nearby_asymmetric_units ( molecule,  distance )

Find nearby asymmetric units in a crystal by looking for overlapping bounding boxes. Contacts with each non-crystallographic symmetry (NCS) position are considered. Returns a list of triples, the first item being the NCS matrix, the second being a another matrix for symmetry placing an asymmetric unit nearby, and the third being identifiers for these two matrices positions (NCS1, NCS2, SMTRY2, unitcell2). The matrices are relative to the given molecule's local coordinates.

create_unit_cell (
        marker_set,
        axes,
        color,
        thickness,
        )

Create markers and links outlining unit cell.

bounding_box ( xyz )

asymmetric_unit_contacts (
        molecule,
        distance,
        angle_tolerance,
        shift_tolerance,
        )

Angle and shift tolerance values are used to eliminate equivalent pairs of asymmetric units.

translate_matrix ( t,  m )

zoom_to_fit ( padding )

pad_box ( box,  padding )

unit_cell_translation ( ijk,  axes )

Translation vector for a unit cell with given indices.

nearby_boxes ( box,  crystal )

Apply crystal symmetry to given box and find all boxes that intersect any NCS symmetry of the given box.

atom_coordinates ( atoms )

zero_translation ( m )

unique_asymmetric_unit_pairs (
        plist,
        angle_tolerance,
        shift_tolerance,
        )

Group pairs of asymmetric units that have the same relative orientation together.

transformed_bounding_box ( box,  tf )

crystal_contact_atoms (
        molecule,
        distance,
        angle_tolerance=None,
        shift_tolerance=None,
        )

Find the atoms of the asymmetric unit that make contacts with other asymmetric units anywhere in the crystal.

contacting_asymmetric_units (
        clist,
        crystal,
        include_000_unit_cell=None,
        )

From list of clashing pairs of asymmetric units determine list of asymmetric units to display.

contact_marker_model (
        molecule,
        crystal,
        clist,
        asu_list,
        )

average_xyz ( xyz )

transform_as_numeric_array ( tf )

make_asu_copies (
        m,
        asu_list,
        crystal,
        )

print_matrix ( m,  format )

basis_coordinate_transform ( axes )

Transformation from xyz position to unit cell indices.

distance ( xyz1,  xyz2 )

check_orthogonality (
        matrices,
        name,
        tolerance,
        )

make_molecule_copies (
        m,
        xflist,
        names,
        )

create_asymmetric_unit_markers (
        marker_set,
        asu_list,
        asu_center,
        identity_smtry_index,
        rgba_ncs,
        rgba_uc,
        rgba_ouc,
        radius_ncs,
        radius_copies,
        )

Create a sphere representing each asymmetric unit. The sphere is created using the volume path tracer module.

identity_matrix_index ( matrices )

overlapping_translations (
        box1,
        box2,
        axes,
        )

Boxes are in crystal axes coordinates.

report_crystal_contacts (
        molecule,
        distance,
        angle_tolerance=None,
        shift_tolerance=None,
        )

Determine clashing asymmetric units and print a text list of clashing pairs having unique relative orientations.

box_center ( box )

show_crystal_contacts (
        molecule,
        dist,
        make_copies=None,
        angle_tolerance=None,
        shift_tolerance=None,
        )

Create a ball and stick model where balls represent asymmetric units of a crystal structure and sticks connect clashing asymmetric units. Or make copies of contacting asymmetric units.

create_clash_links (
        clist,
        n,
        link_radius,
        link_rgba,
        markers,
        )

Create cylinders connecting spheres representing asymmetric unit that have close atomic contacts. The cylinders are volume path tracer links.

Crystal

Symmetry matrices and crystal parameters from PDB header.

NCS_Asymmetric_Unit

Non-crystallographic symmetry (NCS) asymmetric unit.