n", + "Reindexed space group : %s\n\n", NewSymm.symbol_xHM().c_str()); } } else { @@ -106,14 +98,41 @@ NewSymm.symbol_xHM().c_str()); } } - bool reindexed = !reindex.IsIdentity(); // true if reindex op is not h,k,l + char history[MTZRECORDLENGTH]; + char date[11]; + char time[9]; + CCP4::ccp4_utils_date(date); + CCP4::ccp4_utils_time(time); + std::string text = "POINTLESS, "+std::string(date)+" "+std::string(time); + if (reindexed) { + text += " reindexed "+reindex.as_hkl(); + } + text += " Space group "+spacegroupname; + strcpy(history, text.c_str()); + + int Nhist = MtzAddHistory(mtzin, &history, 1); + + // vectors of pointers to interesting columns + std::vector DanoCol; + // ... and pairs + std::vector PairCol; + // ... phase columns + std::vector PhaseCol; + // ... ABCD columns (1st of set) + std::vector ABCDCol; + + SpaceGroup newspacegroup = NewSymm.GetSpaceGroup(); + // for cell constraints - CCtbxSym::CellGroup CG(NewSymm.GetSpaceGroup()); + CCtbxSym::CellGroup CG(newspacegroup); // Process all crystals, changing cells by reindex // Loop crystals scala::Scell newcell; + if (verbose) { + output.logTab(0,LOGFILE, "Unit Cells: "); + } for (int x=0; x < CMtz::MtzNxtal(mtzin); x++) { CMtz::MTZXTAL* xtl = CMtz::MtzIxtal(mtzin,x); newcell = CG.constrain(scala::Scell(xtl->cell).change_basis(reindex)); @@ -129,33 +148,55 @@ // Loop columns int Ncol = pset->ncol; std::vector ColFree(Ncol,true); - for (int col=0;colcol[col]; + char ctype = pcol->type[0]; // column type + // Check for any phase columns (type P) // or phase coefficient columns (type A) - // These cannot be reindexed by this routine - char ctype = pcol->type[0]; - if (reindexed && (ctype == 'P' || ctype == 'A')) { + // These cannot be reindexed by this routine if there is a translation + if (translation && (ctype == 'P' || ctype == 'A')) { PrintError - ("**** Can't reindex file containing Phase or Phase Coefficient column ****", + ("**** Can't apply translation reindex to Phase or Phase Coefficient column ****", output); output.logTabPrintf(0,LOGFILE," Column label %s Type %c\n\n", pcol->label, pcol->type[0]); return false; } + if (reduce) { - // Check for anomalous difference columns - if (ctype == 'D') { + // mark phase & ABCD columns for later processing + if (ctype == 'P') { // phase column + PhaseCol.push_back(pcol); + } else if (ctype == 'A') { + // Check for 4 columns of type A + bool found = true; + if (col <= Ncol-4) { + for (int col2=col+1;col2col[col2]->type[0] == ctype) { // OK type A + ColFree[col2] = false; // mark as used + } else { + found = false; // wrong type + } + } + } + if (!found) { + Message::message(Message_fatal + ("CopyMergedMTZ: incomplet ABCD set"+ + std::string(pcol->label)+" type"+ctype)); + } + ABCDCol.push_back(pcol); // OK + } else if (ctype == 'D') { // Check for anomalous difference columns DanoCol.push_back(pcol); } // Check for columns of type F+, F- (G, sigma L), // or I+, I- (K, sigma M) else if (ctype == 'G' || ctype == 'L' || ctype == 'K' || ctype == 'M') { // Search forward for a matching column + bool found = false; if (col < Ncol-1) { - bool found = false; for (int col2=col+1;col2col[col2]->type[0] == ctype) { // xtl/set/col & col2 are a matched pair to be swapped @@ -165,16 +206,15 @@ break; } } - if (!found) { - Message::message(Message_fatal - ("CopyMergedMTZ: unmatched anomalous column"+ - std::string(pcol->label)+" type"+ctype)); - - } } - } - } - } + if (!found) { + Message::message(Message_fatal + ("CopyMergedMTZ: unmatched anomalous column"+ + std::string(pcol->label)+" type"+ctype)); + } + } // end F/I+- check + } // end reduce + } // end column not yet assigned } // end column loop } // end dataset loop } // end crystal loop @@ -213,8 +253,31 @@ PairCol[i].second->label, ctype); } output.logTab(0,LOGFILE,"\n"); + } // end paircol + if (PhaseCol.size() > 0) { + output.logTabPrintf(0,LOGFILE, + "\nPhases may be changed if indices hkl are changed in reducing to asymmetric unit\n"); + output.logTabPrintf(0,LOGFILE, + "\n Phase column labels: "); + for (size_t i=0;ilabel); + } + output.logTab(0,LOGFILE,"\n"); } - } // verbose + if (ABCDCol.size() > 0) { + output.logTabPrintf(0,LOGFILE, + "\nABCDs may be changed if indices hkl are changed in reducing to asymmetric unit\n"); + output.logTabPrintf(0,LOGFILE, + "\n ABCD column labels: "); + for (size_t i=0;ilabel,(ABCDCol[i]+1)->label, + (ABCDCol[i]+2)->label,(ABCDCol[i]+3)->label); + } + output.logTab(0,LOGFILE,"\n"); + } + + } // end verbose // Update file cell // ?? don't need to, first crystal cell is used @@ -226,7 +289,7 @@ HorR = 'R'; }} - mtzin->mtzsymm = spg_to_mtz(NewSymm.GetSpaceGroup(), HorR); + mtzin->mtzsymm = spg_to_mtz(newspacegroup, HorR); int Ncolumns = CMtz::MtzNcol(mtzin); // Column offsets ( = number-1) for H,K,L columns @@ -239,6 +302,7 @@ int isym; int Nneg = 0; int Nswap = 0; + int Nphasechange = 0; int Nref = 0; int NfractIdx = 0; std::vector cols(Ncolumns); @@ -250,13 +314,11 @@ // set up with the correct length CMtz::MtzRrefl(mtzin->filein, Ncolumns, &*cols.begin()); - int h = Nint(cols[mtzH]); - int k = Nint(cols[mtzK]); - int l = Nint(cols[mtzL]); + scala::Hkl oldhkl(Nint(cols[mtzH]), Nint(cols[mtzK]), Nint(cols[mtzL])); // Reindex scala::Hkl newhkl; // returns false if non-integral indices - bool HklOK = scala::Hkl(h,k,l).change_basis(newhkl, reindex); + bool HklOK = oldhkl.change_basis(newhkl, reindex); if (!HklOK) { NfractIdx++; continue; @@ -264,14 +326,15 @@ if (reduce) { // Reduce to asymmetric unit - newhkl = NewSymm.put_in_asu(newhkl, isym); + oldhkl = newhkl; + newhkl = NewSymm.put_in_asu(oldhkl, isym); + bool hklprint = true; // If hand has changed (isym even), do any necessary swaps if (isym%2 == 0 && !NewSymm.is_centric(newhkl)) { // Anomalous difference swaps, acentric reflections only // NB Data has to be swapped as there is no reliable way just to // change the column names - bool hklprint = true; - if (DanoCol.size() > 0) { + if (DanoCol.size() > 0) { // DANO column for (size_t i=0;isource - 1; @@ -292,8 +355,8 @@ output.logTab(0,LOGFILE, " ... more negated"); } Nneg++; - } - if (PairCol.size() > 0) { + } // end DANO column + if (PairCol.size() > 0) { // Paired +/- column for (size_t i=0;isource - 1; int k = PairCol[i].second->source - 1; @@ -317,9 +380,53 @@ output.logTab(0,LOGFILE, " ... more swapped"); } Nswap++; + } // end paired column + } // end swap + // --- + if (PhaseCol.size() > 0 || ABCDCol.size() > 0) { // Phase columns + // Phase shift for +hkl, degrees + double phaseshift = oldhkl.HKL().sym_phase_shift(newspacegroup.SymopFromIsym(isym)); + if (verbose) { + if (std::abs(phaseshift) > 0.001) { + if (Nphasechange < 20) { + if (hklprint) { + output.logTab(0,LOGFILE,newhkl.format()); + hklprint = false; + } + std::string s = "Phase shift "+clipper::String(clipper::Util::rad2d(phaseshift)); + if (isym%2 == 0) s += " negated"; + output.logTab(0,LOGFILE, s); + Nphasechange++; + } + } } - } - } + if (PhaseCol.size() > 0) { // phase columns + for (size_t i=0;isource - 1; + cols[j] = cols[j] + clipper::Util::rad2d(phaseshift); + if (isym%2 == 0) { // change of hand, negate phase + cols[j] = -cols[j]; + } + } + } // end phase columns + + if (ABCDCol.size() > 0) { // ABCD columns + for (size_t i=0;isource - 1; + // Make ABCD object + clipper::datatypes::ABCD HL(cols[j], cols[j+1], cols[j+2], cols[j+3]); + HL.shift_phase(phaseshift); // shift phase + if (isym%2 == 0) {HL.friedel();} // Friedel symmetry if required + cols[j] = HL.a(); + cols[j+1] = HL.b(); + cols[j+2] = HL.c(); + cols[j+3] = HL.d(); + } + } // end ABCD + } // end phase columns + } // end reduce cols[mtzH] = newhkl[0]; cols[mtzK] = newhkl[1]; @@ -327,7 +434,7 @@ CMtz::MtzWrefl(mtzin->fileout, Ncolumns, &*cols.begin()); Nref++; - } + } // end loop reflections // Reset global resolution limits float minres, maxres; diff -r -u 20110907/ccp4-6.2.0/src/pointless/copymergedmtz.hh 20110921/ccp4-6.2.0/src/pointless/copymergedmtz.hh --- 20110907/ccp4-6.2.0/src/pointless/copymergedmtz.hh 2007-11-12 10:28:20.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/pointless/copymergedmtz.hh 2011-09-06 17:49:04.000000000 +0100 @@ -28,7 +28,6 @@ const std::string& filename_out, const std::string& SpaceGroup, const scala::ReindexOp& reindex, - const bool& reindexedTestData, const bool& reduce, const bool& verbose, phaser_io::Output& output); diff -r -u 20110907/ccp4-6.2.0/src/pointless/fix_merged_scores.cpp 20110921/ccp4-6.2.0/src/pointless/fix_merged_scores.cpp --- 20110907/ccp4-6.2.0/src/pointless/fix_merged_scores.cpp 2011-05-09 10:24:52.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/fix_merged_scores.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -35,9 +35,6 @@ { ASSERT (latticeSymm.Nelement() == int(scores.size())); ASSERT (scores.size() == CCsig.size()); // sanity checks - hkl_symmetry fileSymmtoLat = fileSymm; - // reindex file symmetry to current lattice symmetry if necessary - if (!latticereindex.IsIdentity()) fileSymmtoLat.ChangeBasis(latticereindex); RefListType IsMerged = hklinListType; // if (IsMerged == MERGED) { @@ -47,14 +44,13 @@ // std::cout << "\nLattice symmetry: " << latticeSymm.symbol_xHM() <<"\n"; // latticeSymm.print_elements(); //^- - // We have now decided that the file is merged, reset scores for symmetry elements - // previously merged, ie in fileSymmtoLat + // previously merged, ie in fileSymm reindexed for (int islat=0;islat mergeOps = mergeGroup.PrimRotSymops(); const double tol = 0.001; for (size_t i=0;i& subgroups, - const hkl_symmetry& mergeSymm) - // mergeSymm reindexed into lattice frame + const hkl_symmetry& mergeSymm, const ReindexOp& reindex) + // symops from mergeSymm can be reindexed into lattice frame by reindex { std::vector keepsubgroup(subgroups.size(), true); // flags to keep subgroup bool anyremoved = false; @@ -83,7 +83,9 @@ // loop symmetry elements in mergeSymm for (int iel=0;iel Rmatrix = mergeSymm.SymopInElement(0,iel); + clipper::Symop invsymop = mergeSymm.ClipperSymopInElement(0,iel); + invsymop = reindex.Symop(invsymop); // reindex to lattice cell + std::vector Rmatrix = MVutil::SetVMat33(invsymop.rot()); // ... as matrix // Is this element in the subgroup? if (!subgroups[igl].HasElement(Rmatrix)) { // fail, all elements must be present diff -r -u 20110907/ccp4-6.2.0/src/pointless/getsubgroups.hh 20110921/ccp4-6.2.0/src/pointless/getsubgroups.hh --- 20110907/ccp4-6.2.0/src/pointless/getsubgroups.hh 2009-10-14 16:14:36.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/getsubgroups.hh 2011-09-06 17:49:04.000000000 +0100 @@ -13,10 +13,10 @@ // if forceI2 true, convert any C2/m setting to I std::vector GetSubGroups(const hkl_symmetry& symm); //-------------------------------------------------------------- - // If file is merged, remove all subgroups wich are subgroups of original group + // If file is merged, remove all subgroups which are subgroups of original group // since these are implicit void RemoveImplicitSubgroups(std::vector& subgroups, - const hkl_symmetry& OrigSymm); + const hkl_symmetry& OrigSymm, const ReindexOp& reindex); } // scala diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_controls.cpp 20110921/ccp4-6.2.0/src/pointless/hkl_controls.cpp --- 20110907/ccp4-6.2.0/src/pointless/hkl_controls.cpp 2010-11-24 12:39:48.000000000 +0000 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_controls.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -21,6 +21,8 @@ range_sel = input.getRESO(); // batch exclusions batchexclude = input.BatchExclusions(); + //P // batch inclusions from explicit RUN specification + //P batchinclude = input.RunBatches(); // Check that fileSeries specified on selection commands match // specified files. Fail here if not batchexclude.CheckSeries(NumFileSeries); @@ -55,7 +57,15 @@ // any renumbering (fileSeriesList == 0), no test will be done // (ie always returns true) unless fileSeries == 0 { - return !(batchexclude.InSelection(batch_number, fileSeries)); + bool accept = true; + if (!batchinclude.Null()) { + // We have inclusions from specified RUNs + // accept if within selection + accept = batchinclude.InSelection(batch_number, fileSeries); + } + if (batchexclude.InSelection(batch_number, fileSeries)) { + accept = false; + } + return accept; } - } diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_controls.hh 20110921/ccp4-6.2.0/src/pointless/hkl_controls.hh --- 20110907/ccp4-6.2.0/src/pointless/hkl_controls.hh 2010-05-17 16:24:30.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_controls.hh 2011-09-06 17:49:04.000000000 +0100 @@ -68,6 +68,7 @@ int nrej_mflag, nrej_reso; ResoRange range_sel; BatchSelection batchexclude; // List/ranges of batches to exclude + BatchSelection batchinclude; // List/ranges of batches to include (from RUN) float inputscale; // scale factor to apply on input // fraction of maximum resolution to use in test for blank batches float nullResolutionfraction; diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_datatypes.cpp 20110921/ccp4-6.2.0/src/pointless/hkl_datatypes.cpp --- 20110907/ccp4-6.2.0/src/pointless/hkl_datatypes.cpp 2011-06-18 21:59:54.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_datatypes.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -228,6 +228,16 @@ // << symm.symop(kbest).rot().inverse().format() << "\n\n"; //^- } //-------------------------------------------------------------- + //! change basis of symmetry operator + clipper::Symop ReindexOp::Symop(const clipper::Symop& symop) const + { + // S' = H^-1 S H + // t' = H^-1 t + clipper::Mat33 HR = rot(); + clipper::RTop Sp(HR.inverse()*symop.rot()*HR, HR.inverse() * symop.trn()); + return clipper::Symop(Sp); + } + //-------------------------------------------------------------- bool operator == (const ReindexOp& a,const ReindexOp& b) { return a.equals(b); @@ -673,10 +683,9 @@ Vec3 v = vh * reindex_op; Newhkl = Hkl(Nint(v[0]), Nint(v[1]), Nint(v[2])); bool OK = true; - for (int i=0;i<3;i++) - { - if (std::abs(v[i]-double(Newhkl[i])) > 0.05) OK = false; - } + for (int i=0;i<3;i++) { + if (std::abs(v[i]-double(Newhkl[i])) > 0.05) OK = false; + } return OK; } //-------------------------------------------------------------- @@ -1248,10 +1257,10 @@ std::vector lims(2); std::vector > xylims(2); lims[0] = batchinfo.detlm[0][0][0]; // XDET - lims[1] = batchinfo.detlm[1][0][0]; + lims[1] = batchinfo.detlm[0][0][1]; xylims[0] = lims; lims[0] = batchinfo.detlm[0][1][0]; // YDET - lims[1] = batchinfo.detlm[1][1][0]; + lims[1] = batchinfo.detlm[0][1][1]; xylims[1] = lims; return xylims; } diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_datatypes.hh 20110921/ccp4-6.2.0/src/pointless/hkl_datatypes.hh --- 20110907/ccp4-6.2.0/src/pointless/hkl_datatypes.hh 2011-06-18 21:59:55.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_datatypes.hh 2011-09-06 17:49:04.000000000 +0100 @@ -146,7 +146,13 @@ //! returns true if determinant is positive (desirable!) bool Positive() const { return (rot().det() > 0.0);} - + //! Returns true if there is a translation component + bool IsTranslation() const { + return trn() != clipper::Vec3(0.0,0.0,0.0);} + + //! change basis of symmetry operator + clipper::Symop Symop(const clipper::Symop& symop) const; + //! format as string [h,k,l] std::string as_hkl() const; //! format as matrix @@ -680,6 +686,9 @@ //! Return range of detector pixel coordinates std::vector > DetectorCoordinateRange() const; + //! return number of detectors + int Ndet() const {return batchinfo.ndet;} + //! return MTZ batch: only use this for writing MTZ file /*! otherwise information retrieval should be through explicit calls */ CMtz::MTZBAT batchdata() const {return batchinfo;} @@ -769,7 +778,6 @@ void AddRange(const int& batch1, const int& batch2, const int& fileSeriesList, const int& flag=-1); - //! Return index in list if in selection, for given file series, else -1 int FindInSelection(const int& batch, const int& fileSeriesTest) const; @@ -840,5 +848,4 @@ }; } // namespace scala #endif - // end hkl_datatypes.hh diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp 20110921/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp --- 20110907/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp 2011-05-09 10:24:57.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_symmetry.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -182,15 +182,15 @@ rotsymops[i] = clipper::Symop(clipper::RTop<>(csymops[i].rot())); invrotsymops[i] = clipper::Symop(clipper::RTop<>(csymops[i].rot()).inverse()); } + if (spacegroupname == "Unknown") { + spacegroupname = CCP4spaceGroupName(); // construct from csymops + } spacegroupname = symbol_hm(); spacegroupnumber = spacegroup_number(); CCP4spacegroupnumber = spacegroupnumber; // Sort out name if unknown //^ std::cout << "SpaceGroup: HM: " << symbol_hm() //^ << " Hall: " << symbol_hall() << "\n"; - if (spacegroupname == "Unknown") { - spacegroupname = CCP4spaceGroupName(); - } // Always consult CCP4 libraries for space group numbers CCP4spaceGroupNumber(); SetLatType(); @@ -236,6 +236,14 @@ else {return h;} } //-------------------------------------------------------------- + //! return the symop corresponding to Isym from put_in_asu + clipper::Symop SpaceGroup::SymopFromIsym(const int& isym) const + { + if (isym < 1 || isym > 2*Nsymp) + Message::message(Message_fatal("SymopFromIsym - ISYM out of range") ); + return csymops[(isym-1)/2]; + } + //-------------------------------------------------------------- SpaceGroup SpaceGroup::NewLatticePointGroup(const char& Lattype) const //! Return group with new lattice, keeping point group operators { @@ -277,15 +285,18 @@ // Change basis by reindex operator { for (size_t js=0;js HR = H.rot(); - clipper::Mat33 S = csymops[js].rot(); - clipper::Vec3 t = csymops[js].trn(); - clipper::RTop Sp(HR.inverse()*S*HR, HR.inverse() * t); - csymops[js] = clipper::Symop(Sp); + csymops[js] = H.Symop(csymops[js]); + // clipper::Mat33 S = csymops[js].rot(); + // clipper::Vec3 t = csymops[js].trn(); + // clipper::RTop Sp(HR.inverse()*S*HR, HR.inverse() * t); + // csymops[js] = clipper::Symop(Sp); + //^ std::cout <<"ChangeBasis Symop out: " << csymops[js].format() <<"\n"; } - init(); + spacegroupname = "Unknown"; // force review of name + init(csymops); } //-------------------------------------------------------------- bool SpaceGroup::IsSymopIdentity(const int& symN) const @@ -392,15 +403,17 @@ } //-------------------------------------------------------------- std::string SpaceGroup::CCP4spaceGroupName() const - // Use CCP4 library routine to get name from operators + // Use CCP4 library routine to get name from operators csymops { int nsym = num_symops(); std::vector ccp4ops(nsym); for (int i=0;isymbol_xHM) <<"\n"; //^ return std::string(ccp4spg->symbol_xHM); } //-------------------------------------------------------------- @@ -829,6 +842,23 @@ return true; } //-------------------------------------------------------------- + bool hkl_symmetry::equals_r_order(const hkl_symmetry& other) const + // true if spacegroup other is same ignoring translations + // with operators in the same order + { + if (Nsymp != other.Nsymp) return false; + if (LatType != other.LatType) return false; + // compare symcodes corresponding to rotation-only parts + // for all symops in same order + bool found = true; + for (int i=0; i < Nsymp; i++) { + if (inv_rot_symcodes[i] != other.inv_rot_symcodes[i]) { + found = false; + } + } + return found; + } + //-------------------------------------------------------------- bool hkl_symmetry::equals_rt(const hkl_symmetry& other) const { if (Nsymp != other.Nsymp) return false; @@ -853,12 +883,19 @@ //-------------------------------------------------------------- std::vector hkl_symmetry::SymopInElement(const int& lsym, const int& kelement) const - // Return rotation part of lsym'th symmetry operator of + // Return rotation part of lsym'th inverse symmetry operator of // kelement'th symmetry element { return MVutil::SetVMat33(spaceGroup.InvRotSymop(elements[kelement].symops[lsym]).rot()); } //-------------------------------------------------------------- + clipper::Symop hkl_symmetry::ClipperSymopInElement(const int& lsym, + const int& kelement) const + // Return lsym'th inverse symmetry operator of kelement'th symmetry element + { + return spaceGroup.InvRotSymop(elements[kelement].symops[lsym]); + } + //-------------------------------------------------------------- std::vector hkl_symmetry::RotSymopsInElement(const int& kelement) const { std::vector ops(elements.at(kelement).symops.size()); diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_symmetry.hh 20110921/ccp4-6.2.0/src/pointless/hkl_symmetry.hh --- 20110907/ccp4-6.2.0/src/pointless/hkl_symmetry.hh 2010-08-25 12:44:14.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_symmetry.hh 2011-09-06 17:49:04.000000000 +0100 @@ -55,6 +55,9 @@ clipper::Symop InvRotSymop(const int& symN) const {return invrotsymops.at(symN);} //!< return symN'th inverse symop + //! return the symop corresponding to Isym from put_in_asu + clipper::Symop SymopFromIsym(const int& isym) const; + //! return symop codes for rotation symmetry operators clipper::Symop_code RotSymopCode(const int& symN) const {return clipper::Symop_code(rotsymops.at(symN));} @@ -225,9 +228,14 @@ //! return number of operators in kelement'th symmetry element int NopInElement(const int& kelement) const; - //! Return rotation part of j'th symmetry operator of kelement'th symmetry element + //! Return rotation part of j'th inverse symmetry operator of kelement'th symmetry element std::vector SymopInElement(const int& j, const int& kelement) const; + //! Return lsym'th inverse symmetry operator of kelement'th symmetry element + clipper::Symop ClipperSymopInElement(const int& lsym, + const int& kelement) const; + + //! Return symmetry-element number (from 0->Nelement-1) relating observations with ISYM = isym1,isym2 /*! Isym = 2 * SymNumber + 1 for h+ Isym = 2 * SymNumber + 2 for h- @@ -269,6 +277,9 @@ /*! not equals_r & equals_rt test number of operators & lattice type (centering) */ bool equals_rt(const hkl_symmetry& other) const; //!< test all operators including translation bool equals_r(const hkl_symmetry& other) const; //!< test just rotation parts + // true if spacegroup other is same ignoring translations + // with operators in the same order + bool equals_r_order(const hkl_symmetry& other) const; //! simple test, ignore translations bool operator==(const hkl_symmetry& other) const {return equals_r(other);} diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_unmerge.cpp 20110921/ccp4-6.2.0/src/pointless/hkl_unmerge.cpp --- 20110907/ccp4-6.2.0/src/pointless/hkl_unmerge.cpp 2011-06-18 21:59:55.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_unmerge.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -83,9 +83,10 @@ // ****************************************************************** //-------------------------------------------------------------- // Initialise static members - int SelectI::selecticolflag = -1; // Use Ipr (if present) + int SelectI::selecticolflag = 0; // No Ipr int SelectI::ipowercomb = 3; // Ipower =3 double SelectI::imid = -1.0; // unset + bool SelectI::iprpresent = false; // true if we have a second intensity Ipr stored //-------------------------------------------------------------- void SelectI::SetIcolFlag(const int& IcolFlag, const double& Imid, const int Ipower) { @@ -105,16 +106,31 @@ } } //-------------------------------------------------------------- - IsigI SelectI::GetCombinedI(const Rtype& Ic, const Rtype& varIc, - const Rtype& Ipr, const Rtype& varIpr) + void SelectI::ResetAverageIntensity(const double& meanI) + // store imid = overall if needed + { + if (selecticolflag > 0) { + imid = meanI; + } + } + //-------------------------------------------------------------- + IsigI SelectI::GetCombinedI(const Rtype& Iraw, const Rtype& Ic, const Rtype& varIc, + const Rtype& Ipr, const Rtype& varIpr) // Return combined I, sigI { // COMBINE option, weighted mean of I & Ipr - double w = 1.0/(1.0 + pow((std::abs(Ic)/imid), ipowercomb)); + double w = 1.0/(1.0 + pow((std::abs(Iraw)/imid), ipowercomb)); return IsigI((w*Ipr+(1.0-w)*Ic), sqrt(w*varIpr + (1.0-w)*varIc)); } //-------------------------------------------------------------- + IsigI SelectI::GetCombinedI(const Rtype& Iraw, const IsigI& Isc, const IsigI& Ispr) + { + Rtype varIc = Isc.sigI()*Isc.sigI(); + Rtype varIpr = Ispr.sigI()*Ispr.sigI(); + return GetCombinedI(Iraw, Isc.I(), varIc, Ispr.I(), varIpr); + } + //-------------------------------------------------------------- std::string SelectI::format() { std::string s; @@ -123,10 +139,11 @@ } else if (selecticolflag == 0) { s = "Summation-integration (or sole) intensities will be used"; } else { - s = "Combined intensities will be used: weighted mean of profile-fitted & integrated intensities\n"; - s += " I = w * Ipr + (1-w) * Iint\n"; + s = "Combined intensities will be used:\n"; + s += " weighted mean of profile-fitted (Ipr) & summation (Isum) intensities\n"; + s += " I = w * Ipr + (1-w) * Isum\n"; - s += " w = 1/(1+(I/"+ + s += " w = 1/(1+(Iraw/"+ StringUtil::Strip(StringUtil::ftos(imid,8,1))+ ")^"+StringUtil::Strip(clipper::String(ipowercomb))+")"; } @@ -243,6 +260,118 @@ } return std::pair(Xd/float(Npart_),Yd/float(Npart_)); } + //-------------------------------------------------------------- + IsigI observation::IsigIsummation() + { + // Return "summation" integration I sigI, summed over partials if necessary + // This is also the sole intensity if there is only one + // Also sets mean phi, time, LP + Rtype Itot = 0.0; + Rtype varItot = 0.0; + IsigI Is; + observation_part this_part; + // Stored values + phi_ = 0.0; + time_ = 0.0; + LP_ = 0.0; + + if (Npart_ == 1) { + // Full + Is = get_part(0).I_sigI(); + phi_ = get_part(0).phi(); + time_ = get_part(0).time(); + LP_ = get_part(0).LP(); + batch_ = get_part(0).batch(); + } else { // partial + Rtype max_bit = -1.0; + batch_ = 0; + for (int kpart = 0; kpart < Npart_; kpart++) { // loop parts + this_part = get_part(kpart); + Itot += this_part.Ic(); + varItot += this_part.sigIc()*this_part.sigIc(); + phi_ += this_part.phi(); + time_ += this_part.time(); + LP_ += this_part.LP(); + // find biggest bit to mark as central batch + if (this_part.fraction_calc() > max_bit) { + max_bit = this_part.fraction_calc(); + batch_ = this_part.batch(); + } + } // end loop parts + phi_ = phi_/Npart_; // average phi over all parts + time_ = time_/Npart_; // average time over all parts + LP_ = LP_/Npart_; + Rtype sigItot = sqrt(varItot); + if (part_flag == SCALE) { + Itot /= totalfraction; + sigItot /= totalfraction; + } + // Central batch + if (batch_ == 0) { + // Not set, use one in the middle + batch_ = get_part(Npart_/2).batch(); + } + Is = IsigI(Itot, sigItot); + } // end if partial + return Is; + } + //-------------------------------------------------------------- + IsigI observation::IsigIpr() const + { + // Return "profile" integration I sigI, summed over partials if necessary + Rtype Itot = 0.0; + Rtype varItot = 0.0; + IsigI Is; + observation_part this_part; + + if (Npart_ == 1) { + // Full + Is = get_part(0).I_sigIpr(); + } else { // partial + for (int kpart = 0; kpart < Npart_; kpart++) { // loop parts + this_part = get_part(kpart); + Itot += this_part.Ipr(); + varItot += this_part.sigIpr()*this_part.sigIpr(); + } // end loop parts + Rtype sigItot = sqrt(varItot); + if (part_flag == SCALE) { + Itot /= totalfraction; + sigItot /= totalfraction; + } + Is = IsigI(Itot, sigItot); + } // end if partial + return Is; + } + //-------------------------------------------------------------- + void observation::sum_partials() + { + // Sum (or scale) all partials for this observation + // Assumes that SelectI has been set up correctly to choose + // either summation, profile or combined intensity measurements + // + // Sets I_, sigI_, phi_, time_, LP_, batch_ + // - - - - + + // Get summation integration or sole intensity, sum parts, set phi, time, LP + IsigI Ic = IsigIsummation(); + IsigI Ipr(0.0, 0.0); + if (SelectI::IsIprPresent()) { + // ... and for Ipr if present + Ipr = IsigIpr(); + } + IsigI Isum; + if (SelectI::Combine()) { + Rtype Iraw = Ic.I(); + if (LP_ > 0.0) Iraw /= LP_; // raw intensity back-corrected for LP + Isum = SelectI::GetCombinedI(Iraw, Ic, Ipr); + } else if (SelectI::SelectIcolFlag() < 0) { // profile + Isum = Ipr; + } else { + Isum = Ic; + } + I_ = Isum.I(); + sigI_ = Isum.sigI(); + } // ****************** reflection ******************* reflection::reflection() {} // dummy // Normal constructor @@ -306,103 +435,21 @@ Npart = 0; Nscaled = 0; NvalidObs = 0; // counts valid and accepted - observation_part this_part; - Rtype sigItot; for (int lobs = 0; lobs < num_observations(); lobs++) { - Rtype Itot = 0.0; - Rtype varItot = 0.0; - Rtype ItotPr = 0.0; - Rtype varItotPr = 0.0; - Rtype phi = 0.0; - Rtype time = 0.0; - Rtype LP = 0.0; - int Ntot = 0; - bool scaled = false; - int NpartObs = observations[lobs].num_parts(); - - if (NpartObs == 1) { - // Full - if (SelectI::Combine()) { - // For combination, we want both Ic & Ipr - Itot = observations[lobs].get_part(0).Ic(); - varItot = observations[lobs].get_part(0).sigIc()* - observations[lobs].get_part(0).sigIc(); - ItotPr = observations[lobs].get_part(0).Ipr(); - varItotPr = observations[lobs].get_part(0).sigIpr()* - observations[lobs].get_part(0).sigIpr(); - IsigI Is = SelectI::GetCombinedI(Itot, varItot, ItotPr, varItotPr); - Itot = Is.I(); - sigItot = Is.sigI(); - } else { - // Select either Ic or Ipr - Itot = observations[lobs].get_part(0).Ic(SelectI::SelectIcolFlag()); - sigItot = observations[lobs].get_part(0).sigIc(SelectI::SelectIcolFlag()); - } - phi = observations[lobs].get_part(0).phi(); - time = observations[lobs].get_part(0).time(); - LP = observations[lobs].get_part(0).LP(); - // Can't be scaled - observations[lobs].set_IsigI_phi_time(Itot, sigItot, phi, time, LP); - observations[lobs].set_batch(observations[lobs].get_part(0).batch()); + observations[lobs].sum_partials(); + if (observations[lobs].IsFull()) { if (observations[lobs].IsAccepted()) {NvalidObs++;} Nfull++; } else { // partial - Rtype max_bit = -1.0; - int central_batch = 0; - for (int kpart = 0; kpart < NpartObs; kpart++) { - this_part = observations[lobs].get_part(kpart); - Ntot++; - if (SelectI::Combine()) { - // For combination, we want both Ic & Ipr - Itot += this_part.Ic(); - varItot += this_part.sigIc()* - this_part.sigIc(); - ItotPr += this_part.Ipr(); - varItotPr += this_part.sigIpr()* - this_part.sigIpr(); - } else { - // Select either Ic or Ipr - Itot += this_part.Ic(SelectI::SelectIcolFlag()); - varItot += this_part.sigIc(SelectI::SelectIcolFlag())* - this_part.sigIc(SelectI::SelectIcolFlag()); - } - phi += this_part.phi(); - time += this_part.time(); - LP += this_part.LP(); - // find biggest bit to mark as central batch - if (this_part.fraction_calc() > max_bit) { - max_bit = this_part.fraction_calc(); - central_batch = this_part.batch(); - } - } - phi = phi/Ntot; // average phi over all parts - time = time/Ntot; // average time over all parts - LP = LP/Ntot; - if (SelectI::Combine()) { - IsigI Is = SelectI::GetCombinedI(Itot, varItot, ItotPr, varItotPr); - Itot = Is.I(); - sigItot = Is.sigI(); - } else { - sigItot = sqrt(varItot); - } - // Store total - // scales incomplete partial if necessary - scaled = observations[lobs].set_IsigI_phi_time(Itot, sigItot, phi, time, LP); - if (scaled) Nscaled++; - // Central batch - if (central_batch == 0) { - // Not set, use one in the middle - central_batch = observations[lobs].get_part(NpartObs/2).batch(); - } - observations[lobs].set_batch(central_batch); + if (observations[lobs].PartFlag() == SCALE) Nscaled++; if (observations[lobs].IsAccepted()) {NvalidObs++;} Npart++; + } // end if partial + if (observations[lobs].sigI() > 0.0) { + sdmin = Min(sdmin, observations[lobs].sigI()); } - if (sigItot > 0.0) { - sdmin = Min(sdmin, sigItot); - } - } + } // end loop observations if (sdmin > sdmin0*0.9) sdmin = -1.0; return sdmin; } @@ -1687,13 +1734,14 @@ return Nobservations; } // end partials //-------------------------------------------------------------- - int hkl_unmerge_list::sum_partials() - // ^^^^^^^^^^^ - // Sum partials within each observation for all reflections - // Returns number of valid partials + int hkl_unmerge_list::sum_partials(const bool& forcesum) + // ^^^^^^^^^^^ + // Sum partials within each observation for all reflections + // If forcesum is true, sum them even if already summed + // Returns number of valid partials { - if (status == SUMMED) return Nobs_partial; - if (status != PREPARED) + if (!forcesum && (status == SUMMED)) return Nobs_partial; + if (!(status == PREPARED) && (status != SUMMED)) Message::message(Message_fatal("hkl_unmerge_list::sum_partials - not PREPARED") ); sigmamin = +1000000.; @@ -1704,21 +1752,19 @@ Nobs_scaled = 0; int Nfull, Npart, Nscaled; - for (size_t j = 0; j < refl_list.size(); j++) // loop all reflections - { - // Sum partials - // reflection.sum_partials returns min sigma found - // (excluding zeroes) - sm = refl_list[j].sum_partials(Nfull, Npart, Nscaled); - if (sm > 0.0) - { - sigmamin = Min(sigmamin, sm); - Nref_valid++; - Nobs_full += Nfull; - Nobs_partial += Npart; - Nobs_scaled += Nscaled; - } + for (size_t j = 0; j < refl_list.size(); j++) { // loop all reflections + // Sum partials + // reflection.sum_partials returns min sigma found + // (excluding zeroes) + sm = refl_list[j].sum_partials(Nfull, Npart, Nscaled); + if (sm > 0.0) { + sigmamin = Min(sigmamin, sm); + Nref_valid++; + Nobs_full += Nfull; + Nobs_partial += Npart; + Nobs_scaled += Nscaled; } + } status = SUMMED; NextRefNum = 0; // point to first reflection in list return Nobs_partial; @@ -1867,6 +1913,30 @@ return true; } //-------------------------------------------------------------- + bool hkl_unmerge_list::acceptableReflection(const int& RefNum) const + // private method, no counting or other internal storage + { + // Accepted? + if (refl_list[RefNum].Status() != 0) { + return false; + } + // Reject if no observations + if (refl_list[RefNum].NvalidObservations() <= 0) + return false; + // Test resolution limits + Rtype s2 = refl_list[RefNum].invresolsq(); + if (ResoLimRange.tbin(s2) < 0) + return false; + // Check ice rings: only "reject" rings are stored + if (Icerings.Nrings() > 0) { + int ir = Icerings.InRing(s2); + if (ir >= 0) { + return false; + } + } + return true; + } + //-------------------------------------------------------------- int hkl_unmerge_list::next_reflection(reflection& refl) const { if (status != SUMMED) @@ -1888,6 +1958,22 @@ return NextRefNum; } //-------------------------------------------------------------- + int hkl_unmerge_list::get_accepted_reflection(const int& jref, reflection& this_refl) const + // Get reflection jref, if accepted, else next acceptable one + // Return index of returned reflection, = -1 if end of list + // Thread safe, no change in mutable data + { + int jr = jref; + while (jr < Nref) { + if (acceptableReflection(jr)) { + this_refl = refl_list[jr]; + return jr; + } + jr++; + } + return -1; + } + //-------------------------------------------------------------- reflection hkl_unmerge_list::get_reflection(const int& jref) const // unconditional ^^^^^^^^^^^^ { @@ -2408,4 +2494,4 @@ return *this; } -} // namespace scala +} // namespace diff -r -u 20110907/ccp4-6.2.0/src/pointless/hkl_unmerge.hh 20110921/ccp4-6.2.0/src/pointless/hkl_unmerge.hh --- 20110907/ccp4-6.2.0/src/pointless/hkl_unmerge.hh 2011-05-16 14:23:51.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/hkl_unmerge.hh 2011-09-06 17:49:04.000000000 +0100 @@ -21,8 +21,7 @@ #include "hash.hh" #include "runthings.hh" -namespace scala -{ +namespace scala { //============================================================== class data_flags //! Data column flags to indicate which columns are present in the file @@ -67,16 +66,26 @@ static int& SelectIcolFlag() {return selecticolflag;} // store imid = overall if needed and not set static void SetAverageIntensity(const double& meanI); + // store imid = overall if needed + static void ResetAverageIntensity(const double& meanI); - static IsigI GetCombinedI(const Rtype& Ic, const Rtype& varIc, + static IsigI GetCombinedI(const Rtype& Iraw, const Rtype& Ic, const Rtype& varIc, const Rtype& Ipr, const Rtype& varIpr); + static IsigI GetCombinedI(const Rtype& Iraw, const IsigI& Isc, const IsigI& Ispr); + + //! set true if we have a second intensity Ipr stored + static void SetIprPresent(const bool& Isiprpresent) {iprpresent = Isiprpresent;} + //! return true if we have a second intensity Ipr stored + static bool IsIprPresent() {return iprpresent;} + static std::string format(); private: static int selecticolflag; static int ipowercomb; static double imid; + static bool iprpresent; // true if we have a second intensity Ipr stored //=================================================================== }; // SelectI @@ -177,7 +186,6 @@ //! An observation of a reflection, which may consist of one or more parts class observation { - // public: observation(); observation(const Hkl hkl_in, @@ -199,6 +207,19 @@ Rtype ksigI() const {return sigI_/gscale;} //!< return scaled sigI IsigI kI_sigI() const {return IsigI(I_/gscale,sigI_/gscale);} //!< return scaled I, sigI + //! Return "summation" integration IsigI, summed over partials if necessary + // This is also the sole intensity if there is only one + // Also sets mean phi, time, LP + IsigI IsigIsummation(); + + // Return "profile" integration I sigI, summed over partials if necessary + IsigI IsigIpr() const; + + // Sum (or scale) all partials for this observation + // Assumes that SelectI has been set up correctly to choose + // either summation, profile or combined intensity measurements + // Sets I_, sigI_, phi_, time_, LP_, batch_ + void sum_partials(); Rtype phi() const {return phi_;} //!< return rotation angle "phi" Rtype time() const {return time_;} //!< return "time" @@ -429,7 +450,6 @@ //! Copy operator throws exception unless object is EMPTY hkl_unmerge_list& operator= (const hkl_unmerge_list& List); - // Set controls, limits, etc ---------- void SetResoLimits(const float& LowReso, const float& HighReso); //!< set resolution @@ -547,6 +567,11 @@ //! replace current reflection with updated version void replace_reflection(const reflection& refl); + //! Get reflection jref, if accepted, else next acceptable one + //! Return index of returned reflection, = -1 if end of list + //! Thread safe, no change in mutable data + int get_accepted_reflection(const int& jref, reflection& this_refl) const; + //! replace lobs'th observation in current reflection with updated version void replace_observation(const observation& obs, const int& lobs); @@ -575,7 +600,8 @@ int prepare(); //! Sum partials /*! return number of partials */ - int sum_partials(); + /*! If forcesum is true, sum them even if already summed */ + int sum_partials(const bool& forcesum=false); //! Calculate all secondary beam directions, in chosen frame /*! On entry: @@ -760,7 +786,9 @@ void set_run(); // set all runs in part list bool accept() const; // true if reflection(NextRefNum) is acceptable - // also counts ice ring + // also counts ice ring + // private method, no counting or other internal storage + bool acceptableReflection(const int& RefNum) const; //! Set runs void SetUpRuns(); diff -r -u 20110907/ccp4-6.2.0/src/pointless/intensitystatistics.cpp 20110921/ccp4-6.2.0/src/pointless/intensitystatistics.cpp --- 20110907/ccp4-6.2.0/src/pointless/intensitystatistics.cpp 2011-05-09 10:25:01.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/intensitystatistics.cpp 2011-09-06 17:50:02.000000000 +0100 @@ -89,8 +89,8 @@ // Probability double mcent = 0.968; double macen = 0.736; - DM_2sqrt DMcentric(macen, mcent); - double pcentro = ProbBiassed(TotE2minus1, SD_E2m1, mcent, DMcentric); + DM_2sqrt *DMcentric = new DM_2sqrt(macen, mcent); + double pcentro = ProbBiassed(TotE2minus1, SD_E2m1, mcent, *DMcentric); // double dc = Max(mcent - TotE2minus1, 0.0)/SD_E2m1; diff -r -u 20110907/ccp4-6.2.0/src/pointless/outputunmergeddata.cpp 20110921/ccp4-6.2.0/src/pointless/outputunmergeddata.cpp --- 20110907/ccp4-6.2.0/src/pointless/outputunmergeddata.cpp 2011-05-09 10:25:14.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/outputunmergeddata.cpp 2011-07-29 15:20:59.000000000 +0100 @@ -53,10 +53,11 @@ //^- if (hklout_filename != "") { - // Only test rotational part of symmetry + // Only test rotational part of symmetry, but check for same order // don't bother to change symmetry just for translations // but use correct space group in writing - if (SPGsymm != hkl_list.symmetry() || ! reindex.IsIdentity()) { + if (!SPGsymm.equals_r_order(hkl_list.symmetry()) || + ! reindex.IsIdentity()) { int NfractIdx = hkl_list.change_symmetry(SPGsymm, reindex, true); if (NfractIdx > 0) { output.logTabPrintf(0,LOGFILE, diff -r -u 20110907/ccp4-6.2.0/src/pointless/pgscore.cpp 20110921/ccp4-6.2.0/src/pointless/pgscore.cpp --- 20110907/ccp4-6.2.0/src/pointless/pgscore.cpp 2011-05-09 10:25:15.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/pgscore.cpp 2011-09-06 17:50:02.000000000 +0100 @@ -112,19 +112,19 @@ if (NAveragedZCCfor == 0 && NAveragedZCCagainst == 0) return; IntgrtProb IP1; - if (Close(exponent, 2.0)) { - DM_2sqrt DM(0.0,CCTrueScore); // Model for CC- if true, most likely 0.0 + if (Close(exponent, 2.0)) { + DM_2sqrt *DM = new DM_2sqrt(0.0,CCTrueScore); // Model for CC- if true, most likely 0.0 //DM_2sqrt DM(0.0,1.0); // Model for CC- if true, most likely 0.0 // DM_lin DM(0.0,CCTrueScore); // DM_cubic DM(0.0,CCTrueScore); // DM_cubicsu DM(0.0,CCTrueScore); // DM_1minusmSq DM(0.0,CCTrueScore); // DM_1minusmCu DM(0.0,CCTrueScore); - IP1.init(DM); + IP1.init(*DM); } else { - DM_power DM(0.0,CCTrueScore); - DM.SetPower(exponent); - IP1.init(DM); + DM_power *DM = new DM_power(0.0,CCTrueScore); + DM->SetPower(exponent); + IP1.init(*DM); } const bool DEBUG = false; diff -r -u 20110907/ccp4-6.2.0/src/pointless/pointgroup.cpp 20110921/ccp4-6.2.0/src/pointless/pointgroup.cpp --- 20110907/ccp4-6.2.0/src/pointless/pointgroup.cpp 2011-05-09 10:25:16.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/pointgroup.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -663,20 +663,28 @@ // only, no change otherwise // Return true if accepted { + // compare = -1 int compare = -1; if (CrysSys == ORTHORHOMBIC && sameGroup) { compare = best_cell.compare_orthorhombic(test_cell); } else if (CrysSys == MONOCLINIC) { compare = best_cell.compare_monoclinic (test_cell, UniqueAxis, angular_tolerance); + // Accept new one anyway if beta >= 90 and old best had beta < 90 + if (compare < 1) { + if (best_cell.parameters()[UniqueAxis+3] < 90.0 && test_cell.parameters()[UniqueAxis+3] >= 90.0) { + compare = +1; + }} } if (compare > 0) { //^ - // std::cout << "Updating cell: " << CrysSys << " " - // << sameGroup << " " << angular_tolerance << "\n" - // << "Old best cell: " << UcellFormat(best_cell) <<"\n" - // << "New best cell: " << UcellFormat(test_cell) <<"\n"; + // std::cout << "Updating cell: " << CrysSys << " " + // << sameGroup << " " << angular_tolerance << "\n" + // << "Old best cell: " << UcellFormat(best_cell) <<"\n" + // << "New best cell: " << UcellFormat(test_cell) <<"\n"; + // for (int i=0;i<6;++i) {std::cout <<" "< 0 && BestCell) ChBasisVec.resize(1); return ChBasisVec; - } + } // GetAlterntiveBases //-------------------------------------------------------------- std::vector ChangeBasesList(const std::vector& CBlist, @@ -1139,7 +1147,7 @@ uctbx::unit_cell uccell_chb = ChBasis.apply(uccell); //^ // std::cout << "\n>>> SetCell " << RefLGname() << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"; - + //^- // Try to get "best" setting of cell and new reference // cb_op_best transforms reference to "best" sgtbx::change_of_basis_op cb_op_best = GetBestCell(LaueGrp_ref, uccell_chb, AllowI2); @@ -1147,14 +1155,14 @@ //^ // std::cout << "Reindex original->constructor ChBasis_cell): " - // << ChangeBasisFormat_as_Reindex(ChBasis_cell) << "\n" - // << "Reindex original->reference ChBasis): " - // << ChangeBasisFormat_as_Reindex(ChBasis) << "\n" - // << "Reindex constructor->reference ChBasis_ref): " - // << ChangeBasisFormat_as_Reindex(ChBasis_ref) << "\n" - // << "CellIn: " << UcellFormat(uccell) << "\n" - // << "CellChB: " << UcellFormat(uccell_chb) << "\n" - // << "CellRef: " << UcellFormat(uccell_ref) << "\n"; + // << ChangeBasisFormat_as_Reindex(ChBasis_cell) << "\n" + // << "Reindex original->reference ChBasis): " + // << ChangeBasisFormat_as_Reindex(ChBasis) << "\n" + // << "Reindex constructor->reference ChBasis_ref): " + // << ChangeBasisFormat_as_Reindex(ChBasis_ref) << "\n" + // << "CellIn: " << UcellFormat(uccell) << "\n" + // << "CellChB: " << UcellFormat(uccell_chb) << "\n" + // << "CellRef: " << UcellFormat(uccell_ref) << "\n"; //-! // Test for change of symmetry, C2 to I2 @@ -1168,15 +1176,15 @@ LaueGrp_ref_type = sgtbx::space_group_type(LaueGrp_ref); LatType = CentringSymbol(LaueGrp_ref); //^ - // std::cout << "\n==== SetCell: updated groups " << LatType << " " - // << LaueGrp_ref_type.hall_symbol() << "\n"; - // std::cout << "Cell_ref: " << UcellFormat(uccell_ref) << "\n"; - // std::cout << "ChBasis:\n"; - // PrintChBOp(ChBasis); - // std::cout << "ChBasis_ref:\n"; - // PrintChBOp(ChBasis_ref); - // std::cout << "cb_op_best:\n"; - // PrintChBOp(cb_op_best); + // std::cout << "\n==== SetCell: updated groups " << LatType << " " + // << LaueGrp_ref_type.hall_symbol() << "\n"; + // std::cout << "Cell_ref: " << UcellFormat(uccell_ref) << "\n"; + // std::cout << "ChBasis:\n"; + // PrintChBOp(ChBasis); + // std::cout << "ChBasis_ref:\n"; + // PrintChBOp(ChBasis_ref); + // std::cout << "cb_op_best:\n"; + // PrintChBOp(cb_op_best); //^- } // ChBasis is operator for Original(cell) -> reference @@ -1197,8 +1205,8 @@ } //^ // std::cout << "End of SetCell:\n" - // << " Reindex original->reference ChBasis): " - // << ChangeBasisFormat_as_Reindex(ChBasis) << "\n"; + // << " Reindex original->reference ChBasis): " + // << ChangeBasisFormat_as_Reindex(ChBasis) << "\n"; //^- // Maximum angular deviation of cell from that // required by rotation group diff -r -u 20110907/ccp4-6.2.0/src/pointless/pointgroup.hh 20110921/ccp4-6.2.0/src/pointless/pointgroup.hh --- 20110907/ccp4-6.2.0/src/pointless/pointgroup.hh 2010-07-01 09:11:54.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/pointgroup.hh 2011-09-06 17:49:04.000000000 +0100 @@ -286,6 +286,9 @@ // Constructor -> reference sgtbx::change_of_basis_op ChBasis_ref; + // Reference -> "best" + sgtbx::change_of_basis_op ChBasis_best; + // Symmetry element list std::vector ElementNums; diff -r -u 20110907/ccp4-6.2.0/src/pointless/pointless.cpp 20110921/ccp4-6.2.0/src/pointless/pointless.cpp --- 20110907/ccp4-6.2.0/src/pointless/pointless.cpp 2011-06-18 21:59:59.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/pointless.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -561,8 +561,7 @@ // file is merged, remove all subgroups which are subgroups of original group // since these are implicit hkl_symmetry mergeSymm = OrigSymm; - mergeSymm.ChangeBasis(reindex_op); - RemoveImplicitSubgroups(subgroups, mergeSymm); + RemoveImplicitSubgroups(subgroups, mergeSymm, reindex_op); } //^ // std::cout << "=== Subgroup size " <CCP4 Program Suite: pointless @@ -160,20 +166,22 @@ HKLIN file is a merged file, then any anomalous difference columns will be negated, and F+/- I+/- columns swapped, if the hand of the index is changed by the reduction process. Note that in this case -there is no check made that the reindexing operator is consistent +there is no reliable check made that the reindexing operator is +consistent with the space group: if a SPACEGROUP command is not given, the reindexed space group will be used if it is valid, otherwise you will have to specify the space group. Any reflections with non-integral indices after reindexing are discarded, so this may be used to select reflections -corresponding to a sub-cell. Files containing phase columns cannot be -reindexed.

+corresponding to a sub-cell. Files containing phase columns can now be +reindexed, as long as you are just changing the setting, not the space +group (eg I2<->C2, P2 21 21 <-> P21 21 2 etc).

5. Converting XDS, Scalepack, SHELX or SAINT format to MTZ

The command line option "-copy" (or "-c") may be used just to convert an XDS, Scalepack or SHELX file to the MTZ format. The NAME keyword is required, and for -SCALEPACK or SHELX input the CELL must be given. For SAINT input it is recommended to give a CELL (as it will be more accurate).

+SCALEPACK or SHELX input the CELL must be given. For SAINT input it is recommended to give a CELL (as it may be more accurate).

Choice of solution for the output file

A “solution” is a space group (or point group) and a reindexing operator. In INDEX mode, the solution @@ -948,8 +956,31 @@


Release notes

+

1.6.4

+Reindexing merged files now deals properly with phase and ABCD columns, +eg for I2<->C2 or  P2 21 21 <-> P21 21 2 conversions
+Improved/fixed detection of new space group after reindexing
+ +

1.6.3

Trap "*****" fields from format overflow in XDS headers, just to give a sensible error message
+

1.6.2

+ +XDS XSCALE now puts [U] = [I] to +evade bug in Reindex, used in Xia2. Also restored the History record in +the MTZ header (lost at some previous point)
+

1.6.1
+

+

+

+fixed serious bug present in all 1.5.x versions. If an MTZ file +input is in the highest point group of the higher symmetry group, +specifically 422, 622, R32 or 432, and the final output file is in the +same point group, then the symmetry operators were scrambled relative +to the ISYM flags on the observations, leading to wrong original hkl +being genereated in Scala/Aimless: this then affects the secondary beam +calculation and hence the absorption correction   

1.5.22

+ WILDFILE option
For enantiomorpic space groups, prefer to pick the one that matches the input file
Minor fix to reading XSCALE output files
diff -r -u 20110907/ccp4-6.2.0/src/pointless/probfunctions.cpp 20110921/ccp4-6.2.0/src/pointless/probfunctions.cpp --- 20110907/ccp4-6.2.0/src/pointless/probfunctions.cpp 2011-05-09 10:25:23.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/probfunctions.cpp 2011-09-06 17:50:02.000000000 +0100 @@ -12,6 +12,7 @@ // Gaussian probability density function // returns p = (1/(sd*sqrt(twopi))) exp (-1/2 z^2) // where z = (val-mean)/sd + // { if (sd <= 0.0) clipper::Message::message(clipper::Message_fatal diff -r -u 20110907/ccp4-6.2.0/src/pointless/probfunctions.hh 20110921/ccp4-6.2.0/src/pointless/probfunctions.hh --- 20110907/ccp4-6.2.0/src/pointless/probfunctions.hh 2011-05-09 10:25:23.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/probfunctions.hh 2011-09-06 17:50:02.000000000 +0100 @@ -153,6 +153,7 @@ { public: IntgrtProb() : nd(10000) {} + ~IntgrtProb() { delete DMeanModel; } // Note that this stores a pointer to the external function // which therefore must continue to exist while this class diff -r -u 20110907/ccp4-6.2.0/src/pointless/scala_util.cpp 20110921/ccp4-6.2.0/src/pointless/scala_util.cpp --- 20110907/ccp4-6.2.0/src/pointless/scala_util.cpp 2011-06-18 22:00:06.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/scala_util.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -49,7 +49,7 @@ break; } } - if (i < name.size()-1) { + if (dot && i < int(name.size())-1) { return name.substr(i+1, name.size()-1-i); } } diff -r -u 20110907/ccp4-6.2.0/src/pointless/scsignificance.cpp 20110921/ccp4-6.2.0/src/pointless/scsignificance.cpp --- 20110907/ccp4-6.2.0/src/pointless/scsignificance.cpp 2011-05-09 10:25:30.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/scsignificance.cpp 2011-09-06 17:50:02.000000000 +0100 @@ -37,7 +37,7 @@ // P(S|score)/[P(S|score) + P(!S|score)] // E(score|S) = TrueScore (eg 1.0 for correlation coefficient) // E(score|!S) is in range 0.0 to TrueScore - // + // Returns = 0.0 if SDUnrelSC = 0.0 // = 1.0 if SDUnrelSC < 0 { @@ -47,18 +47,18 @@ IntgrtProb IP; if (Close(exponent, 2.0)) { - DM_2sqrt DM(0.0,truescore); // Model for CC- if true, most likely 0.0 + DM_2sqrt *DM = new DM_2sqrt(0.0,truescore); // Model for CC- if true, most likely 0.0 // DM_2sqrt DM(0.0,1.0); // Model for CC- if true, most likely 0.0 // DM_lin DM(0.0,1.0); // DM_cubic DM(0.0,1.0); // DM_cubicsu DM(0.0,1.0); // DM_1minusmSq DM(0.0,1.0); // DM_1minusmCu DM(0.0,1.0); - IP.init(DM); + IP.init(*DM); } else { - DM_power DM(0.0,truescore); - DM.SetPower(exponent); - IP.init(DM); + DM_power *DM = new DM_power(0.0,truescore); + DM->SetPower(exponent); + IP.init(*DM); } double PS, PnotS; diff -r -u 20110907/ccp4-6.2.0/src/pointless/spacegroupreindex.cpp 20110921/ccp4-6.2.0/src/pointless/spacegroupreindex.cpp --- 20110907/ccp4-6.2.0/src/pointless/spacegroupreindex.cpp 2010-06-17 10:02:38.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/spacegroupreindex.cpp 2011-09-06 17:49:04.000000000 +0100 @@ -19,7 +19,7 @@ // in same crystal system // Mainly (only?) for C2<->I2 and H3<->R3 // Throws a clipper::Message_warn exception if the space groups are - // not just alternative settings (ie have differnt reference groups) + // not just alternative settings (ie have different reference groups) { // from space group std::string frname = CCtbxSym::CCTBX_SGsymbol_HorR(from_SGname); @@ -28,7 +28,7 @@ // Change of basis to reference setting sgtbx::change_of_basis_op ChB_ref_from = from_SG.type().cb_op(); sgtbx::space_group from_SG_ref = from_SG.change_basis(ChB_ref_from); - //^ CCtbxSym::PrintChBOp(ChB_ref_from); + //^ CCtbxSym::PrintChBOp(ChB_ref_from); //^ // to space group sgtbx::space_group to_SG = @@ -37,7 +37,7 @@ // Change of basis to reference setting sgtbx::change_of_basis_op ChB_ref_to = to_SG.type().cb_op(); sgtbx::space_group to_SG_ref = to_SG.change_basis(ChB_ref_to); - //^ CCtbxSym::PrintChBOp(ChB_ref_to); + //^ CCtbxSym::PrintChBOp(ChB_ref_to); //^ // Reference groups should be the same if (from_SG_ref != to_SG_ref) { @@ -64,12 +64,14 @@ bool SpacegroupReindex(const GlobalControls& GC, const hkl_symmetry& HKLINsymm, const Scell& cell, ReindexOp& Reindex, phaser_io::Output& output) -// If SPACEGROUP is specified but no REINDEX operator, generate appropriate reindexing -// to convert from input HKLIN file HKLINsymm to desired spacegroup -// Probably really only useful (or indeed valid) for C2 <-> I2 & H3<->R3 -// -// Returns true if Reindex is set -// fails if the symmetries do not belong to same lattice group + // If SPACEGROUP is specified but no REINDEX operator, generate appropriate reindexing + // to convert from input HKLIN file HKLINsymm to desired spacegroup + // Probably really only useful (or indeed valid) for C2 <-> I2 & H3<->R3, or P222 groups + // + // input cell corresponds to HKLINsymm + // + // Returns true if Reindex is set + // fails if the symmetries do not belong to same lattice group { if (GC.Spacegroup() == "" || GC.Spacegroup() == "HKLIN" || GC.IsReindexSet()) return false; @@ -85,6 +87,7 @@ } try { + // Get reindex operator Reindex = SpacegroupReindexOp(HKLIN_SGname, Input_SGname); } catch (Message_warn& warn) { @@ -95,10 +98,14 @@ Message::message(Message_fatal(message)); } - CCtbxSym::PointGroup PG(Input_SGname); - PG.SetCell(cell.UnitCell(), Reindex, GC.AllowI2()); + int AllowI2 = GC.AllowI2(); + if (NewSymm.lattice_type() != 'I') { + AllowI2 = 0; // don't allow I lattice if we've asked for C2 + } - Reindex = PG.RefSGreindex(); + CCtbxSym::PointGroup PG(Input_SGname); + PG.SetCell(cell.UnitCell(), Reindex, AllowI2); + Reindex = PG.RefSGreindex(); // reindex cell -> best output.logTab(0,LOGFILE, "Reindexing data with operator "+Reindex.as_hkl()+ diff -r -u 20110907/ccp4-6.2.0/src/pointless/version.hh 20110921/ccp4-6.2.0/src/pointless/version.hh --- 20110907/ccp4-6.2.0/src/pointless/version.hh 2011-06-18 22:00:09.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/version.hh 2011-09-06 17:49:04.000000000 +0100 @@ -4,9 +4,9 @@ #define PROGRAM_VERSION_HEADER #define PROGRAM_NAME std::string("POINTLESS") -#define PROGRAM_VERSION "1.5.22" -#define PROGRAM_DATE "18th May 2011" -#define PROGRAM_DATE2 "2011/05/18" +#define PROGRAM_VERSION "1.6.4" +#define PROGRAM_DATE "17th August 2011" +#define PROGRAM_DATE2 "2011/08/17" #define PROGRAM_EXPIRES bool(false) #define EXPIRE_DAY int(1) #define EXPIRE_MONTH int(1) diff -r -u 20110907/ccp4-6.2.0/src/pointless/writeunmergedmtz.cpp 20110921/ccp4-6.2.0/src/pointless/writeunmergedmtz.cpp --- 20110907/ccp4-6.2.0/src/pointless/writeunmergedmtz.cpp 2011-05-16 14:24:03.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/writeunmergedmtz.cpp 2011-08-03 11:11:26.000000000 +0100 @@ -26,6 +26,7 @@ #include "openinputfile.hh" #include "observationflags.hh" #include "cellgroup.hh" +#include "version.hh" using namespace CMtz; @@ -155,10 +156,11 @@ char time[9]; CCP4::ccp4_utils_date(date); CCP4::ccp4_utils_time(time); - std::string text = "POINTLESS, "+std::string(date)+" "+ + std::string text = "Pointless, version "+std::string(PROGRAM_VERSION)+ + ", run on "+std::string(date)+" at "+ std::string(time); strcpy(history, text.c_str()); - // int Nhist = MtzAddHistory(mtzout, &history, 1); + int Nhist = MtzAddHistory(mtzout, &history, 1); // Count observation parts in each batch std::vector nobsbatch(hkl_list.num_batches(),0); diff -r -u 20110907/ccp4-6.2.0/src/pointless/xds_unmerge.cpp 20110921/ccp4-6.2.0/src/pointless/xds_unmerge.cpp --- 20110907/ccp4-6.2.0/src/pointless/xds_unmerge.cpp 2011-06-18 22:00:10.000000000 +0100 +++ 20110921/ccp4-6.2.0/src/pointless/xds_unmerge.cpp 2011-09-06 17:31:31.000000000 +0100 @@ -193,6 +193,7 @@ nxpix = 0; nypix = 0; Umat = Mat33::identity(); + mosaicrange = 0.0; if (verbose > 0) { output += FormatOutput::logTab(0, @@ -222,12 +223,23 @@ // Header line // echo to log file if (verbose > 0) output += FormatOutput::logTab(0, line); - + + // Header lines should not contain "*" character + // This will occur if things are horribly wrong, format overflow + if (line.find("*") != std::string::npos) { + Message::message(Message_fatal + ("XDS: Header line corrupt:\n"+line)); + } + + // remove leading "!" line = line.substr(1, line.length()-1); // line = std::string(line, 1, line.length()-1); + std::vector keyvalues = SSplit(line); + + for (size_t ik=0;ik