From 0d06927a50f11418c36190e7808f351d78655515 Mon Sep 17 00:00:00 2001 From: dennisbrookner Date: Thu, 21 Dec 2023 12:32:51 -0500 Subject: [PATCH] complete alpha support in matchmaps.mr --- src/matchmaps/_compute_mr_diff.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/matchmaps/_compute_mr_diff.py b/src/matchmaps/_compute_mr_diff.py index 7043d28..9d8f453 100644 --- a/src/matchmaps/_compute_mr_diff.py +++ b/src/matchmaps/_compute_mr_diff.py @@ -49,6 +49,7 @@ def compute_mr_difference_map( eff : str = None, keep_temp_files: str = None, radius : float = 5, + alpha : float = 0, no_bss = False, ): """ @@ -98,6 +99,8 @@ def compute_mr_difference_map( If not None, the name of a subdirectory of the output_dir into which intermediate matchmaps files are moved upon program completion. radius : float, optional Maximum distance away from protein model to include voxels. Only applies to the "unmasked" difference map output. + alpha : float, optional + Alpha to use in error weighting of F-obs prior to Fourier Transform. Defaults to 0, e.g. no weighting. no_bss : bool, optional If True, skip bulk solvent scaling feature of phenix.refine """ @@ -197,10 +200,10 @@ def compute_mr_difference_map( # TO-DO: Figure out why phenix outputs are sometimes still split into (+) and (-) columns, even when I specify that anomalous=False # As a workaround, even anomalous files have a single 'F-obs-filtered' column, so I can always just use that. fg_off = make_floatgrid_from_mtz( - mtzoff, spacing, F="F-obs-filtered", Phi="PH2FOFCWT", spacegroup="P1", dmin=dmin + mtzoff, spacing, F="F-obs-filtered", SigF="SIGF-obs-filtered", Phi="PH2FOFCWT", spacegroup="P1", dmin=dmin, alpha=alpha, ) fg_on = make_floatgrid_from_mtz( - mtzon, spacing, F="F-obs-filtered", Phi="PH2FOFCWT", spacegroup="P1", dmin=dmin + mtzon, spacing, F="F-obs-filtered", SigF="SIGF-obs-filtered", Phi="PH2FOFCWT", spacegroup="P1", dmin=dmin, alpha=alpha, ) if rbr_gemmi is None: