def crystal_symmetry_as_sg_uc_list(crystal_symmetry):
u = crystal_symmetry.unit_cell()
s = crystal_symmetry.space_group_info()
if (u is None): uc = ["None"]*6
else: uc = ["%.6g" % v for v in u.parameters()]
sg = cns_format(space_group_info=s)
if (sg is None): sg = str(s).replace(" ","")
return sg, uc
def crystal_symmetry_as_sg_uc_list(crystal_symmetry):
u = crystal_symmetry.unit_cell()
s = crystal_symmetry.space_group_info()
if (u is None): uc = ["None"]*6
else: uc = ["%.6g" % v for v in u.parameters()]
sg = cns_format(space_group_info=s)
if (sg is None): sg = str(s).replace(" ","")
return sg, uc
def write_header(s,
file=None,
description=None,
comment=None,
space_group_info=None,
n_rows=None):
assert n_rows is not None
if (file is not None):
print >> s, "{+ file: %s +}" % str(file)
if (description is not None):
print >> s, "{+ description: %s +}" % str(description)
if (comment is not None):
print >> s, "{+ comment:"
for line in comment:
print >> s, line
print >> s, "+}"
print >> s
print >> s, "{- begin block parameter definition -} define("
print >> s
if (space_group_info is not None):
print >> s, """\
{============================ space group ============================}
{* space group *}
{* use International Table conventions with subscripts substituted
by parenthesis *}
{===>} sg="%s";
""" % space_group_symbols.cns_format(space_group_info)
print >> s, """\
{==================== derivative/MAD coordinates =====================}
{+ list: for each site define:
- whether the site is to be refined, fixed or ignored
- derivative name (must be the same for all sites in a derivative)
- chemical type (note: wavelength-dependent form factors
are specified in mad_refine.inp)
- coordinates (x, y, z)
- B-value (b)
- occupancy (q)
- group name (g) +}
{+ list: the optional group name (g) is a string of upto 4 characters.
If a group is left blank, each site is refined individually.
If a group is specified, all sites with the same group name
and the same derivative name are treated as a rigid body, and their
occupancies, B-values, and form factors are refined as a group. +}
{+ table: rows=%d numbered
cols=9 "action" "derivative name" "chemical type"
"x coordinate" "y coordinate" "z coordinate"
"B-value" "occupancy" "group" +}
""" % n_rows
def write_header(s, file=None, description=None, comment=None,
space_group_info=None, n_rows=None):
assert n_rows is not None
if (file is not None):
print >> s, "{+ file: %s +}" % str(file)
if (description is not None):
print >> s, "{+ description: %s +}" % str(description)
if (comment is not None):
print >> s, "{+ comment:"
for line in comment: print >> s, line
print >> s, "+}"
print >> s
print >> s, "{- begin block parameter definition -} define("
print >> s
if (space_group_info is not None):
print >> s, """\
{============================ space group ============================}
{* space group *}
{* use International Table conventions with subscripts substituted
by parenthesis *}
{===>} sg="%s";
""" % space_group_symbols.cns_format(space_group_info)
print >> s, """\
{==================== derivative/MAD coordinates =====================}
{+ list: for each site define:
- whether the site is to be refined, fixed or ignored
- derivative name (must be the same for all sites in a derivative)
- chemical type (note: wavelength-dependent form factors
are specified in mad_refine.inp)
- coordinates (x, y, z)
- B-value (b)
- occupancy (q)
- group name (g) +}
{+ list: the optional group name (g) is a string of upto 4 characters.
If a group is left blank, each site is refined individually.
If a group is specified, all sites with the same group name
and the same derivative name are treated as a rigid body, and their
occupancies, B-values, and form factors are refined as a group. +}
{+ table: rows=%d numbered
cols=9 "action" "derivative name" "chemical type"
"x coordinate" "y coordinate" "z coordinate"
"B-value" "occupancy" "group" +}
""" % n_rows
def do_dirty_work(params, fo, hl_coeffs):
fo.export_as_cns_hkl(file_object=open("f_obs.hkl", "wb"),
file_name="f_obs.hkl")
hl_coeffs.export_as_cns_hkl(file_object=open("hl_coeffs.hkl", "wb"),
file_name="hl_coeffs.hkl")
cns_solve_dir = os.environ.get("CNS_SOLVE")
if cns_solve_dir is None:
raise RuntimeError("Environment variable CNS_SOLVE is not defined")
shutil.copyfile("%s/inputs/xtal_phase/density_modify.inp" % cns_solve_dir,
"tmp.inp")
cns_params = {}
cns_params.setdefault(
"space_group", cns_format(space_group_info=params.input.space_group))
uc_params = params.input.unit_cell.parameters()
cns_params["a"] = uc_params[0]
cns_params["b"] = uc_params[1]
cns_params["c"] = uc_params[2]
cns_params["alpha"] = uc_params[3]
cns_params["beta"] = uc_params[4]
cns_params["gamma"] = uc_params[5]
if params.d_min is None:
if params.phase_extension:
params.d_min = fo.d_min()
else:
params.d_min = hl_coeffs_start.d_min()
if params.initial_d_min is None:
params.initial_d_min = params.d_min
assert params.initial_d_min >= params.d_min
cns_params["d_min"] = params.d_min
cns_params["initial_d_min"] = params.initial_d_min
cns_params["phase_extend"] = str(params.phase_extension).lower()
cns_params["prot_to_solv"] = params.protein_solvent_ratio
cns_params["trunc_min"] = params.density_truncation.fraction_min
cns_params["trunc_max"] = params.density_truncation.fraction_max
cns_params["trunc_max"] = 1
cns_params["solcon"] = params.solvent_fraction
if params.solvent_mask.averaging_radius.final is None:
params.solvent_mask.averaging_radius.final = params.d_min
if params.solvent_mask.averaging_radius.initial is None:
params.solvent_mask.averaging_radius.initial \
= params.solvent_mask.averaging_radius.final + 1
cns_params[
"start_ave_radius"] = params.solvent_mask.averaging_radius.initial
cns_params[
"finish_ave_radius"] = params.solvent_mask.averaging_radius.final
cns_params["initial_steps"] = params.initial_steps
cns_params["shrink_steps"] = params.shrink_steps
cns_params["final_steps"] = params.final_steps
cns_params["grid_resolution_factor"] = params.grid_resolution_factor
cns_params["averaging"] = "false"
cns_params["ncs_infile"] = "ncs.def"
params_file = open("params.inp", "wb")
params_file.write(cns_density_modify_inp_template % cns_params)
params_file.close()
cmd = "%s/bin/cns_transfer -def params.inp -inp tmp.inp -out density_modify.inp" % (
cns_solve_dir)
print cmd
result = easy_run.fully_buffered(command=cmd).raise_if_errors_or_output()
cmd = "cns_solve < density_modify.inp > density_modify.out"
print cmd
t0 = time.time()
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
print "CNS time: %.2f" % (time.time() - t0)
result.show_stdout()
import iotbx.xplor.map
modified_map = iotbx.xplor.map.reader(file_name="density_modify.map")
modified_map = modified_map.data[:-1, :-1, :-1]
return group_args(modified_map=modified_map)
def do_dirty_work(params, fo, hl_coeffs):
fo.export_as_cns_hkl(
file_object=open("f_obs.hkl", "wb"),
file_name="f_obs.hkl")
hl_coeffs.export_as_cns_hkl(
file_object=open("hl_coeffs.hkl", "wb"),
file_name="hl_coeffs.hkl")
cns_solve_dir = os.environ.get("CNS_SOLVE")
if cns_solve_dir is None:
raise RuntimeError("Environment variable CNS_SOLVE is not defined")
shutil.copyfile(
"%s/inputs/xtal_phase/density_modify.inp" % cns_solve_dir, "tmp.inp")
cns_params = {}
cns_params.setdefault("space_group", cns_format(
space_group_info=params.input.space_group))
uc_params = params.input.unit_cell.parameters()
cns_params["a"] = uc_params[0]
cns_params["b"] = uc_params[1]
cns_params["c"] = uc_params[2]
cns_params["alpha"] = uc_params[3]
cns_params["beta"] = uc_params[4]
cns_params["gamma"] = uc_params[5]
if params.d_min is None:
if params.phase_extension:
params.d_min = fo.d_min()
else:
params.d_min = hl_coeffs_start.d_min()
if params.initial_d_min is None:
params.initial_d_min = params.d_min
assert params.initial_d_min >= params.d_min
cns_params["d_min"] = params.d_min
cns_params["initial_d_min"] = params.initial_d_min
cns_params["phase_extend"] = str(params.phase_extension).lower()
cns_params["prot_to_solv"] = params.protein_solvent_ratio
cns_params["trunc_min"] = params.density_truncation.fraction_min
cns_params["trunc_max"] = params.density_truncation.fraction_max
cns_params["trunc_max"] = 1
cns_params["solcon"] = params.solvent_fraction
if params.solvent_mask.averaging_radius.final is None:
params.solvent_mask.averaging_radius.final = params.d_min
if params.solvent_mask.averaging_radius.initial is None:
params.solvent_mask.averaging_radius.initial \
= params.solvent_mask.averaging_radius.final + 1
cns_params["start_ave_radius"] = params.solvent_mask.averaging_radius.initial
cns_params["finish_ave_radius"] = params.solvent_mask.averaging_radius.final
cns_params["initial_steps"] = params.initial_steps
cns_params["shrink_steps"] = params.shrink_steps
cns_params["final_steps"] = params.final_steps
cns_params["grid_resolution_factor"] = params.grid_resolution_factor
cns_params["averaging"] = "false"
cns_params["ncs_infile"] = "ncs.def"
params_file = open("params.inp", "wb")
params_file.write(cns_density_modify_inp_template % cns_params)
params_file.close()
cmd = "%s/bin/cns_transfer -def params.inp -inp tmp.inp -out density_modify.inp" %(
cns_solve_dir)
print cmd
result = easy_run.fully_buffered(command=cmd).raise_if_errors_or_output()
cmd = "cns_solve < density_modify.inp > density_modify.out"
print cmd
t0 = time.time()
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
print "CNS time: %.2f" %(time.time()-t0)
result.show_stdout()
import iotbx.xplor.map
modified_map = iotbx.xplor.map.reader(file_name="density_modify.map")
modified_map = modified_map.data[:-1,:-1,:-1]
return group_args(modified_map=modified_map)