def merge_ligand_into_protein(self,widget):
print '===> XCE: merge ligand into protein structure'
# merge_molecules(list(imols), imol) e.g. merge_molecules([1],0)
coot.merge_molecules_py([self.mol_dict['ligand']],self.mol_dict['protein'])
print '===> XCE: deleting ligand molecule'
coot.close_molecule(self.mol_dict['ligand'])
def RefreshData(self):
# initialize Refinement library
self.Refine=XChemRefine.Refine(self.project_directory,self.xtalID,self.compoundID,self.data_source)
self.Serial=self.Refine.GetSerial()
if self.Serial==1:
# i.e. no refinement has been done; data is probably straight out of dimple
if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.pdb_style)):
print '==> XCE: updating quality indicators in data source for '+self.xtalID
XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID,self.data_source,os.path.join(self.project_directory,self.xtalID,self.pdb_style))
XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID,self.data_source,'') # '' because file does not exist
elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')):
print '==> XCE: updating quality indicators in data source for '+self.xtalID
XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID,self.data_source,os.path.join(self.project_directory,self.xtalID,'dimple.pdb'))
XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID,self.data_source,'') # '' because file does not exist
# all this information is now updated in the datasource after each refinement cycle
self.QualityIndicators=self.db.get_db_dict_for_sample(self.xtalID)
if int(self.selected_site[0]) > 0:
self.spider_plot_data=self.db.get_db_pandda_dict_for_sample_and_site(self.xtalID,self.selected_site[0])
self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id'])
try:
self.ligand_occupancyValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_occupancy']),2)) )
self.ligand_BaverageValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_B_average']),2)) )
self.ligand_BratioSurroundingsValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']),2)) )
self.ligand_RSCCValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_RSCC']),2)) )
self.ligand_rmsdValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_rmsd']),2)) )
self.ligand_RSRValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_RSR']),2)) )
self.ligand_RSZDValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_RSZD']),2)) )
except ValueError:
self.ligand_occupancyValue.set_label('-')
self.ligand_BaverageValue.set_label('-')
self.ligand_BratioSurroundingsValue.set_label('-')
self.ligand_RSCCValue.set_label('-')
self.ligand_rmsdValue.set_label('-')
self.ligand_RSRValue.set_label('-')
self.ligand_RSZDValue.set_label('-')
#########################################################################################
# history
# if the structure was previously refined, try to read the parameters
# self.hbox_for_info_graphics.remove(self.canvas)
if self.Serial > 1:
self.RefmacParams=self.Refine.ParamsFromPreviousCycle(self.Serial-1)
# refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory()
# self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst))
# else:
# self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea
# self.canvas.set_size_request(190, 190)
# self.hbox_for_info_graphics.add(self.canvas)
# self.canvas.show()
#########################################################################################
# Spider plot
# Note: refinement history was shown instead previously
if os.path.isfile(self.spider_plot):
spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot)
else:
spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join(os.getenv('XChemExplorer_DIR'),'image','NO_SPIDER_PLOT_AVAILABLE.png'))
self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR)
self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic)
#########################################################################################
# update pdb & maps
#########################################################################################
# delete old PDB and MAP files
# - get a list of all molecules which are currently opened in COOT
# - remove all molecules/ maps before loading a new set
if len(coot_utils_XChem.molecule_number_list()) > 0:
for item in coot_utils_XChem.molecule_number_list():
coot.close_molecule(item)
#########################################################################################
# read new PDB files
# read protein molecule after ligand so that this one is the active molecule
coot.set_nomenclature_errors_on_read("ignore")
if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.pdb')):
imol=coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.pdb'),0)
self.mol_dict['ligand']=imol
coot.read_cif_dictionary(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.cif'))
if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.pdb_style)):
os.chdir(os.path.join(self.project_directory,self.xtalID))
# we want to be able to check dimple results immediately, but don't want to interfere with refinement
# if not os.path.isfile('REFINEMENT_IN_PROGRESS'):
# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-ensemble-model.pdb')):
# os.symlink(self.xtalID+'-ensemble-model.pdb',self.pdb_style)
# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')):
# os.symlink('dimple.pdb',self.pdb_style)
# else:
# self.go_to_next_xtal()
if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.pdb_style)):
os.chdir(os.path.join(self.project_directory,self.xtalID))
imol=coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory,self.xtalID,self.pdb_style),0)
elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')):
os.chdir(os.path.join(self.project_directory,self.xtalID))
imol=coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory,self.xtalID,'dimple.pdb'),0)
else:
self.go_to_next_xtal()
self.mol_dict['protein']=imol
for item in coot_utils_XChem.molecule_number_list():
if coot.molecule_name(item).endswith(self.pdb_style):
coot.set_show_symmetry_master(1) # master switch to show symmetry molecules
coot.set_show_symmetry_molecule(item,1) # show symm for model
#########################################################################################
# read fofo maps
# - read ccp4 map: 0 - 2fofc map, 1 - fofc.map
# read 2fofc map last so that one can change its contour level
if os.path.isfile(os.path.join(self.project_directory,self.xtalID,'2fofc.map')):
coot.set_default_initial_contour_level_for_difference_map(3)
coot.handle_read_ccp4_map(os.path.join(self.project_directory,self.xtalID,'fofc.map'),1)
coot.set_default_initial_contour_level_for_map(1)
coot.handle_read_ccp4_map(os.path.join(self.project_directory,self.xtalID,'2fofc.map'),0)
coot.set_last_map_colour(0,0,1)
else:
# try to open mtz file with same name as pdb file
coot.set_default_initial_contour_level_for_map(1)
# if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)):
# os.chdir(os.path.join(self.project_directory,self.xtalID))
# if not os.path.isfile('REFINEMENT_IN_PROGRESS'):
# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')):
# os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style)
# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')):
# os.symlink('dimple.mtz',self.mtz_style)
if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)):
coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory,self.xtalID,self.mtz_style))
elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')):
coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory,self.xtalID,'dimple.mtz'))
#########################################################################################
# check for PANDDAs EVENT maps
if os.path.isfile(self.event_map):
coot.handle_read_ccp4_map((self.event_map),0)
for imol in coot_utils_XChem.molecule_number_list():
if self.event_map in coot.molecule_name(imol):
coot.set_contour_level_in_sigma(imol,2)
# coot.set_contour_level_absolute(imol,0.5)
coot.set_last_map_colour(0.4,0,0.4)
# #########################################################################################
# # update Ligand Confidence combobox
# if str(self.ligand_confidence_of_sample)=='None':
# self.ligand_confidence_of_sample='Analysis Pending'
# db_dict={'RefinementLigandConfidence': self.ligand_confidence_of_sample}
## self.db.update_data_source(self.xtalID,db_dict)
# for n,criteria in enumerate(self.ligand_confidence):
# if criteria.replace('Ligand Confidence: ','')==self.ligand_confidence_of_sample:
# self.cb_ligand_confidence.set_active(n)
#########################################################################################
# update Quality Indicator table
try:
self.RRfreeValue.set_label( str(round(float(self.QualityIndicators['RefinementRcryst']),3)) +' / '+str(round(float(self.QualityIndicators['RefinementRfree']),3)))
except ValueError:
self.RRfreeValue.set_label('-')
try:
self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight']))
except ValueError:
pass
self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution'])
try:
self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL']))
except ValueError:
pass
self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore'])
try:
self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementMolProbityScoreTL']))
except ValueError:
pass
self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers'])
try:
self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRamachandranOutliersTL']))
except ValueError:
pass
self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored'])
try:
self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRamachandranFavoredTL']))
except ValueError:
pass
self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds'])
try:
self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL']))
except ValueError:
pass
self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles'])
try:
self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL']))
except ValueError:
pass
self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight'])
try:
pic = gtk.gdk.pixbuf_new_from_file(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.png'))
except gobject.GError:
pic = gtk.gdk.pixbuf_new_from_file(os.path.join(os.getenv('XChemExplorer_DIR'),'image','NO_COMPOUND_IMAGE_AVAILABLE.png'))
self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR)
self.image.set_from_pixbuf(self.pic)
