def _showVolumesChimera(self):
tmpFileNameCMD = self.protocol._getExtraPath("chimera.cxc")
f = open(tmpFileNameCMD, "w")
dim = self.protocol.inputVolumes.get().getDim()[0]
sampling = self.protocol.inputVolumes.get().getSamplingRate()
tmpFileName = os.path.abspath(self.protocol._getExtraPath("axis.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=tmpFileName,
sampling=sampling)
f.write("open %s\n" % tmpFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
_inputVol = self.protocol.inputVolumes.get()
_outputVol = self.protocol.outputVolume
inputVolFileName = os.path.abspath(ImageHandler.removeFileType(
_inputVol.getFileName()))
# input vol origin coordinates
x_input, y_input, z_input = _inputVol.getShiftsFromOrigin()
f.write("open %s\n" % inputVolFileName)
f.write("volume #2 style mesh level 0.001 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n"
% (_inputVol.getSamplingRate(), x_input, y_input, z_input))
outputVolFileName = os.path.abspath(ImageHandler.removeFileType(
_outputVol.getFileName()))
# output vol origin coordinates
x_output, y_output, z_output = _outputVol.getShiftsFromOrigin()
f.write("open %s\n" % outputVolFileName)
f.write("volume #3 style surface level 0.001 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n"
% (_outputVol.getSamplingRate(), x_output, y_output, z_output))
cMap = ['red', 'yellow', 'green', 'cyan', 'blue']
d = {}
innerRadius = self.protocol.innerRadius.get()
d['outerRadius'] = self.protocol.outerRadius.get() * sampling
if innerRadius < 0:
innerRadius = 0
d['innerRadius'] = innerRadius * sampling
d['innerRadius'] = self.protocol.innerRadius.get() * sampling
d['symmetry'] = Chimera.getSymmetry(XMIPP_TO_SCIPION[self.protocol.symmetryGroup.get()])
if self.protocol.symmetryGroup >= XMIPP_I222:
f.write("shape icosahedron mesh true radius %(outerRadius)d "
"orientation %(symmetry)s\n" % d)
step = (d['outerRadius'] - d['innerRadius']) / float(len(cMap) - 1)
f.write("color radial #3 center 0,0,0 palette -")
counter = 0
s = ""
for color in cMap:
s += "%d,%s:" % (d['innerRadius'] + counter * step, color)
counter += 1
f.write(s[:-1] + '\n')
f.close()
return [ChimeraView(tmpFileNameCMD)]
def _visualize(self, obj, **args):
# The input pdb is a parameter from the protocol
# and from the parent protocol.
inputAtomStruct = self.protocol.pdbFileToBeRefined.get()
# To show pdbs only
dim = 150.
sampling = 1.
bildFileName = os.path.abspath(self.protocol._getTmpPath(
"axis_output.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCmd = self.protocol._getTmpPath("chimera_output.cxc")
f = open(fnCmd, 'w')
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
f.write("open %s\n"
% os.path.abspath(inputAtomStruct.getFileName()))
f.write("style stick\n")
if self.protocol.hasAttribute('rotatedAtomStruct'):
outputAtomStruct = self.protocol.rotatedAtomStruct.getFileName()
f.write("open %s\n" % os.path.abspath(outputAtomStruct))
f.close()
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera', 'Plugin', doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(), fnCmd + "&")
return []
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
tmpFileNameCMD = self.protocol._getExtraPath("chimera.cxc")
f = open(tmpFileNameCMD, "w")
sampling, _setOfVolumes = self._createSetOfVolumes()
count = 1 # chimeraX stars counting in 1 (chimera in 0)
if len(_setOfVolumes) == 1:
# if we have a single volume then create axis
# as bild file. Chimera must read the bild file first
# otherwise system of coordinates will not
# be in the center of the window
dim = self.protocol.outputVolume.getDim()[0]
tmpFileNameBILD = os.path.abspath(
self.protocol._getExtraPath("axis.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=tmpFileNameBILD,
sampling=sampling)
f.write("open %s\n" % tmpFileNameBILD)
f.write("cofr 0,0,0\n") # set center of coordinates
count = 2 # skip first model because is not a 3D map
for vol in _setOfVolumes:
localVol = os.path.abspath(
image.ImageHandler.removeFileType(vol.getFileName()))
if localVol.endswith("stk"):
errorWindow(None, "Extension .stk is not supported")
f.write("open %s\n" % localVol)
f.write("volume #%d style surface level 0.001 voxelSize %f\n" %
(count, sampling))
count += 1
if len(_setOfVolumes) > 1:
f.write('tile\n')
else:
x, y, z = vol.getShiftsFromOrigin()
f.write("volume #2 origin %0.2f,%0.2f,%0.2f\n" % (x, y, z))
if vol.getHalfMaps():
for halfMap in vol.getHalfMaps().split(','):
if not os.path.abspath(halfMap).endswith(".mrc"):
f.write(
"open %s\n" %
(os.path.abspath(halfMap).split(".")[0] + ".mrc"))
else:
f.write("open %s\n" % os.path.abspath(halfMap))
f.write(
"volume #%d style surface level 0.001 voxelSize %f\n" %
(count, sampling))
f.write("volume #%d origin %0.2f,%0.2f,%0.2f\n" %
(count, x, y, z))
f.write("tile\n")
count += 1
f.write("view\n")
f.close()
return [ChimeraView(tmpFileNameCMD)]
def _displayMapModel(self, e=None):
bildFileName = self.protocol._getExtraPath("axis_output.bild")
_inputVol = self.protocol.inputVolume.get()
if _inputVol is None:
_inputVol = self.protocol.inputStructure.get().getVolume()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
counter = 1
fnCmd = self.protocol._getExtraPath("chimera_output.cxc")
f = open(fnCmd, 'w')
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
# reference axis model = 0
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
# input 3D map
counter += 1 # 1
fnVol = self._getInputVolume()
if fnVol is not None:
EMRINGERFILENAME = self.protocol._getExtraPath(
self.protocol.EMRINGERFILE)
f.write("open %s\n" % EMRINGERFILENAME)
x, y, z = fnVol.getOrigin(force=True).getShifts()
sampling = fnVol.getSamplingRate()
f.write("volume #%d style surface voxelSize %f\nvolume #%d origin "
"%0.2f,%0.2f,%0.2f\n" %
(counter, sampling, counter, x, y, z))
# input PDB (usually from coot)
counter += 1 # 2
pdbFileName = self.protocol.inputStructure.get().getFileName()
f.write("open %s\n" % pdbFileName)
f.close()
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera',
'Plugin',
doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(),
fnCmd + "&",
cwd=os.getcwd())
return []
def _visualize(self, obj, **args):
fnCmd = self.protocol._getExtraPath("chimera_output.cxc")
self._getVols()
self._getPdbs()
dim = float()
sampling = float()
if len(self.vols) > 0:
if self.vols[0] is not None:
dim, sampling = self._getDimSamplingFromVol(self.vols[0])
elif self.vols[1] is not None:
dim, sampling = self._getDimSamplingFromVol(self.vols[1])
else:
# To show pdbs only
dim = 150.
sampling = 1.
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
with open(fnCmd, 'w') as f:
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
if len(self.vols) > 0:
for vol in self.vols:
sampling, volFileName, x, y, z = self._getXYZFromVol(vol)
f.write("open %s\n" % volFileName)
f.write("volume #2 style surface voxelSize %f\n"
"volume #2 origin %0.2f,%0.2f,%0.2f\n" %
(sampling, x, y, z))
for filename in self.pdbList:
f.write("open %s\n" % filename)
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera',
'Plugin',
doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(),
fnCmd + "&",
cwd=os.getcwd())
return []
def _validate(self):
if (self.displayVol == VOLUME_CHIMERA
and find_executable(Chimera.getProgram()) is None):
return [
"chimera is not available. "
"Either install it or choose option 'slices'. "
]
return []
def main():
fileName = sys.argv[1]
# Clean filename in case it comes annotated like 1@xxxmrc:mrcs
fileName = fileName.split(":")[0]
# if contains @
if "@" in fileName:
fileName = fileName.split("@")[1]
Chimera().runProgram(args=fileName)
def _insertAllSteps(self):
dim = 150.
sampling = 1.
bildFileName = os.path.abspath(self._getExtraPath("axis_output.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCmd = self._getExtraPath("chimera_output.cxc")
f = open(fnCmd, 'w')
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
f.close()
if self.Operation == self.operationsDictInv['addChain']:
listStructFileName = []
for aStruct in self.InputAtomStruct2:
listStructFileName.append(aStruct.get().getFileName())
self._insertFunctionStep(
'addChainStep',
self.pdbFileToBeRefined.get().getFileName(),
listStructFileName)
elif self.Operation == self.operationsDictInv['extractChain']:
self._insertFunctionStep(
'extractChainStep',
self.pdbFileToBeRefined.get().getFileName())
elif self.Operation == self.operationsDictInv['extractAllChains']:
self._insertFunctionStep(
'extractAllChainsStep',
self.pdbFileToBeRefined.get().getFileName())
elif self.Operation == self.operationsDictInv['reNumberChain']:
self._insertFunctionStep(
'reNumberChainStep',
self.pdbFileToBeRefined.get().getFileName())
elif self.Operation == self.operationsDictInv['reNameChain']:
self._insertFunctionStep(
'reNameChainStep',
self.pdbFileToBeRefined.get().getFileName())
else:
raise Exception("ERROR: Invalid operation *%s* I quit" %
self.Operation)
def _displayModel(self, e=None):
# bildFileName = os.path.abspath(self.protocol._getTmpPath(
# "axis_output.bild"))
bildFileName = self.protocol._getTmpPath("axis_output.bild")
# Axis Dim
dim = 150.
sampling = 1.
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCmd = self.protocol._getTmpPath("chimera_output.cxc")
f = open(fnCmd, 'w')
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
# reference axis model = 0
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
# f.write("open %s\n" % os.path.abspath(
# self.protocol.pdbFileToBeRefined.get().getFileName()))
f.write("open %s\n" %
self.protocol.pdbFileToBeRefined.get().getFileName())
if self.protocol.SYMMETRY.get() and \
os.path.exists(self.protocol.getSymmetrizedModelName()):
f.write("open %s\n" % self.protocol.getSymmetrizedModelName())
f.close()
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera',
'Plugin',
doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(),
fnCmd + "&",
cwd=os.getcwd())
return []
def __applyTransform(suffix, pdbFileName, shift, angles, sampling):
""" auxiliary function, transform PDB and 3dmap files"""
# create a Scipion transformation matrix
from numpy import deg2rad
rotation_matrix = emconv.euler_matrix(deg2rad(angles[0]),
deg2rad(angles[1]),
deg2rad(angles[2]), 'szyz')
translation = emconv.translation_matrix(shift)
M = emconv.concatenate_matrices(rotation_matrix, translation)
# apply it to the pdb file
# if rotation move to center
aSH = emconv.AtomicStructHandler(pdbFileName)
if angles[0] != 0. or angles[1] != 0. or angles[2] != 0.:
ih = ImageHandler()
x, y, z, n = ih.getDimensions("emd_%s.map" % EMDBID)
x /= 2.
y /= 2.
z /= 2.
localShift = [-x, -y, -z]
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.concatenate_matrices(rotation_matrix,
translation)
aSH.transform(localM, sampling=sampling)
aSH.transform(M, sampling=sampling)
if angles[0] != 0. or angles[1] != 0. or angles[2] != 0.:
localShift = [x, y, z]
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.concatenate_matrices(rotation_matrix,
translation)
aSH.transform(localM, sampling=sampling)
aSH.write("%s_%s_transformed.ent" % (suffix, PDBID.lower()))
# get equivalent xmipp transformation
shift, angles = __getXmippEulerAngles(M)
# shift 3map and set sampling
__runXmippProgram(
"xmipp_transform_geometry", '-i emd_%s.map '
'-o %s_emd_%s_transform.map '
'--interp linear '
'--shift %f %f %f '
'--rotate_volume euler %f %f %f ' %
(EMDBID, suffix, EMDBID, shift[0], shift[1], shift[2],
angles[0], angles[1], angles[2]))
header = Ccp4Header("%s_emd_%s_transform.map" % (suffix, EMDBID),
readHeader=True)
header.setSampling(sampling)
# put the sampling back, xmipp_transform_geometry erased it
header.writeHeader()
# view the results with chimera
from pwem.viewers import Chimera
args = "%s %s %s %s" % (
pdbFileName, "emd_%s.map" % EMDBID, "%s_%s_transformed.ent" %
(suffix, PDBID.lower()), "%s_emd_%s_transform.map" %
(suffix, EMDBID))
Chimera.runProgram(args)
def _visualize(self, obj, **args):
# Input map(s) are a parameter from the protocol
dim = 150.
sampling = 1.
_inputVol = None
_inputHalf1 = None
_inputHalf2 = None
listVol = []
directory = self.protocol._getExtraPath()
if self.protocol.useHalfMapsInsteadVol.get():
if self.protocol.halfMapsAttached.get():
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
listVol.append(_inputVol)
else:
if self.protocol.inputHalf1.get() is not None:
_inputHalf1 = self.protocol.inputHalf1.get()
_inputHalf2 = self.protocol.inputHalf2.get()
dim = _inputHalf1.getDim()[0]
sampling = _inputHalf1.getSamplingRate()
listVol.append(_inputHalf1)
listVol.append(_inputHalf2)
else:
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
listVol.append(_inputVol)
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCxc = self.protocol._getExtraPath("chimera_output.cxc")
f = open(fnCxc, 'w')
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
counter = 1
for vol in listVol:
counter += 1
self._visInputVolume(f, vol, counter)
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
counter += 1
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
if self.protocol.useHalfMapsInsteadVol.get():
if self.protocol.halfMapsAttached.get():
inVol = self.protocol.inputVolume.get()
else:
inVol = self.protocol.inputHalf1.get()
else:
inVol = self.protocol.inputVolume.get()
vol.setSamplingRate(inVol.getSamplingRate())
vol.setOrigin(inVol.getOrigin(True))
self._visInputVolume(f, vol, counter)
f.write("volume #%d level %0.3f\n" % (counter, 0.001))
f.close()
return [ChimeraView(fnCxc)]
def _validate(self):
if find_executable(Chimera.getProgram()) is None:
return ["chimerax is not available. Either install it or choose"
" option 'slices'. "]
return []