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 openVolumeData(self):
"""
open MRC file
set step size to 1, set contour, show surface
create self.voldata
"""
self.writeMessageToLog("Opening volume type: %s file: %s" %
(self.fileformat, self.tmpfilepath))
default_settings.set('limit_voxel_count', self.voxellimit)
default_settings.set('surface_smoothing', True)
default_settings.set('smoothing_iterations', 10)
self.voldata = open_volume_file(self.tmpfilepath, self.fileformat)[0]
#self.writeMessageToLog(str(dir(self.voldata)))
self.voldata.set_parameters(
show_outline_box=False,
surface_smoothing=True,
two_sided_lighting=False,
)
if self.contour is not None:
self.voldata.set_parameters(surface_levels=[self.contour])
self.voldata.show('surface')
self.surfaces = openModels.list(modelTypes=[SurfaceModel])
self.setZoom()
### This does not work on CentOS and Chimera v1.2509, but does with Chimera v1.4
result = re.search("([0-9]\.[0-9]*)", chimera.version.release)
if not result or not result.groups():
self.writeMessageToLog(
"Failed to get numeric version of Chimera: %s" %
(chimera.version.release))
sys.exit(1)
version = float(result.groups()[0])
self.writeMessageToLog("Chimera numeric version: %lf" % (version))
if version > 1.3:
### draw scale bar if version greater than 1.3
self.drawScaleBar()
else:
self.writeMessageToLog("Skipping scale bar")
def openVolumeData(self):
"""
open MRC file
set step size to 1, set contour, show surface
create self.voldata
"""
self.writeMessageToLog("Opening volume type: %s file: %s"%(self.fileformat, self.tmpfilepath))
default_settings.set('limit_voxel_count', self.voxellimit)
default_settings.set('surface_smoothing', True)
default_settings.set('smoothing_iterations', 10)
self.voldata = open_volume_file(self.tmpfilepath, self.fileformat)[0]
#self.writeMessageToLog(str(dir(self.voldata)))
self.voldata.set_parameters(
show_outline_box=False,
surface_smoothing=True,
two_sided_lighting=False,
)
if self.contour is not None:
self.voldata.set_parameters(surface_levels = [self.contour])
self.voldata.show('surface')
self.surfaces = openModels.list(modelTypes=[SurfaceModel])
self.setZoom()
### This does not work on CentOS and Chimera v1.2509, but does with Chimera v1.4
result = re.search("([0-9]\.[0-9]*)", chimera.version.release)
if not result or not result.groups():
self.writeMessageToLog("Failed to get numeric version of Chimera: %s"
%(chimera.version.release))
sys.exit(1)
version = float(result.groups()[0])
self.writeMessageToLog("Chimera numeric version: %lf"%(version))
if version > 1.3:
### draw scale bar if version greater than 1.3
self.drawScaleBar()
else:
self.writeMessageToLog("Skipping scale bar")