def show_start_model(self, file_name):
'''
Load the starting model from file. Takes the filename (including full
path) as an argument.
'''
if self._start_model is not None and not self._start_model.deleted:
self.session.models.close([self._start_model])
from chimerax.open_command.cmd import provider_open
m = self._start_model = provider_open(self.session, [file_name])[0]
m.bonds.radii=0.05
from chimerax.clipper.symmetry import get_symmetry_handler
get_symmetry_handler(m)
self.set_default_atom_coloring()
return True
def spotlight_mode(self):
'''
Force a return to "spotlight" viewing mode.
'''
from chimerax.clipper.symmetry import get_symmetry_handler
sh = get_symmetry_handler(self._current_model)
sh.spotlight_mode=True
def close_maps(self):
if self._current_model is None or self._current_model.deleted:
raise RuntimeError('No PHENIX model/maps currently open!')
from chimerax.clipper.symmetry import get_symmetry_handler
sh = get_symmetry_handler(self._current_model)
if len(sh.map_mgr.xmapsets):
self.session.models.close(sh.map_mgr.xmapsets)
return True
def load_phenix_refine_final_xn_files(self, output_dir, file_base):
'''
Load the final phenix.refine results for a joint x-ray/neutron
refinement. Will automatically close the temporary files.
'''
self._load_phenix_refine_final_files(output_dir, file_base,
joint_xray_neutron=True)
m = self._current_model
from chimerax.clipper.symmetry import get_symmetry_handler
sh = get_symmetry_handler(m)
xmapset = sh.map_mgr.xmapsets[0]
return True
def isolate(session, atoms,
surround_distance=0,
context_distance=5,
mask_radius=3,
hide_surrounds=True,
focus=False):
from chimerax.clipper.symmetry import get_symmetry_handler
us = atoms.unique_structures
for s in us:
sel = us.atoms.intersect(atoms)
sh = get_symmetry_handler(s, create=True)
sh.isolate_and_cover_selection(sel,
include_surrounding_residues = surround_distance,
show_context = context_distance,
mask_radius = mask_radius,
hide_surrounds = hide_surrounds,
focus = focus)
def test_clipper_sym(session, radius=12):
import os
from chimerax.open_command.cmd import provider_open
libdir = os.path.abspath(os.path.dirname(__file__))
m = provider_open(session, [os.path.join(libdir, '3io0.pdb')])[0]
m.atoms.displays = True
from chimerax.std_commands import cofr
cofr.cofr(session, method='center of view', show_pivot=True)
from chimerax.clipper import symmetry
sym_handler = symmetry.get_symmetry_handler(m, create=True)
sym_handler.spotlight_radius = radius
sym_handler.map_mgr.add_xmapset_from_mtz(os.path.join(
libdir, '3io0_combined.mtz'),
oversampling_rate=1.5)
sym_handler.map_mgr.nxmapset.add_nxmap_handler_from_file(
os.path.join(libdir, '3io0_real_space.ccp4'))
return sym_handler
def spotlight(session, models=None, enable=True, radius=None):
from chimerax.clipper.symmetry import get_symmetry_handler, SymmetryManager
if models is None:
from chimerax.atomic import AtomicStructure
models = session.models.list(type=AtomicStructure)
sym_mgrs = session.models.list(type=SymmetryManager)
models = [m for m in models if m.parent not in sym_mgrs]
models = models+sym_mgrs
create = False
else:
create = True
for m in models:
if isinstance(m, SymmetryManager):
sh = m
else:
sh = get_symmetry_handler(m, create=create, auto_add_to_session=True)
if sh is not None:
sh.spotlight_mode=enable
if radius is not None:
sh.spotlight_radius = radius