def runChimeraStep(self):
# create CMD file
parentSessionFileName = self.parentProt._getExtraPath(sessionFile)
# if len(self.extraCommands.get()) > 2:
# f.write(self.extraCommands.get())
# args = " --nogui --cmd " + self._getTmpPath(
# chimeraScriptFileName)
program = Chimera.getProgram()
config = configparser.ConfigParser()
_chimeraPdbTemplateFileName = \
os.path.abspath(self._getExtraPath(
chimeraPdbTemplateFileName))
_chimeraMapTemplateFileName = \
os.path.abspath(self._getExtraPath(
chimeraMapTemplateFileName))
_sessionFile = os.path.abspath(self._getExtraPath(sessionFile))
protId = self.getObjId()
config['chimerax'] = {
'chimerapdbtemplatefilename': _chimeraPdbTemplateFileName % protId,
'chimeramaptemplatefilename': _chimeraMapTemplateFileName % protId,
'sessionfile': _sessionFile,
'enablebundle': True,
'protid': self.getObjId()
}
with open(self._getExtraPath(CHIMERA_CONFIG_FILE), 'w') as configfile:
config.write(configfile)
# run in the background
cwd = os.path.abspath(self._getExtraPath())
Chimera.runProgram(program,
os.path.abspath(parentSessionFileName),
cwd=cwd)
def _displayMask(self, e=None):
if self.protocol.generateMaskedVolume.get():
maskedMapFileName = os.path.abspath(
self.protocol._getExtraPath(
self.protocol._getMapMaskedByPdbBasedMaskFileName()))
ccp4header = Ccp4Header(maskedMapFileName, readHeader=True)
dim, _, _ = ccp4header.getDims()
x, y, z = ccp4header.getOrigin()
sampling, _, _ = ccp4header.getSampling()
counter = 1
fnCmd = self.protocol._getExtraPath("chimera_mask.cxc")
f = open(fnCmd, 'w')
maskFileName = os.path.abspath(maskedMapFileName)
f.write("open %s\n" % maskFileName)
f.write("volume #%d style surface voxelSize %f\n" %
(counter, sampling))
# No origin information in header :-(
#f.write("volume #%d origin %0.2f,%0.2f,%0.2f\n" %
# (counter, x, y, z))
f.close()
# run in the background
Chimera.runProgram(Chimera.getProgram(), fnCmd + "&")
return []
else:
errorWindow(
self.getTkRoot(), "This protocol has been executed "
"without the mask option")
return []
def _visualizeMapModel(self, e=None):
bildFileName = os.path.abspath(
self.protocol._getExtraPath("axis_output.bild"))
if self.protocol.inputVolume.get() is None:
_inputVol = self.protocol.inputStructure.get().getVolume()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
else:
dim = self.protocol.inputVolume.get().getDim()[0]
sampling = self.protocol.inputVolume.get().getSamplingRate()
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
counter = 1
fnCmd = self.protocol._getExtraPath("chimera_output.cxc")
f = open(fnCmd, 'w')
# reference axis model = 0
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n")
# input 3D map
counter += 1 # 2
fnVol = self.protocol._getInputVolume()
fnVolName = os.path.abspath(fnVol.getFileName())
if fnVolName.endswith(":mrc"):
fnVolName = fnVolName.split(":")[0]
f.write("open %s\n" % fnVolName)
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 # 3
pdbFileName = os.path.abspath(
self.protocol.inputStructure.get().getFileName())
f.write("open %s\n" % pdbFileName)
# second refmac step output -> refined PDB
counter += 1 # 4
pdbFileName = os.path.abspath(self.protocol.outputPdb.getFileName())
f.write("open %s\n" % pdbFileName)
f.close()
# run in the background
Chimera.runProgram(Chimera.getProgram(), fnCmd + "&")
return []
def _visualize(self, obj, **args):
fnCmd = self.protocol._getTmpPath("chimera_restore_session.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())
path1 = os.path.join(self.protocol._getExtraPath(), sessionFile)
if os.path.exists(path1):
# restored SESSION
path = path1
else:
# SESSION from inputProtocol
path2 = os.path.join(
self.protocol.inputProtocol.get()._getExtraPath(), sessionFile)
path = path2
f.write("open %s\n" % path)
Chimera.runProgram(Chimera.getProgram(), fnCmd + "&")
return []
def _visualize(self, obj, **args):
# Create minimalistic coordinate axis
dim = 150.
sampling = 1.
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
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())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
# show vol
_showVol = self.protocol.outputVolume #.get()
showVolFileName = ImageHandler.removeFileType(_showVol.getFileName())
f.write("open %s\n" % showVolFileName)
if _showVol.hasOrigin():
x, y, z = _showVol.getOrigin().getShifts()
else:
x, y, z = _showVol.getOrigin(force=True).getShifts()
f.write("volume #2 style surface voxelSize %f\n"
"volume #2 origin %0.2f,%0.2f,%0.2f\n"
% (_showVol.getSamplingRate(), x, y, z))
# show atom struct)
atomstruct = self.protocol.atomStruct.get()
if atomstruct is not None:
f.write("open %s\n" % atomstruct.getFileName())
# run in the background
Chimera.runProgram(Chimera.getProgram(), fnCmd + "&")
return []
def chimeraInstalled(): return Chimera.getHome() and os.path.exists(Chimera.getProgram())
import pyworkflow.protocol.params as params
import pyworkflow.gui.plotter as plotter
import pyworkflow.gui.dialog as dialog
import pwem.constants as emcts
import pwem.protocols as emprot
from pwem import emlib, splitRange
from pwem.objects import AtomStruct, SetOfAtomStructs
from pwem.viewers.viewer_chimera import mapVolsWithColorkey, Chimera, ChimeraView, generateColorLegend
from pwem.convert.atom_struct import *
from .plotter import EmPlotter, plt
CHIMERA_ERROR = 'Chimera program is not found were it was expected: \n\n{}\n\n' \
'Either install ChimeraX in this path or install our ' \
'scipion-em-chimera plugin'.format(Chimera.getProgram())
class LocalResolutionViewer(pwviewer.ProtocolViewer):
"""
Visualization tools for local resolution results.
"""
binaryCondition = ('(colorMap == %d) ' % emcts.COLOR_OTHER)
def __init__(self, *args, **kwargs):
pwviewer.ProtocolViewer.__init__(self, **kwargs)
def getImgData(self, imgFile, minMaskValue=0.1, maxMaskValue=None):
import numpy as np
# if image ends in .mrc or .map :mrc
def _visualize(self, obj, **args):
# THe input map or pdb may be a parameter from the protocol
# or from the parent protocol.
dim = 150.
sampling = 1.
_inputVol = None
directory = self.protocol._getExtraPath()
try:
try:
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
elif self.protocol.pdbFileToBeRefined.get().getVolume(
) is not None:
_inputVol = self.protocol.pdbFileToBeRefined.get(
).getVolume()
elif self.protocol.inputVolumes[0] is not None:
_inputVol = self.protocol.inputVolumes[0].get()
except:
output3DMapList = []
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
output3DMapList.append(filename.split('.')[0])
output3DMap = str(output3DMapList[0])
if len(output3DMap) > 0:
_inputVol = self.protocol.output3DMap
except:
# TODO: I do not know if we still need this part
# Remark that inputProtocol does not longer exist, it has been replaced by inputProtocolDict
# Compare with the previous code, specially the alternative directory
for item in list(self.protocol.inputProtocolDict().values()):
if item.hasAttribute(
'inputVolume') and item.inputVolume.get() is not None:
_inputVol = item.inputVolume.get()
break
elif item.hasAttribute('pdbFileToBeRefined') and \
item.pdbFileToBeRefined.get().getVolume() is not None:
_inputVol = item.pdbFileToBeRefined.get().getVolume()
break
# directory = item._getExtraPath()
if _inputVol is not None:
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
bildFileName = self.protocol._getTmpPath("axis_output.bild")
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())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
inputVolFileName = ''
counter = 2
if _inputVol is not None:
# In case we have PDBs only, _inputVol is None:
self.visInputVolume(f, _inputVol, counter)
else:
counter = 1
if (self.protocol.hasAttribute("inputVolume2") and\
self.protocol.inputVolume2.get() is not None):
counter += 1
_inputVol2 = self.protocol.inputVolume2.get()
self.visInputVolume(f, _inputVol2, counter)
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc") and filename != inputVolFileName:
counter += 1
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
f.write("open %s\n" % volFileName)
f.write("volume #%d style surface voxelSize %f\n"
"volume #%d origin %0.2f,%0.2f,%0.2f\n" %
(counter, sampling, counter, shifts[0], shifts[1],
shifts[2]))
f.write("volume #%d level %0.3f\n" % (counter, 0.001))
for filename in os.listdir(directory):
if filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
# f.write("open %s\n" % os.path.abspath(path))
f.write("open %s\n" % path)
f.close()
# run in the background
Chimera.runProgram(Chimera.getProgram(), fnCmd + "&")
return []