#! /usr/bin/env ccp4-python # # Copyright (C) 2005 Ronan Keegan # # This code is distributed under the terms and conditions of the # CCP4 Program Suite Licence Agreement as a CCP4 Application. # A copy of the CCP4 licence can be obtained by writing to the # CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. # # Top level wrapper for launcing Molecular Replacement and Refinement jobs # Ronan Keegan 10/03/06 # import os, sys, string import Model_Queue import MRBUMP_Phaser import MRBUMP_Molrep import MRBUMP_cpirate import MRBUMP_writebest #import MRBUMP_cbuccaneer_ref import Phase_improve class MR_submit: def __init__(self): self.DB_fail=False try: self.debug=eval(os.environ['MRBUMP_DEBUG']) except: self.debug=False def setDEBUG(self, flag): self.debug=flag def MR_isdone(self, init, mstat): """ A function that returns True if there are no more jobs to submit """ for model in mstat.sorted_model_list: # Loop over the list of molecular replacement programs that are being used in this job for MRPROGRAM in init.keywords.MR_PROGRAM_LIST: # Set the MR program mstat.setMRPROGRAM(MRPROGRAM.upper()) MODEL=mstat.model_list[model] # Find any jobs that have not already been submitted if mstat.MRPROGRAM == "MOLREP" and not MODEL.isMolrepSubmitted() or \ mstat.MRPROGRAM == "PHASER" and not MODEL.isPhaserSubmitted(): return False return True def MR_start(self, target_info, init, mstat, job_limit, pyrvapi): """ A function to start a molecular replacement job (Molrep or Phaser).""" sys.stdout.write("MR log: Checking to see if we can launch more molecular replacement jobs\n") sys.stdout.write("\n") # If an enantiomorph exists and we want to do a search in that spacegroup too, report it if init.keywords.ENANT: sys.stdout.write("MR log: The spacegroup of the target data (%s) has an enantiomorph (%s)\n" \ % (target_info.space_group, target_info.enant_spacegroup)) sys.stdout.write(" Molecular replacement will be carried out in this spacegroup also.\n") sys.stdout.write("\n") # Sort the model list so that jobs with a higher sequence identity are started first self.sort_model_list(mstat) jl_file=os.path.join(init.search_dir, "logs", "jobs.txt") if os.path.isfile(jl_file): job_id_log = open(jl_file, 'a') else: job_id_log = open(jl_file, 'w') # Loop over all of the search models and submit them to one of the MR programs model_count=0 loop_count=0 for model in mstat.sorted_model_list: FIRSTPASS=True #pyrvapi.rvapi_add_section ( "tree_sec1","Section for NODE 1","tree1",0,0,1,1,True ), #pyrvapi.rvapi_add_text ( "Text for NODE 1","tree_sec1",0,0,1,1 ), #pyrvapi.rvapi_add_section ( "tree_sec2","Section for NODE 2","tree1",0,0,1,1,True ), #pyrvapi.rvapi_add_text ( "Text for NODE 2","tree_sec2",0,0,1,1 ), #pyrvapi.rvapi_add_section ( "tree_sec21","Section for NODE 21","tree1",0,0,1,1,True ), #pyrvapi.rvapi_add_text ( "Text for NODE 21","tree_sec21",0,0,1,1 ), #pyrvapi.rvapi_add_section ( "tree_sec22","Section for NODE 22","tree1",0,0,1,1,True ), #pyrvapi.rvapi_add_text ( "Text for NODE 22","tree_sec22",0,0,1,1 ), # # pyrvapi.rvapi_set_tree_node ( "tree1","tree_sec1","Node 1","auto","" ), # pyrvapi.rvapi_set_tree_node ( "tree1","tree_sec2","Node 2","auto","" ), # pyrvapi.rvapi_set_tree_node ( "tree1","tree_sec21","Node 21 make this long","auto","tree_sec2" ), # pyrvapi.rvapi_set_tree_node ( "tree1","tree_sec22","Node 22","auto","tree_sec2" ), # If we have submitted enough jobs, then exit if model_count>=job_limit: break # If a solution is found output the results and exit from the models loop if mstat.solution_found: if init.keywords.TRYALL == False: break # Loop over the list of molecular replacement programs that are being used in this job for MRPROGRAM in init.keywords.MR_PROGRAM_LIST: # Set the MR program mstat.setMRPROGRAM(MRPROGRAM.upper()) MODEL=mstat.model_list[model] # Skip jobs that have already been submitted if mstat.MRPROGRAM == "MOLREP" and MODEL.isMolrepSubmitted() or \ mstat.MRPROGRAM == "PHASER" and MODEL.isPhaserSubmitted(): continue # Set the job number MODEL.setMR_JobNumber(mstat.mr_counter) # Print some details about this job self.print_job_details(MODEL, mstat, init) # if we are using Phaser as the MR program then we start the MR job accordingly. if mstat.MRPROGRAM=='PHASER': # Set the model variable for the name of the MR program MODEL.setMRPROGRAM("PHASER") # Setup for Phaser MODEL.setPhaserLogFile(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'phaser_' + MODEL.name + '.log')) MODEL.setPhaserSummary(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'phaser_' + MODEL.name + '.sum')) MODEL.setPhaserSolnFile(os.path.join(MODEL.model_directory,'mr', 'phaser', 'phaser_' + MODEL.name + '.sol')) MODEL.setPhaserMTZfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'phaser_' + MODEL.name + '.1.mtz')) MODEL.setPhaserPDBfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'phaser_' + MODEL.name + '.1.pdb')) MODEL.setPhaserJobName("MRB_" + MODEL.name) # Specify the PDB summary log file name for phaser MODEL.setMRPDBSummaryFile(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'mr_pdb_summary_phaser_' + MODEL.name + '.log')) # Specify the PDBcur log file name MODEL.setPDBcurSummaryFile(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'pdbcur_summary_phaser_' + MODEL.name + '.log')) # Create specific files for the Refmac Rigid Body MTZ, PDB, solution file and logfile for Phaser. if init.keywords.RBODREF: MODEL.setRefmacRBPhaserLogFile(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'refine', 'refmacRB_phaser_' + MODEL.name + '.log')) MODEL.setRefmacRBPhaserPDBfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "refine", "refmacRB_phaser_" + MODEL.name + ".pdb")) #MODEL.setRefmacRBPhaserMTZINfile(os.path.join(MODEL.model_directory, "refine", "phaser", "refmac_phaser_HKLIN_" + MODEL.name + ".mtz")) MODEL.setRefmacRBPhaserMTZOUTfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "refine", "refmacRB_phaser_HKLOUT_" + MODEL.name + ".mtz")) #MODEL.setRefmacRBPhaserMTZINfile(target_info.refinement_hklin) # Create specific files for the Refmac MTZ, PDB, solution file and logfile for Phaser. MODEL.setRefmacPhaserLogFile(os.path.join(MODEL.model_directory, 'mr', 'phaser', 'refine', 'refmac_phaser_' + MODEL.name + '.log')) MODEL.setRefmacPhaserPDBfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "refine", "refmac_phaser_" + MODEL.name + ".pdb")) #MODEL.setRefmacPhaserMTZINfile(os.path.join(MODEL.model_directory, "refine", "phaser", "refmac_phaser_HKLIN_" + MODEL.name + ".mtz")) MODEL.setRefmacPhaserMTZOUTfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "refine", "refmac_phaser_HKLOUT_" + MODEL.name + ".mtz")) #MODEL.setRefmacPhaserMTZINfile(target_info.refinement_hklin) # Model building settings if init.keywords.BUCCANEER: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build", "buccaneer"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build", "buccaneer")) MODEL.setBuccaneerPhaserPDBOUTfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "build", "buccaneer", "buccaneer_phaser_" + MODEL.name + ".pdb")) MODEL.setBuccaneerPhaserWorkingDIR(os.path.join(MODEL.model_directory, 'mr', 'phaser', "build", "buccaneer")) MODEL.setBuccaneerPhaserPDBrefinedfile(os.path.join(MODEL.buccaneer_phaser_directory, "buccaneer_pipeline", "refined.pdb")) MODEL.setBuccaneerPhaserMTZrefinedfile(os.path.join(MODEL.buccaneer_phaser_directory, "buccaneer_pipeline", "refined.mtz")) if init.keywords.ARPWARP: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build", "arpwarp"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build", "arpwarp")) MODEL.setArpwarpPhaserPDBOUTfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "build", "arpwarp", "arpwarp_phaser_" + MODEL.name + ".pdb")) if init.keywords.SHELXE: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build", "shelxe"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "phaser", "build", "shelxe")) MODEL.setShelxePhaserPDBfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "build", "shelxe", "shelxe_phaser_" + MODEL.name + ".pdb")) MODEL.setShelxePhaserPHSfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "build", "shelxe", "shelxe_phaser_" + MODEL.name + ".phs")) MODEL.setShelxePhaserMTZfile(os.path.join(MODEL.model_directory, 'mr', 'phaser', "build", "shelxe", "shelxe_phaser_" + MODEL.name + ".mtz")) # Set this as submitted, and increment counter MODEL.setPhaserSubmitted(True) model_count += 1 # Complete the jobs script to be Phaser specific phaser_job=MRBUMP_Phaser.Phaser() phaser_job.submit_job(init, mstat, MODEL, target_info) # or if we are using molrep... if mstat.MRPROGRAM=='MOLREP': # Set the model variable for the name of the MR program MODEL.setMRPROGRAM("MOLREP") # Make sure not to try the phaser ensemble model if we are running Molrep #if "ensemble_model" in MODEL.name: # if self.debug: # sys.stdout.write("Ignoring ensemble model in Molrep\n") # sys.stdout.write("\n") # else: # Setup for Molrep if init.keywords.QTYPE=="CONDOR": # Condor needs all file in one directory MODEL.setMolrepLogFile(os.path.join(MODEL.model_directory, 'molrep1.log')) MODEL.setMolrepSolnFile(os.path.join(MODEL.model_directory, 'molrep1.log')) MODEL.setMolrepMTZfile(os.path.join(MODEL.model_directory, 'molrep_' + MODEL.name + '.1.mtz')) MODEL.setMolrepPDBfile(os.path.join(MODEL.model_directory, 'molrep_' + MODEL.name + '.1.pdb')) else: MODEL.setMolrepLogFile(os.path.join(MODEL.model_directory, 'mr', 'molrep', 'molrep.log')) MODEL.setMolrepSolnFile(os.path.join(MODEL.model_directory, 'mr', 'molrep', 'molrep.log')) MODEL.setMolrepMTZfile(os.path.join(MODEL.model_directory, 'mr', 'molrep', 'molrep_' + MODEL.name + '.1.mtz')) MODEL.setMolrepPDBfile(os.path.join(MODEL.model_directory, 'mr', 'molrep', 'molrep_' + MODEL.name + '.1.pdb')) MODEL.setMolrepJobName("MRB_" + MODEL.name) # Specify the PDB summary log file name for molrep MODEL.setMRPDBSummaryFile(os.path.join(MODEL.model_directory, "mr", 'molrep',"mr_pdb_summary_molrep_" + MODEL.name + ".log")) # Specify the PDBcur log file name MODEL.setPDBcurSummaryFile(os.path.join(MODEL.model_directory, "mr", 'molrep',"pdbcur_summary_molrep_" + MODEL.name + ".log")) # Create specific files for the Refmac Rigid Body solution file and logfile for Molrep. if init.keywords.RBODREF: MODEL.setRefmacRBMolrepLogFile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmacRB_molrep_" + MODEL.name + ".log")) MODEL.setRefmacRBMolrepPDBfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmacRB_molrep_" + MODEL.name + ".pdb")) #MODEL.setRefmacRBMolrepMTZINfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_HKLIN_" + MODEL.name + ".mtz")) MODEL.setRefmacRBMolrepMTZOUTfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmacRB_molrep_HKLOUT_" + MODEL.name + ".mtz")) #MODEL.setRefmacRBMolrepMTZINfile(target_info.refinement_hklin) # Create specific files for the Refmac solution file and logfile for Molrep. if init.keywords.QTYPE=="CONDOR": # Condor needs all file in one directory MODEL.setRefmacMolrepLogFile(os.path.join(MODEL.model_directory, "refmac_molrep_" + MODEL.name + ".log")) MODEL.setRefmacMolrepPDBfile(os.path.join(MODEL.model_directory, "refmac_molrep_" + MODEL.name + ".pdb")) #MODEL.setRefmacMolrepMTZINfile(os.path.join(MODEL.model_directory, "refmac_molrep_HKLIN_" + MODEL.name + ".mtz")) MODEL.setRefmacMolrepMTZOUTfile(os.path.join(MODEL.model_directory, "refmac_molrep_HKLOUT_" + MODEL.name + ".mtz")) #MODEL.setRefmacMolrepMTZINfile(target_info.refinement_hklin) else: MODEL.setRefmacMolrepLogFile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_" + MODEL.name + ".log")) MODEL.setRefmacMolrepPDBfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_" + MODEL.name + ".pdb")) #MODEL.setRefmacMolrepMTZINfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_HKLIN_" + MODEL.name + ".mtz")) MODEL.setRefmacMolrepMTZOUTfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_HKLOUT_" + MODEL.name + ".mtz")) #MODEL.setRefmacMolrepMTZINfile(target_info.refinement_hklin) # Model building settings if init.keywords.BUCCANEER: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer")) MODEL.setBuccaneerMolrepPDBOUTfile(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer", "buccaneer_molrep_" + MODEL.name + ".pdb")) MODEL.setBuccaneerMolrepWorkingDIR(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer")) MODEL.setBuccaneerMolrepPDBrefinedfile(os.path.join(MODEL.buccaneer_molrep_directory, "buccaneer_pipeline", "refined.pdb")) MODEL.setBuccaneerMolrepMTZrefinedfile(os.path.join(MODEL.buccaneer_molrep_directory, "buccaneer_pipeline", "refined.mtz")) if init.keywords.ARPWARP: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "arpwarp"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "arpwarp")) MODEL.setArpwarpPhaserPDBOUTfile(os.path.join(MODEL.model_directory, 'mr', 'molrep', "build", "arpwarp", "arpwarp_molrep_" + MODEL.name + ".pdb")) # Create specific files for the Refmac Rigid Body solution file and logfile for Molrep. if init.keywords.RBODREF: MODEL.setRefmacRBMolrepLogFile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmacRB_molrep_" + MODEL.name + ".log")) MODEL.setRefmacRBMolrepPDBfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmacRB_molrep_" + MODEL.name + ".pdb")) #MODEL.setRefmacRBMolrepMTZINfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_HKLIN_" + MODEL.name + ".mtz")) MODEL.setRefmacRBMolrepMTZOUTfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmacRB_molrep_HKLOUT_" + MODEL.name + ".mtz")) #MODEL.setRefmacRBMolrepMTZINfile(target_info.refinement_hklin) # Create specific files for the Refmac solution file and logfile for Molrep. MODEL.setRefmacMolrepLogFile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_" + MODEL.name + ".log")) MODEL.setRefmacMolrepPDBfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_" + MODEL.name + ".pdb")) #MODEL.setRefmacMolrepMTZINfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_HKLIN_" + MODEL.name + ".mtz")) MODEL.setRefmacMolrepMTZOUTfile(os.path.join(MODEL.model_directory, "mr", "molrep", "refine", "refmac_molrep_HKLOUT_" + MODEL.name + ".mtz")) #MODEL.setRefmacMolrepMTZINfile(target_info.refinement_hklin) # Model building settings if init.keywords.BUCCANEER: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer")) MODEL.setBuccaneerMolrepPDBOUTfile(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer", "buccaneer_molrep_" + MODEL.name + ".pdb")) MODEL.setBuccaneerMolrepWorkingDIR(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "buccaneer")) MODEL.setBuccaneerMolrepPDBrefinedfile(os.path.join(MODEL.buccaneer_molrep_directory, "buccaneer_pipeline", "refined.pdb")) MODEL.setBuccaneerMolrepMTZrefinedfile(os.path.join(MODEL.buccaneer_molrep_directory, "buccaneer_pipeline", "refined.mtz")) if init.keywords.ARPWARP: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "arpwarp"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "arpwarp")) MODEL.setArpwarpPhaserPDBOUTfile(os.path.join(MODEL.model_directory, 'mr', 'molrep', "build", "arpwarp", "arpwarp_molrep_" + MODEL.name + ".pdb")) if init.keywords.SHELXE: if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build")) if os.path.isdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "shelxe"))==False: os.mkdir(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "shelxe")) MODEL.setShelxeMolrepPDBfile(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "shelxe", "shelxe_molrep_" + MODEL.name + ".pdb")) MODEL.setShelxeMolrepPHSfile(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "shelxe", "shelxe_molrep_" + MODEL.name + ".phs")) MODEL.setShelxeMolrepMTZfile(os.path.join(MODEL.model_directory, "mr", "molrep", "build", "shelxe", "shelxe_molrep_" + MODEL.name + ".mtz")) # Set this as submitted, and increment counter MODEL.setMolrepSubmitted(True) model_count += 1 # Complete the jobs script to be Molrep specific molrep_job=MRBUMP_Molrep.Molrep() molrep_job.submit_job(init, mstat, MODEL, target_info) # If we are using the cluster we do not do the following: if init.keywords.CLUSTER == False: # If we are running on a single machine we do the following. Uses the same script sys.stdout.write("Finished job, checking results....\n") # Check the results for this job queue=Model_Queue.Queue_info() queue.check_result_serial(mstat, init, model, target_info) # Run Acorn if the solution looks ok and the resolution is good enough SOLUTION=False if mstat.MRPROGRAM == "MOLREP": if MODEL.good_solution_MOLREP or MODEL.marginal_solution_MOLREP: SOLUTION=True if mstat.MRPROGRAM == "PHASER": if MODEL.good_solution_PHASER or MODEL.marginal_solution_PHASER: SOLUTION=True if init.acorn_found and SOLUTION and init.keywords.USEACORN: if target_info.resolution <= init.keywords.ACORNRES: sys.stdout.write("##############################################################\n") sys.stdout.write("Running Acorn using output MTZ from Refmac to improve the map\n") sys.stdout.write("##############################################################\n") sys.stdout.write("\n") sys.stdout.write("Collected data resolution = %.3f Angstroms\n" % target_info.resolution) sys.stdout.write("\n") phase_imp=Phase_improve.PhaseImprove() # Make the building directory if os.path.exists(os.path.join(MODEL.model_directory, "building")) == False: os.mkdir(os.path.join(MODEL.model_directory, "building")) # Set the input PDB file for Acorn (experiment with this) #if init.keywords.XYZACORN = "REFINED": #MODEL.acorn_XYZINfile = MODEL.refmac_PDBfile # sys.stdout.write("Using PDB # Set the various file names if mstat.MRPROGRAM == "MOLREP": MODEL.acorn_XYZINfile = MODEL.refmac_molrep_PDBfile MODEL.acorn_MTZOUTfile = os.path.join(MODEL.model_directory, "building", MODEL.name + "_molrep_acorn_out.mtz") MODEL.acorn_logfile = os.path.join(MODEL.model_directory, "building", MODEL.name + "_molrep_acorn.log") if mstat.MRPROGRAM == "PHASER": MODEL.acorn_XYZINfile = MODEL.refmac_phaser_PDBfile MODEL.acorn_MTZOUTfile = os.path.join(MODEL.model_directory, "building", MODEL.name + "_phaser_acorn_out.mtz") MODEL.acorn_logfile = os.path.join(MODEL.model_directory, "building", MODEL.name + "_phaser_acorn.log") # Run acorn to calculate new phases if self.debug: sys.stdout.write("Running Acorn to calculate new phases...\n") sys.stdout.write("\n") # Set the ecalc output MTZ (original target or enantiomorphic) if init.keywords.ENANT and MODEL.enant_solution: target_info.ecalc_MTZOUTfile = target_info.enant_ecalc_MTZOUTfile else: target_info.ecalc_MTZOUTfile = target_info.target_ecalc_MTZOUTfile # Run Acorn phase_imp.run_acorn(init, mstat, target_info, MODEL) # Check the results from Acorn phase_imp.read_logfile(MODEL.acorn_logfile) # Get the final cc value and the no. of cycles used MODEL.acorn_CC_value = phase_imp.cc_value MODEL.acorn_cycles = phase_imp.no_cycles ### CPIRATE: ################################################################################################################# # Run Cpirate if the solution looks ok and the resolution is not high enough for Acorn NO_GOOD_SOLUTION=False if mstat.MRPROGRAM == "MOLREP": if MODEL.poor_solution_MOLREP or MODEL.marginal_solution_MOLREP: NO_GOOD_SOLUTION=True if mstat.MRPROGRAM == "PHASER": if MODEL.poor_solution_PHASER or MODEL.marginal_solution_PHASER: NO_GOOD_SOLUTION=True if init.cpirate_found and NO_GOOD_SOLUTION \ and init.keywords.USECPIRATE and mstat.MRPROGRAM == "PHASER": sys.stdout.write("##################################################################\n") sys.stdout.write("Running Cpirate using output MTZ from Phaser to improve the phases\n") sys.stdout.write("##################################################################\n") sys.stdout.write("\n") sys.stdout.write("Collected data resolution = %.3f Angstroms\n" % target_info.resolution) sys.stdout.write("\n") # Instantiate a cpirate job cp=MRBUMP_cpirate.Cpirate() # Make the directory if os.path.isdir(os.path.join(MODEL.model_directory, 'mr', 'build')) == False: os.mkdir(os.path.join(MODEL.model_directory, 'mr', 'build')) # Set the Cpirate logfile, command file and output MTZ file MODEL.setCpirateMTZfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'cpirate_' + MODEL.name + '.mtz')) MODEL.setCpirateLogfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'cpirate_' + MODEL.name + '.log')) MODEL.setCpirateCmdfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'cpirate_' + MODEL.name + '_commandline.txt')) # Set the log file and command file cp.setLogfile(MODEL.cpirate_logfile) cp.setCommandfile(MODEL.cpirate_cmdfile) # Set the Column labels for the phaser output HL coeffiecients (assume phaser has these as HLA, HLB,...) target_info.mtz_coldata['HLA'] = 'HLA' target_info.mtz_coldata['HLB'] = 'HLB' target_info.mtz_coldata['HLC'] = 'HLC' target_info.mtz_coldata['HLD'] = 'HLD' # Set up the keyword input for Cpirate cp.keywords["mtzin-ref"]=init.cpirate_MTZref_file cp.keywords["mtzin-wrk"]=MODEL.phaser_MTZfile cp.keywords["mtzout"]=MODEL.cpirate_MTZfile cp.keywords["colin-ref-fo"]="/*/*/[%s,%s]" % (init.cpirate_mtz_coldata['F'], init.cpirate_mtz_coldata['SIGF']) cp.keywords["colin-ref-hl"]="/*/*/[%s,%s,%s,%s]" % (init.cpirate_mtz_coldata['HLA'], init.cpirate_mtz_coldata['HLB'], \ init.cpirate_mtz_coldata['HLC'], init.cpirate_mtz_coldata['HLD']) cp.keywords["colin-wrk-fo"]="/*/*/[%s,%s]" % (target_info.mtz_coldata['F'], target_info.mtz_coldata['SIGF']) cp.keywords["colin-wrk-hl"]="/*/*/[%s,%s,%s,%s]" % (target_info.mtz_coldata['HLA'], target_info.mtz_coldata['HLB'], \ target_info.mtz_coldata['HLC'], target_info.mtz_coldata['HLD']) cp.keywords["colin-wrk-free"] = "/*/*/[%s]" % target_info.mtz_coldata['FREE'] cp.keywords["colout"] = "pirate" cp.keywords["ncycles"] = init.keywords.PIRCYC cp.keywords["unbias"] = True # Run cpirate cp.run() # Display location of Log and MTZ files from cpirate sys.stdout.write("Output Log file from cpirate written to:\n %s\n" % MODEL.cpirate_logfile) sys.stdout.write("\n") sys.stdout.write("Output MTZ file from cpirate written to:\n %s\n" % MODEL.cpirate_MTZfile) sys.stdout.write("\n") ############################################################################################################################## ### BUCC_REFMAC: ############################################################################################################# # Run CCP4_pipeline_simple to cycle buccaneer and refmac to build the model if init.cpirate_found and NO_GOOD_SOLUTION \ and init.keywords.USECPIRATE and mstat.MRPROGRAM == "PHASER": cbr=MRBUMP_buccaneer_ref.Buc_Ref() cbr.debug = True # Make the directory if os.path.isdir(os.path.join(MODEL.model_directory, 'mr', 'build')) == False: os.mkdir(os.path.join(MODEL.model_directory, 'mr', 'build')) # Set the log file, the command file and any other files MODEL.setbucc_ref_logfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'buccref_' + MODEL.name + '.log')) MODEL.setbucc_ref_cmdfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'buccref_' + MODEL.name + '.com')) MODEL.setbucc_MTZINfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'bucc_' + MODEL.name + '_in.mtz')) MODEL.setbucc_MTZOUTfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'bucc_' + MODEL.name + '_out.mtz')) MODEL.setbucc_refmac_PDBOUTfile(os.path.join(MODEL.model_directory, 'mr', 'build', 'bucc_refmac_' + MODEL.name + '_out.pdb')) # Copy the output MTZ file from cpirate to the input MTZ file for the first loop os.copyfile(MODEL.cpirate_MTZfile, MODEL.bucc_MTZINfile) cbr.setLogfile(MODEL.bucc_ref_logfile) cbr.setCommandfile(MODEL.bucc_ref_cmdfile) cbr.setbucc_title("Mrbump buccaneer run") cbr.setbucc_SEQIN(target_info.seqfile) cbr.setbucc_workMTZIN(MODEL.bucc_MTZINfile) cbr.setbucc_workPDBIN(MODEL.bucc_refmac_PDBOUTfile) cbr.setbucc_workPDBOUT(MODEL.bucc_MTZOUTfile) cbr.bucc_workCol["FP"]=target_info.mtz_coldata["F"] cbr.bucc_workCol["SIGFP"]=target_info.mtz_coldata["SIGF"] cbr.bucc_workCol["HLA"]=target_info.mtz_coldata["HLA"] cbr.bucc_workCol["HLB"]=target_info.mtz_coldata["HLB"] cbr.bucc_workCol["HLC"]=target_info.mtz_coldata["HLC"] cbr.bucc_workCol["HLD"]=target_info.mtz_coldata["HLD"] cbr.bucc_workCol["PHCOMB"]="PHCOMB" cbr.bucc_workCol["FOM"]="FOM" cbr.bucc_cycles.append(3) for i in range(cbr.ncycles-1): cbr.bucc_cycles.append(1) cbr.bucc_seqReliability.append(0.95) for i in range(cbr.ncycles-1): cbr.bucc_seqReliability.append(0.95) cbr.setbucc_Resolution(2.0) cbr.setrefmac_title("Bucc Refmac run") cbr.setrefmac_MTZIN(MODEL.cpirate_MTZfile) cbr.setrefmac_PDBIN(MODEL.bucc_MTZOUTfile) cbr.setrefmac_MTZOUT(MODEL.bucc_MTZINfile) cbr.setrefmac_PDBOUT(MODEL.bucc_refmac_PDBOUTfile) cbr.refmac_Col["FP"]=target_info.mtz_coldata["F"] cbr.refmac_Col["SIGFP"]=target_info.mtz_coldata["SIGF"] cbr.refmac_Col["HLA"]=target_info.mtz_coldata["HLA"] cbr.refmac_Col["HLB"]=target_info.mtz_coldata["HLB"] cbr.refmac_Col["HLC"]=target_info.mtz_coldata["HLC"] cbr.refmac_Col["HLD"]=target_info.mtz_coldata["HLD"] cbr.run() ############################################################################################################################## # If a solution is found output the results and exit from the MRPROGRAM loop if mstat.solution_found: if init.keywords.TRYALL == False: mstat.mr_results.copy_solution_files(mstat, os.path.join(mstat.results_dir, 'solution')) mstat.mr_results.display_results(mstat, init, target_info) break ############################################################################################## ############################################################################################## # Jsrview ############################################################################################## if init.keywords.JSRVIEW: if loop_count==0 and FIRSTPASS: print pyrvapi.rvapi_add_tree_widget ( "tree1","MR Results","tab5",0,0,1,1 ), if FIRSTPASS: print pyrvapi.rvapi_add_section ( "tree_sec%d" % (loop_count+1),"Details for model: %s" % str(model),"tree1",0,0,1,1,True ), print pyrvapi.rvapi_set_tree_node ( "tree1","tree_sec%d" % (loop_count+1),str(model),"auto","" ), if "MOLREP" in init.keywords.MR_PROGRAM_LIST: print pyrvapi.rvapi_add_section ( "tree_sec%d1" % (loop_count+1),"%s using Molrep" % str(model),"tree1",0,0,1,1,True ), print pyrvapi.rvapi_set_tree_node ( "tree1","tree_sec%d1" % (loop_count+1),"Molrep","auto","tree_sec%d" % (loop_count+1)), if "PHASER" in init.keywords.MR_PROGRAM_LIST: print pyrvapi.rvapi_add_section ( "tree_sec%d2" % (loop_count+1),"%s using Phaser" % str(model),"tree1",0,0,1,1,True ), print pyrvapi.rvapi_set_tree_node ( "tree1","tree_sec%d2" % (loop_count+1),"Phaser","auto","tree_sec%d" % (loop_count+1)), if FIRSTPASS: print pyrvapi.rvapi_add_table1 ( "tree_sec%d/model_table%d" % (loop_count+1, loop_count+1), "Model details", 1, 0, 1, 1, True), print pyrvapi.rvapi_put_vert_theader ( "model_table%d" % (loop_count+1), "Name:", "Tooltip 1", 0), print pyrvapi.rvapi_put_table_string ( "model_table%d" % (loop_count+1), str(model), 0, 0), print pyrvapi.rvapi_put_vert_theader ( "model_table%d" % (loop_count+1), "Source:", "Tooltip 1", 1), print pyrvapi.rvapi_put_table_string ( "model_table%d" % (loop_count+1), mstat.model_list[model].source, 1, 0), print pyrvapi.rvapi_put_vert_theader ( "model_table%d" % (loop_count+1), "Parent PDB:", "Tooltip 1", 2), print pyrvapi.rvapi_put_table_string ( "model_table%d" % (loop_count+1), mstat.model_list[model].PDBName, 2, 0), print pyrvapi.rvapi_put_vert_theader ( "model_table%d" % (loop_count+1), "Sequence ID:", "Tooltip 1", 3), print pyrvapi.rvapi_put_table_string ( "model_table%d" % (loop_count+1), str(mstat.model_list[model].seqID), 3, 0), FIRSTPASS=False if mstat.MRPROGRAM == "MOLREP": print pyrvapi.rvapi_add_data1("tree_sec%d1/dat%d1" % (loop_count+1, loop_count+1), "Molrep solution structure", mstat.model_list[model].molrep_PDBfile, "xyz", 2, 0, 1, 1, False), print pyrvapi.rvapi_append_to_data("dat%d1" % (loop_count+1), mstat.model_list[model].molrep_MTZfile, "hkl:map"), print mstat.model_list[model].molrep_PDBfile print pyrvapi.rvapi_flush(), if mstat.MRPROGRAM == "PHASER": print pyrvapi.rvapi_add_data1("tree_sec%d2/dat%d2" % (loop_count+1, loop_count+1), "Phaser solution structure and electron density", mstat.model_list[model].phaser_PDBfile, "xyz", 2, 0, 1, 1, False), print pyrvapi.rvapi_append_to_data("dat%d2" % (loop_count+1), mstat.model_list[model].phaser_MTZfile, "hkl:map"), print pyrvapi.rvapi_flush(), ############################################################################################## # Increment the counter mstat.mr_counter=mstat.mr_counter+1 mstat.model_list[model]=MODEL if init.keywords.CLUSTER == False: # Print out the summary of results so far, but only for non-parallel best=MRBUMP_writebest.BestLog() best.write_results_log(init, mstat) mstat.sorted_soln_list=best.sorted_soln_list sys.stdout.write(best.report) # If we have submitted enough jobs, then exit if model_count>=job_limit: break loop_count=loop_count+1 job_id_log.close() def print_job_details(self, MODEL, mstat, init): """ A function to output the details of the MR job to be submitted for execution. """ # Print some details about this job sys.stdout.write("*********************************************************************************\n") sys.stdout.write("*********************************************************************************\n") sys.stdout.write("*********************************************************************************\n") sys.stdout.write("\n") sys.stdout.write("#####################################################\n") sys.stdout.write("Template Model %s: %s\n" % (MODEL.MR_job_number, MODEL.name)) sys.stdout.write("#####################################################\n") sys.stdout.write("\n") sys.stdout.write("Working directory:\n %s\n" % MODEL.model_directory) # List the models being used as input to the MR job if MODEL.num_per_ensem > 1: sys.stdout.write("Input search models: \n") for i in range(MODEL.num_per_ensem): if init.keywords.MDLCHAINSAW: sys.stdout.write(" " + MODEL.PDBfile[i] + "\n") else: sys.stdout.write(" " + MODEL.PDBfile[i] + "\n") sys.stdout.write(" Sequence ID: %.3f" % MODEL.seqID[i]) if MODEL.rms[i] != 0.0: sys.stdout.write(" RMS value: %.3f" % MODEL.rms[i]) sys.stdout.write("\n") else: sys.stdout.write("Input search model:\n %s\n" % MODEL.PDBfile[0]) if MODEL.resolution_low == 0.0 and MODEL.resolution_high == 0.0: sys.stdout.write("Resolution Range for this model: Not Known\n") else: sys.stdout.write("Resolution Range for this model: %.2lf - %.2lf Angstroms\n" % (MODEL.resolution_low, MODEL.resolution_high)) sys.stdout.write("Search model type: %s\n" % MODEL.type) sys.stdout.write("Molecular Replacement Program: %s\n" % mstat.MRPROGRAM) sys.stdout.write("Refinement Program: Refmac5\n") sys.stdout.write("\n") # FIXED components if init.keywords.FIXED: sys.stdout.write("Fixed component(s) being used in search:\n") for i in init.keywords.fixed_list.keys(): sys.stdout.write("File name: %s, Seq ID: %.3f\n" \ % (init.keywords.fixed_list[i].filename, init.keywords.fixed_list[i].identity)) if mstat.MRPROGRAM == "MOLREP" and init.keywords.fixedfile_count > 1: sys.stdout.write("For Molrep these have been merged into the PDB file:\n %s\n" % init.molrep_fixed_PDBfile) sys.stdout.write("\n") def sort_model_list(self, mstat): """ Sort the models in the list according to sequence identity with the target structure. """ for name in mstat.sorted_MR_list: for model in mstat.model_list.keys(): if mstat.model_list[model].chain_source == name and model not in mstat.sorted_model_list: mstat.sorted_model_list.append(model)