def start(self):
self.setFileName()
scale = float(self.params['oldapix'])/self.params['newapix']
mrcname = os.path.join(self.params['rundir'], self.params['name']+".mrc")
origmodel = self.params['file']
if os.path.isfile(mrcname):
apDisplay.printError("File exists")
if (abs(self.params['oldapix'] - self.params['newapix']) > 1.0e-2 or
abs(self.params['oldbox'] - self.params['newbox']) > 1.0e-1):
### rescale old model to a new size
apDisplay.printWarning("rescaling original model to a new size")
scale = float(self.params['oldapix'])/self.params['newapix']
apDisplay.printMsg("rescaling model by scale factor of %.4f"%(scale))
apVolume.rescaleVolume(origmodel, mrcname,
self.params['oldapix'], self.params['newapix'], self.params['newbox'])
else:
### simple upload, just copy file to models folder
apDisplay.printMsg("copying original model to a new location: "+mrcname)
shutil.copyfile(origmodel, mrcname)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['newapix'])
### render chimera images of model
contour = self.params['contour']
if self.params['mass'] is not None:
apChimera.setVolumeMass(mrcname, self.params['newapix'], self.params['mass'])
contour = 1.0
apChimera.renderSnapshots(mrcname, contour=contour,
zoom=self.params['zoom'], sym=self.params['symdata']['eman_name'])
self.insertModel(mrcname)
def convertPDBtoMRC(self, pdbfile):
### create density from pdb
spidername = self.params['name']+".spi"
mrcname = self.params['name']+".mrc"
if self.params['method'] == 'spider':
if self.params['bunit'] is True:
pdbfile = self.removeModelFlags(pdbfile)
volFun.pdb2vol(pdbfile, self.params['apix'], self.params['boxsize'], spidername)
if not os.path.isfile(spidername):
apDisplay.printError("SPIDER did not create density file: "+spidername)
### convert spider to mrc format
apDisplay.printMsg("converting spider file to mrc")
emancmd='proc3d %s %s apix=%.4f lp=%.2f norm=0,1 origin=0,0,0' % (spidername, mrcname,
self.params['apix'], self.params['lowpass'])
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
apFile.removeFile(spidername)
elif self.params['method'] == 'eman':
mult = 1.0
### use resolution of mult*apix, because this is slow and lowpass is fast
emancmd='pdb2mrc %s %s apix=%.4f res=%.2f box=%d center allmdl' % (pdbfile, mrcname,
self.params['apix'], mult*self.params['apix'], self.params['boxsize'])
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
### lowpass to desired resolution minus the res factor specified
lp = math.sqrt(self.params['lowpass']**2 - (mult*self.params['apix'])**2)
emancmd='proc3d %s %s apix=%.4f lp=%.2f norm=0,1 origin=0,0,0' % (mrcname, mrcname,
self.params['apix'], lp)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['apix'])
return mrcname
def convertPDBtoMRC(self, pdbfile):
### create density from pdb
spidername = self.params['name']+".spi"
mrcname = self.params['name']+".mrc"
if self.params['method'] == 'spider':
if self.params['bunit'] is True:
pdbfile = self.removeModelFlags(pdbfile)
volFun.pdb2vol(pdbfile, self.params['apix'], self.params['boxsize'], spidername)
if not os.path.isfile(spidername):
apDisplay.printError("SPIDER did not create density file: "+spidername)
### convert spider to mrc format
apDisplay.printMsg("converting spider file to mrc")
emancmd='proc3d %s %s apix=%.4f lp=%.2f norm=0,1 origin=0,0,0' % (spidername, mrcname,
self.params['apix'], self.params['lowpass'])
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
apFile.removeFile(spidername)
elif self.params['method'] == 'eman':
mult = 1.0
### use resolution of mult*apix, because this is slow and lowpass is fast
emancmd='pdb2mrc %s %s apix=%.4f res=%.2f box=%d center allmdl' % (pdbfile, mrcname,
self.params['apix'], mult*self.params['apix'], self.params['boxsize'])
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
### lowpass to desired resolution minus the res factor specified
lp = math.sqrt(self.params['lowpass']**2 - (mult*self.params['apix'])**2)
emancmd='proc3d %s %s apix=%.4f lp=%.2f norm=0,1 origin=0,0,0' % (mrcname, mrcname,
self.params['apix'], lp)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['apix'])
return mrcname
def convertRefineModelIcosSymmetry(self,modelname,extname,modelfile,apix): # EMAN uses (5 3 2) only symmetry_description = self.model['data']['symmetry']['symmetry'] tempfile = os.path.join(self.params['rundir'], "temp.%s" % (extname)) if '(2 3 5)' in symmetry_description: apVolume.viper2eman(modelfile, tempfile, apix=self.stack['apix']) shutil.copy(tempfile,modelfile) if '(2 5 3)' in symmetry_description: apVolume.crowther2eman(modelfile, tempfile, apix=self.stack['apix']) shutil.copy(tempfile,modelfile)
def start(self):
self.setFileName()
scale = float(self.params['oldapix']) / self.params['newapix']
mrcname = os.path.join(self.params['rundir'],
self.params['name'] + ".mrc")
origmodel = self.params['file']
if os.path.isfile(mrcname):
apDisplay.printError("File exists")
if (abs(self.params['oldapix'] - self.params['newapix']) > 1.0e-2 or
abs(self.params['oldbox'] - self.params['newbox']) > 1.0e-1):
### rescale old model to a new size
apDisplay.printWarning("rescaling original model to a new size")
scale = float(self.params['oldapix']) / self.params['newapix']
apDisplay.printMsg("rescaling model by scale factor of %.4f" %
(scale))
apVolume.rescaleVolume(origmodel, mrcname, self.params['oldapix'],
self.params['newapix'],
self.params['newbox'])
else:
### simple upload, just copy file to models folder
apDisplay.printMsg("copying original model to a new location: " +
mrcname)
shutil.copyfile(origmodel, mrcname)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['newapix'])
### render chimera images of model
contour = self.params['contour']
if self.params['mass'] is not None:
apChimera.setVolumeMass(mrcname, self.params['newapix'],
self.params['mass'])
contour = 1.0
apChimera.renderSnapshots(mrcname,
contour=contour,
zoom=self.params['zoom'],
sym=self.params['symdata']['eman_name'])
self.insertModel(mrcname)
def start(self):
self.apix = None
self.mass = None
self.setFileName()
mrcname = self.params['name'] + ".mrc"
ccp4name = self.params['name'] + ".ccp4"
### get emdb from web
emdbfile = self.fetchEMDB(self.params['emdbid'], ccp4name)
### create density from emdb
self.getXMLInfoFromEMDB(self.params['emdbid'])
emancmd = ("proc3d " + ccp4name + " " + mrcname)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
apFile.removeFile(ccp4name)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.apix)
### lowpass filter, do both atan2 and Gaussian filter to sum up to requested lowpass
### total lowpass = sqrt( lp1^2 + lp2^2 )
if self.params['lowpass'] is not None:
lp = self.params['lowpass'] / math.sqrt(2.0)
emancmd = "proc3d %s %s apix=%.3f origin=0,0,0 norm=0,1 " % (
mrcname, mrcname, self.apix)
if self.params['lowpass'] is not None:
emancmd += "tlp=%.2f lp=%.2f" % (lp, lp)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
if self.mass is not None:
apChimera.setVolumeMass(mrcname, apix=self.apix, mass=self.mass)
### chimera imaging
apChimera.renderSnapshots(mrcname,
contour=1.0,
zoom=1.0,
sym=self.params['symdata']['eman_name'])
### upload it
self.uploadDensity(mrcname)
def start(self):
self.apix = None
self.mass = None
self.setFileName()
mrcname = self.params['name']+".mrc"
ccp4name = self.params['name']+".ccp4"
### get emdb from web
emdbfile = self.fetchEMDB(self.params['emdbid'], ccp4name)
### create density from emdb
self.getXMLInfoFromEMDB(self.params['emdbid'])
emancmd = ("proc3d "+ccp4name+" "+mrcname)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
apFile.removeFile(ccp4name)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.apix)
### lowpass filter, do both atan2 and Gaussian filter to sum up to requested lowpass
### total lowpass = sqrt( lp1^2 + lp2^2 )
if self.params['lowpass'] is not None:
lp = self.params['lowpass']/math.sqrt(2.0)
emancmd = "proc3d %s %s apix=%.3f origin=0,0,0 norm=0,1 " %(mrcname, mrcname, self.apix)
if self.params['lowpass'] is not None:
emancmd += "tlp=%.2f lp=%.2f" % (lp, lp)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
if self.mass is not None:
apChimera.setVolumeMass(mrcname, apix=self.apix, mass=self.mass)
### chimera imaging
apChimera.renderSnapshots(mrcname, contour=1.0, zoom=1.0, sym=self.params['symdata']['eman_name'])
### upload it
self.uploadDensity(mrcname)