diff options
| -rw-r--r-- | libcrystfel/src/index.c | 4 | ||||
| -rw-r--r-- | src/indexamajig.c | 13 |
2 files changed, 10 insertions, 7 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index a62dfcf1..b20c689a 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -316,9 +316,9 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, ERROR("To disable prediction refinement ('norefine'), use --no-refine.\n"); ERROR("To check cell axes only ('axes'), use --no-cell-combinations.\n"); ERROR("To disable all unit cell checks ('raw'), use --no-check-cell.\n"); + ERROR("To disable peak alignment check ('bad'), use --no-check-peaks.\n"); ERROR("To disable indexing retry ('noretry'), use --no-retry.\n"); - ERROR("Multi-lattice indexing ('multi') is now the default: " - "use --no-multi to disable it.\n"); + ERROR("To enable multi-lattice indexing by 'delete and retry', use --multi\n"); ERROR("------------------\n"); free(methods); return NULL; diff --git a/src/indexamajig.c b/src/indexamajig.c index a6651497..3cfe2c6e 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -124,11 +124,11 @@ static void show_help(const char *s) " --no-check-cell Don't check lattice parameters against input cell\n" " --no-cell-combinations\n" " Don't use axis combinations when checking cell\n" -" --no-multi Don't repeat indexing to index multiple hits\n" +" --multi Repeat indexing to index multiple hits\n" " --no-retry Don't repeat indexing to increase indexing rate\n" " --no-refine Skip the prediction refinement step\n" -" --check-peaks Check that most of the peaks can be accounted for\n" -" by the indexing solution\n" +" --no-check-peaks Don't check that most of the peaks can be accounted\n" +" for by the indexing solution\n" "\n" " --taketwo-member-threshold\n" " Minimum number of members in network\n" @@ -239,8 +239,8 @@ int main(int argc, char *argv[]) int if_refine = 1; int if_nocomb = 0; int if_nocheck = 0; - int if_peaks = 0; - int if_multi = 1; + int if_peaks = 1; + int if_multi = 0; int if_retry = 1; int serial_start = 1; @@ -343,8 +343,11 @@ int main(int argc, char *argv[]) {"no-check-cell", 0, &if_nocheck, 1}, {"no-cell-check", 0, &if_nocheck, 1}, {"check-peaks", 0, &if_peaks, 1}, + {"no-check-peaks", 0, &if_peaks, 0}, {"no-retry", 0, &if_retry, 0}, + {"retry", 0, &if_retry, 1}, {"no-multi", 0, &if_multi, 0}, + {"multi", 0, &if_multi, 1}, {"overpredict", 0, &iargs.overpredict, 1}, /* Long-only options which don't actually do anything */ |