def runAlign():
# -----------------------------------------------------------------------------
### set files
#maindir = '/ami/data16/appion/09mar04b/models/emanmodel28'
default_settings.set('limit_voxel_count', False)
maindir = '/home/vossman/Documents/papers/initmodel/initmodels-figure'
map1_path = os.path.join(maindir, 'reconemdb.mrc')
map1 = open_volume_file(map1_path)[0]
map1.set_parameters(surface_levels = [1.0])
mrcfiles = glob.glob(os.path.join(maindir, '*.mrc'))
aligndir = os.path.join(maindir, 'align/')
if not os.path.isdir(aligndir):
os.mkdir(aligndir)
N = len(mrcfiles)
random.shuffle(mrcfiles)
for i,mrcfile in enumerate(mrcfiles):
if os.path.basename(mrcfile)[:5] == "align":
continue
new_path = os.path.join(aligndir, 'align'+os.path.basename(mrcfile))
if os.path.isfile(new_path):
print "----------", os.path.basename(mrcfile)
continue
print ("\n==============================\n",
os.path.basename(mrcfile),
"\n==============================\n")
map2 = open_volume_file(mrcfile)[0]
map2.set_parameters(surface_levels = [1.0])
new_path = os.path.join(aligndir, 'align'+os.path.basename(mrcfile))
fit_map_in_map(map1, map2, map1_threshold=1.0)
runCommand('vop #1 resample onGrid #0 modelId %d'%(i+N))
runCommand('volume #%d save %s'%(i+N, new_path))
map2.close()
runCommand('close #1')
runCommand('close #%d'%(i+N))
def fit_map_in_map(map1_path, map2_path, xformName,
initial_map1_transform = None,
map1_threshold = None,
ijk_step_size_min = 0.01, # Grid index units
ijk_step_size_max = 0.5, # Grid index units
max_steps = 5000,
optimize_translation = True,
optimize_rotation = True):
# Files have to have file suffix indicating volume format.
from VolumeViewer import open_volume_file
map1 = open_volume_file(map1_path)[0] # Assume files contain just one array
map2 = open_volume_file(map2_path)[0]
if initial_map1_transform:
from Matrix import chimera_xform
xf = chimera_xform(initial_map1_transform)
map1.surface_model().openState.globalXform(xf)
use_threshold = (map1_threshold != None)
from FitMap.fitmap import map_points_and_weights, motion_to_maximum
points, point_weights = map_points_and_weights(map1, use_threshold)
if len(points) == 0:
if use_threshold:
print 'No grid points above map threshold.'
else:
print 'Map has no non-zero values.'
return
move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation)
import Matrix
if initial_map1_transform:
move_tf = Matrix.multiply_matrices(move_tf, initial_map1_transform)
header = ('\nFit map %s in map %s using %d points\n'
% (map1.name, map2.name, stats['points']) +
' correlation = %.4g, overlap = %.4g\n'
% (stats['correlation'], stats['overlap']) +
' steps = %d, shift = %.3g, angle = %.3g degrees\n'
% (stats['steps'], stats['shift'], stats['angle']))
print header
f = open(xformName,'w')
for i in range(4):
for j in range(3):
# print move_tf[j][i]
f.write('{:f}'.format(move_tf[j][i]))
f.write("\n")
f.close()
print move_tf
tfs = Matrix.transformation_description(move_tf)
print tfs
def fit_map_in_map(
map1_path,
map2_path,
initial_map1_transform=None,
map1_threshold=None,
ijk_step_size_min=0.01, # Grid index units
ijk_step_size_max=0.5, # Grid index units
max_steps=2000,
optimize_translation=True,
optimize_rotation=True,
metric='sum product'
): # 'sum product' > overlap; other options are 'correlation' and 'correlation about mean'
# Files have to have file suffix indicating volume format.
map1 = open_volume_file(map1_path)[
0] # Assume files contain just one array
map2 = open_volume_file(map2_path)[0]
if initial_map1_transform:
from Matrix import chimera_xform
xf = chimera_xform(initial_map1_transform)
map1.surface_model().openState.globalXform(xf)
use_threshold = (map1_threshold != None)
points, point_weights = map_points_and_weights(map1, use_threshold)
if len(points) == 0:
if use_threshold:
print 'No grid points above map threshold.'
else:
print 'Map has no non-zero values.'
return
move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation,
metric)
if initial_map1_transform:
move_tf = Matrix.multiply_matrices(move_tf, initial_map1_transform)
header = ('\nFit map %s in map %s using %d points\n' %
(map1.name, map2.name, stats['points']) +
' correlation = %.4g, overlap = %.4g\n' %
(stats['correlation'], stats['overlap']) +
' steps = %d, shift = %.3g, angle = %.3g degrees\n' %
(stats['steps'], stats['shift'], stats['angle']))
print header
tfs = Matrix.transformation_description(move_tf)
print tfs
def transform(model_path, fixed_model_path, ea = (0.0, 0.0, 0.0),
t = (0.0, 0.0, 0.0), move_atoms=True):
"""Translates and/or rotates a model.
Parameters
----------
model_path : str
The path to the file containing the model that will be moved.
fixed_model_path : str
The path to the file containing the model that will remain
in place.
ea : tuple
3-tuple of Euler angles for rotating the model.
t : tuple
3-tuple of xyz displacements for translating the model.
move_atoms : bool
Determines whether the atoms or the coordinate system should
be moved.
"""
model = open_volume_file(model_path)[0]
fixed_model = open_volume_file(fixed_model_path)[0]
try:
ea = map(float, ea)
t = map(float, t)
except ValueError:
from chimera.replyobj import warning
warning('Error parsing Euler angle or translation number')
return
if len(ea) != 3:
from chimera.replyobj import warning
warning('Requires 3 Euler angles.')
return
if len(t) != 3:
from chimera.replyobj import warning
warning('Requires 3 translation values.')
return
xf = mt.euler_xform(ea, t)
if isinstance(model, Molecule) and move_atoms:
mt.transform_atom_coordinates(m.atoms, xf)
else:
mt.transform_coordinate_axes(model, xf)
print('Transformation matrix:')
print(xf)
def fetch_eds_map(id, type = '2fofc', open_models = True):
site = 'eds.bmc.uu.se'
url_pattern = 'http://%s/eds/dfs/%s/%s/%s'
# Fetch map.
from chimera.replyobj import status
status('Fetching %s from web site %s...\n' % (id,site), blankAfter = False)
if type == 'fofc':
map_name = id + '_diff.omap'
elif type == '2fofc':
map_name = id + '.omap'
map_url = url_pattern % (site, id[1:3], id, map_name)
name = 'map %s' % id
minimum_map_size = 8192 # bytes
from chimera import fetch
map_path, headers = fetch.fetch_file(map_url, name, minimum_map_size,
'EDS', map_name)
# Display map.
status('Opening map %s...\n' % map_name, blankAfter = False)
from VolumeViewer import open_volume_file
models = open_volume_file(map_path, 'dsn6', map_name, 'mesh',
open_models = open_models)
status('\n')
return models
def draw(self):
"""
Research on Chimera's Volume extensions
"""
try:
grad_file, dens_file = self.data['grad_cube'], self.data['dens_cube']
except KeyError:
raise UserError('NCIPlot has not been run yet!')
else:
gradient = open_volume_file(grad_file, show_dialog=False,
model_id=(self._model_id[0], 1))[0]
density = open_volume_file(dens_file, show_dialog=False,
model_id=(self._model_id[0], 2))[0]
density.display = False
self._model_id[0] += 1
return gradient, density
def open_cb(path, ftype=name):
from VolumeViewer import open_volume_file
vlist = open_volume_file(path, ftype, open_models = False,
show_data = False, show_dialog = False)
import chimera
if len(vlist) > 0 and not chimera.nogui:
from SurfaceColor.gui import show_surface_color_dialog
d = show_surface_color_dialog()
d.use_electrostatics_colormap()
# TODO: Should set volume menu entry, but volumes are not yet opened.
return vlist
def fetch_emdb_map(id, open_fit_pdbs = False, open_models = True):
site = 'ftp.ebi.ac.uk'
url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/map/%s'
xml_url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/header/%s'
from chimera.replyobj import status, info
status('Fetching %s from %s...\n' % (id,site), blankAfter = False)
# Fetch map.
map_name = 'emd_%s.map' % id
map_gz_name = map_name + '.gz'
map_url = url_pattern % (site, id, map_gz_name)
name = 'EMDB %s' % id
minimum_map_size = 8192 # bytes
from chimera import fetch
map_path, headers = fetch.fetch_file(map_url, name, minimum_map_size,
'EMDB', map_name, uncompress = True)
# Display map.
status('Opening map %s...\n' % map_name, blankAfter = False)
from VolumeViewer import open_volume_file
models = open_volume_file(map_path, 'ccp4', map_name, 'surface',
open_models = open_models)
if open_fit_pdbs:
# Find fit pdb ids.
status('EMDB %s: looking for fits PDBs\n' % id)
pdb_ids = fit_pdb_ids_from_web_service(id)
msg = ('EMDB %s has %d fit PDB models: %s\n'
% (id, len(pdb_ids), ','.join(pdb_ids)))
status(msg)
info(msg)
if pdb_ids:
mlist = []
from chimera import _openPDBIDModel, openModels
for pdb_id in pdb_ids:
status('Opening %s\n' % pdb_id)
if open_models:
m = openModels.open(pdb_id, 'PDBID')
else:
m = _openPDBIDModel(pdb_id)
mlist.extend(m)
models.extend(mlist)
return models
def add_volumes(self, paths):
if not paths:
return
if len(paths) != len(self.ensemble):
raise ValueError('Provide exactly one volume per frame.')
volumes = []
for i, path in enumerate(paths):
basename, ext = os.path.splitext(path)
if ext in MULTIWFN_SUPPORTED_EXTENSIONS:
show_message('Converting to cube...')
path = _multiwfn_to_cube(path)
show_message('Converting to cube... Done!', blankAfter=3)
volume = open_volume_file(path,
show_dialog=False,
model_id=1000 + i)[0]
volume.display = False
volumes.append(volume)
self.volumes = volumes
self.isosurface()
self.colorize_by_volume(alpha=0.6)
self.update_volume()
self.volume_ui = self.launch_orbitraj_dialog()
def open_cb(path, ftype=name): from VolumeViewer import open_volume_file drlist = open_volume_file(path, ftype, open_models = False) models = [dr.surface_model() for dr in drlist] drlist = None # Work around numpy bug #454 return models