Python Example Scripts
From Phaserwiki
See Python Interface for introduction to running phaser as a python library.
Example scripts for the most popular modes of running Phaser.
Reading MTZ Files for Molecular Replacement
Example script for reading data from MTZ file beta_blip.mtz.
Note that by default reflections are sorted into resolution order upon reading, to achieve a performance gain in the molecular replacement routines. If reflections are not being read from an MTZ file with this script, reflections should be pre-sorted into resolution order to achieve the same performance gain. Sorting is turned off with the setSORT(False) function.
#beta_blip_data.py
from phaser import *
i = InputMR_DAT()
HKLIN = "beta_blip.mtz"
F = "Fobs"
SIGF = "Sigma"
i.setHKLI(HKLIN)
i.setLABI_F_SIGF(F,SIGF)
i.setMUTE(True)
r = runMR_DAT(i)
print r.logfile()
if r.Success():
hkl = r.getMiller()
fobs = r.getF()
sigma = r.getSIGF()
nrefl = min(10,hkl.size())
print "Data read from: " , HKLIN
print "First ", nrefl , " reflections"
print "%4s %4s %4s %10s %10s" % ("H","K","L",F,SIGF)
for i in range(0,nrefl):
print "%4d %4d %4d %10.4f %10.4f" % \
(hkl[i][0],hkl[i][1],hkl[i][2],fobs[i],sigma[i])
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Automated Molecular Replacement
Example script for automated structure solution of BETA-BLIP
beta_blip_auto.py
from phaser import *
i = InputMR_DAT()
i.setHKLI("beta_blip.mtz")
i.setLABI("Fobs","Sigma")
i.setHIRES(6.0)
i.setMUTE(True)
r = runMR_DAT(i)
if r.Success():
i = InputMR_AUTO()
i.setSPAC_HALL(r.getSpaceGroupHall())
i.setCELL6(r.getUnitCell())
i.setREFL(r.getMiller(),r.getFobs(),r.getSigFobs())
i.setROOT("beta_blip_auto")
i.addENSE_PDB_ID("beta","beta.pdb",1.0)
i.addENSE_PDB_ID("blip","blip.pdb",1.0)
i.addCOMP_PROT_MW_NUM(28853,1)
i.addCOMP_PROT_MW_NUM(17522,1)
i.addSEAR_ENSE_NUM("beta",1)
i.addSEAR_ENSE_NUM("blip",1)
i.setMUTE(True)
del(r)
r = runMR_AUTO(i)
if r.Success():
if r.foundSolutions() :
print "Phaser has found MR solutions"
print "Top LLG = %f" % r.getTopLLG()
print "Top PDB file = %s" % r.getTopPdbFile()
else:
print "Phaser has not found any MR solutions"
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Reading MTZ Files for Experimental Phasing
Example script for reading SAD data from MTZ file S-insulin.mtz
insulin_data.py
from phaser import *
i = InputEP_DAT()
HKLIN = "S-insulin.mtz"
xtalid = "insulin"
waveid = "cuka"
i.setHKLI(HKLIN)
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")
i.setMUTE(True)
r = runEP_DAT(i)
if r.Success():
hkl = r.getMiller()
Fpos = r.getFpos(xtalid,waveid)
Ppos = r.getPpos(xtalid,waveid)
Fneg = r.getFneg(xtalid,waveid)
Pneg = r.getPneg(xtalid,waveid)
print "Data read from: " , HKLIN
print "Spacegroup Name (Hall symbol) = %s (%s)" % \
(r.getSpaceGroupName(), r.getSpaceGroupHall())
print "Unitcell = " , r.getUnitCell()
nrefl = min(10,hkl.size())
print "First ", nrefl , " reflections with anomalous differences"
print "%4s %4s %4s %10s %10s %10s" % ("H","K","L","F(+)","F(-)","D")
i = 0
r = 0
while r < nrefl:
if Ppos[i] and Pneg[i] :
D = abs(Fpos[i]-Fneg[i])
if D > 0
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \
(hkl[i][0],hkl[i][1],hkl[i][2],Fpos[i],Fneg[i],D)
r=r+1
i=i+1
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Automated Experimental Phasing
Example script for SAD phasing for insulin
#insulin_sad.py
from phaser import *
from cctbx import xray
i = InputEP_DAT()
HKLIN = "S-insulin.mtz"
xtalid = "insulin"
waveid = "cuka"
i.setHKLI(HKLIN)
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")
i.setMUTE(True)
r = runEP_DAT(i)
if r.Success():
hkl = r.getMiller()
Fpos = r.getFpos(xtalid,waveid)
Spos = r.getSIGFpos(xtalid,waveid)
Ppos = r.getPpos(xtalid,waveid)
Fneg = r.getFneg(xtalid,waveid)
Sneg = r.getSIGFneg(xtalid,waveid)
Pneg = r.getPneg(xtalid,waveid)
i = InputEP_AUTO()
i.setSPAC_HALL(r.getSpaceGroupHall())
i.setCELL(r.getUnitCell())
i.setCRYS_MILLER(hkl)
i.addCRYS_ANOM_DATA(xtalid,waveid,Fpos,Spos,Ppos,Fneg,Sneg,Pneg)
i.setATOM_PDB(xtalid,"S-insulin_hyss.pdb")
i.setLLGC_CRYS_COMPLETE(xtalid,True)
i.addLLGC_CRYS_SCAT_ELEMENT(xtalid,"S")
i.addCOMP_PROT_FASTA_NUM("S-insulin.seq",1.)
i.setHKLO(False)
i.setSCRI(False)
i.setXYZO(False)
i.setMUTE(True)
r = runEP_AUTO(i)
if r.Success():
print "SAD phasing"
print "Data read from: " , HKLIN
print "Data output to : " , r.getMtzFile()
print "Spacegroup Name (Hall symbol) = %s (%s)" % \
(r.getSpaceGroupName(), r.getSpaceGroupHall())
print "Unitcell = " , r.getUnitCell()
print "LogLikelihood = " , r.getLogLikelihood()
atom = r.getAtoms(xtalid)
print atom.size(), " refined atoms"
print "%5s %10s %10s %10s %10s %10s" % \
("atom","x","y","z","occupancy","u-iso")
for i in range(0,atom.size()):
print "%5s %10.4f %10.4f %10.4f %10.4f %10.4f" % \
(atom[i].scattering_type,atom[i].site[0],atom[i].site[1],atom[i].site[2],atom[i].occupancy,atom[i].u_iso)
hkl = r.getMiller();
fwt = r.getFWT()
phwt = r.getPHWT()
fom = r.getFOM()
nrefl = min(10,hkl.size())
print "First ", nrefl , " reflections"
print "%4s %4s %4s %10s %10s %10s" % \
("H","K","L","FWT","PHWT","FOM")
for i in range(0,nrefl):
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \
(hkl[i][0],hkl[i][1],hkl[i][2],fwt[i],phwt[i],fom[i])
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Anisotropy Correction
Example script script for anisotropy correction of BETA-BLIP data
#beta_blip_ano.py
from phaser import *
i = InputMR_DAT()
HKLIn = "beta_blip.mtz"
F = "Fobs"
SIGF = "Sigma"
i.setHKLI(HKLIn)
i.setLABI(F,SIGF)
i.setMUTE(True)
r = runMR_DAT(i)
if r.Success():
i = InputANO()
i.setSPAC_HALL(r.getSpaceGroupHall())
i.setCELL6(r.getUnitCell())
i.setREFL(r.getMiller(),r.getFobs(),r.getSigFobs())
i.setREFL_ID(F,SIGF)
i.setHKLI(HKLIn)
i.setROOT("beta_blip_ano")
i.setMUTE(True)
del(r)
r = runANO(i)
if r.Success():
print "Anisotropy Correction"
print "Data read from: " , HKLIn
print "Data output to : " , r.getMtzFile()
print "Spacegroup Name (Hall symbol) = %s (%s)" % \
(r.getSpaceGroupName(), r.getSpaceGroupHall())
print "Unitcell = " , r.getUnitCell()
print "Principal components = " , r.getEigenBs()
print "Range of principal components = " , r.getAnisoDeltaB()
print "Wilson Scale = " , r.getWilsonK()
print "Wilson B-factor = " , r.getWilsonB()
hkl = r.getMiller();
f = r.getF()
sigf = r.getSIGF()
f_iso = r.getCorrectedF()
sigf_iso = r.getCorrectedSIGF()
corr = r.getCorrection()
nrefl = min(10,hkl.size())
print "First ", nrefl , " reflections"
print "%4s %4s %4s %10s %10s %10s %10s %10s" % \
("H","K","L",F,SIGF,r.getLaboutF(),r.getLaboutSIGF(),"Corr\'n")
for i in range(0,nrefl):
print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \
(hkl[i][0],hkl[i][1],hkl[i][2],f[i],sigf[i],f_iso[i],sigf_iso[i],corr[i])
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Cell Content Analysis
Example script for cell content analysis of BETA-BLIP
#beta_blip_cca.py
from phaser import *
i = InputMR_DAT()
HKLIN = "beta_blip.mtz"
F = "Fobs"
SIGF = "Sigma"
i.setHKLI(HKLIN)
i.setLABI(F,SIGF)
i.setMUTE(True)
r = runMR_DAT(i)
if r.Success():
i = InputCCA()
i.setSPAC_HALL(r.getSpaceGroupHall())
i.setCELL6(r.getUnitCell())
i.addCOMP_PROT_MW_NUM(28853,1)
i.addCOMP_PROT_MW_NUM(17522,1)
i.setMUTE(True)
del(r)
r = runCCA(i)
if r.Success():
print "Cell Content Analysis"
print "Molecular weight of assembly = " , r.getAssemblyMW()
print "Best Z value = " , r.getBestZ()
print "Best VM value = " , r.getBestVM()
print "Probability of Best VM = " , r.getBestProb()
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Translational NCS Analysis
Example script for translational NCS analysis of BETA-BLIP
#beta_blip_ncs.py
from phaser import *
i = InputMR_DAT()
HKLIN = "beta_blip.mtz"
F = "Fobs"
SIGF = "Sigma"
i.setHKLI(HKLIN)
i.setLABI(F,SIGF)
i.setMUTE(True)
r = runMR_DAT(i)
if r.Success():
i = InputNCS()
i.setSPAC_HALL(r.getSpaceGroupHall())
i.setCELL6(r.getUnitCell())
i.setREFL(r.getMiller(),r.getF(),r.getSIGF())
i.addCOMP_PROT_MW_NUM(28853,1)
i.addCOMP_PROT_MW_NUM(17522,1)
i.setMUTE(True)
del(r)
r = runNCS(i)
if r.Success():
print "Translational NCS analysis"
print "Translational NCS present = ", r.hasTNCS()
if r.hasTNCS():
print "Translational NCS vecor = ", r.hasTNCS()
print "Twinning alpha = ", r.getTwinAlpha()
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Normal Mode Analysis
Example script for normal mode analysis of BETA-BLIP. Note that the space group and unit cell are not required, and so the MTZ file does not need to be read to extract these parameters.
#beta_nma.py
from phaser import *
i = InputNMA()
i.setROOT("beta_nma")
i.addENSE_PDB_ID("beta","beta.pdb",1.0)
i.setNMAP_MODES([7,10])
i.setNMAP_FORWARD()
i.setMUTE(True)
r = runNMA(i)
if r.Success():
print "Normal Mode Analysis"
for i in range(0,r.getNum()):
print "PDB file = ", r.getPdbFile(i)
displacement = r.getDisplacements(i)
mode = r.getModes(i)
for j in range(0,mode.size()):
print " Mode = " , mode[j], " Displacement = ", displacement[j]
else:
print "Job exit status FAILURE"
print r.ErrorName(), "ERROR :", r.ErrorMessage()
Logfile Handling
Example of how to redirect phaser output to a python string for real-time viewing of output, but not via standard output. Output to standard out is silenced with setMUTE(True).
beta_blip_logfile.py
from phaser import *
from cStringIO import StringIO
i = InputMR_DAT()
i.setHKLI("beta_blip.mtz")
i.setLABI("Fobs","Sigma")
i.setMUTE(True)
o = Output()
redirect_str = StringIO()
o.setPackagePhenix(file_object=redirect_str)
r = runMR_DAT(i,o)
