Difference between revisions of "Python Example Scripts"

From Phaserwiki
(→‎Automated Molecular Replacement)
(→‎Anisotropy Correction: Change example script to include the new resharpen Boolean, set by default to True)
 
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Line 1: Line 1:
 
<div style="margin-left: 25px; float: right;">__TOC__</div>
 
<div style="margin-left: 25px; float: right;">__TOC__</div>
  
−
Example scripts for the most popular modes of running Phaser.
+
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==
 
== Reading MTZ Files for Molecular Replacement==
Line 7: Line 9:
  
 
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.
 
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.
−
<pre>
+
 
 
       #beta_blip_data.py
 
       #beta_blip_data.py
 
       from phaser import *
 
       from phaser import *
 
       i = InputMR_DAT()
 
       i = InputMR_DAT()
−
       HKLIN = "beta_blip.mtz"
+
       HKLIN = "beta_blip_P3221.mtz"
−
      F = "Fobs"
 
−
      SIGF = "Sigma"
 
 
       i.setHKLI(HKLIN)
 
       i.setHKLI(HKLIN)
−
      i.setLABI(F,SIGF)
 
 
       i.setMUTE(True)
 
       i.setMUTE(True)
 
       r = runMR_DAT(i)
 
       r = runMR_DAT(i)
Line 25: Line 24:
 
         nrefl = min(10,hkl.size())
 
         nrefl = min(10,hkl.size())
 
         print "Data read from: " , HKLIN
 
         print "Data read from: " , HKLIN
−
        print "Spacegroup Name (Hall symbol) = %s (%s)" % \
 
−
          (r.getSpaceGroupName(), r.getSpaceGroupHall())
 
−
        print "Unitcell = " , r.getUnitCell()
 
 
         print "First ", nrefl , " reflections"
 
         print "First ", nrefl , " reflections"
 
         print "%4s %4s %4s %10s %10s" % ("H","K","L",F,SIGF)
 
         print "%4s %4s %4s %10s %10s" % ("H","K","L",F,SIGF)
Line 36: Line 32:
 
         print "Job exit status FAILURE"
 
         print "Job exit status FAILURE"
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
−
</pre>
 
−
 
  
 
==Automated Molecular Replacement==
 
==Automated Molecular Replacement==
 
Example script for automated structure solution of BETA-BLIP
 
Example script for automated structure solution of BETA-BLIP
−
<pre>
+
 
−
       beta_blip_auto.py
+
       #beta_blip_auto.py
 
       from phaser import *
 
       from phaser import *
 
       i = InputMR_DAT()
 
       i = InputMR_DAT()
−
       i.setHKLI("beta_blip.mtz")
+
       i.setHKLI("beta_blip_P3221.mtz")
−
      i.setLABI("Fobs","Sigma")
 
 
       i.setHIRES(6.0)
 
       i.setHIRES(6.0)
 
       i.setMUTE(True)
 
       i.setMUTE(True)
Line 52: Line 45:
 
       if r.Success():
 
       if r.Success():
 
         i = InputMR_AUTO()
 
         i = InputMR_AUTO()
−
         i.setSPAC_HALL(r.getSpaceGroupHall())
+
         i.setREFL_DATA(r.getREFL_DATA())
−
        i.setCELL(r.getUnitCell())
 
−
        i.setREFL(r.getMiller(),r.getFobs(),r.getSigFobs())
 
 
         i.setROOT("beta_blip_auto")
 
         i.setROOT("beta_blip_auto")
 
         i.addENSE_PDB_ID("beta","beta.pdb",1.0)
 
         i.addENSE_PDB_ID("beta","beta.pdb",1.0)
Line 70: Line 61:
 
             print "Top LLG = %f" % r.getTopLLG()
 
             print "Top LLG = %f" % r.getTopLLG()
 
             print "Top PDB file = %s" % r.getTopPdbFile()
 
             print "Top PDB file = %s" % r.getTopPdbFile()
−
            print "Spacegroup Name (Hall symbol) = %s (%s)" % \
 
−
              (r.getSpaceGroupName(), r.getSpaceGroupHall())
 
 
           else:
 
           else:
 
             print "Phaser has not found any MR solutions"
 
             print "Phaser has not found any MR solutions"
Line 80: Line 69:
 
         print "Job exit status FAILURE"
 
         print "Job exit status FAILURE"
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
−
</pre>
 
  
 
==Reading MTZ Files for Experimental Phasing==
 
==Reading MTZ Files for Experimental Phasing==
 
Example script for reading SAD data from MTZ file S-insulin.mtz
 
Example script for reading SAD data from MTZ file S-insulin.mtz
 
<pre>
 
<pre>
−
       insulin_data.py
+
       #insulin_data.py
 
       from phaser import *
 
       from phaser import *
 
       i = InputEP_DAT()
 
       i = InputEP_DAT()
Line 122: Line 110:
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
 
</pre>
 
</pre>
 +
 
==Automated Experimental Phasing==
 
==Automated Experimental Phasing==
  
Line 198: Line 187:
 
Example script script for anisotropy correction of BETA-BLIP data
 
Example script script for anisotropy correction of BETA-BLIP data
 
        
 
        
−
<pre>
 
 
       #beta_blip_ano.py
 
       #beta_blip_ano.py
 
       from phaser import *
 
       from phaser import *
 
       i = InputMR_DAT()
 
       i = InputMR_DAT()
−
       HKLIn = "beta_blip.mtz"
+
       HKLIn = "beta_blip_P3221.mtz"
−
      F = "Fobs"
 
−
      SIGF = "Sigma"
 
 
       i.setHKLI(HKLIn)
 
       i.setHKLI(HKLIn)
−
      i.setLABI(F,SIGF)
 
 
       i.setMUTE(True)
 
       i.setMUTE(True)
 
       r = runMR_DAT(i)
 
       r = runMR_DAT(i)
Line 212: Line 197:
 
         i = InputANO()
 
         i = InputANO()
 
         i.setSPAC_HALL(r.getSpaceGroupHall())
 
         i.setSPAC_HALL(r.getSpaceGroupHall())
−
         i.setCELL(r.getUnitCell())
+
         i.setREFL_DATA(r.getREFL_DATA())
−
        i.setREFL(r.getMiller(),r.getFobs(),r.getSigFobs())
 
−
        i.setREFL_ID(F,SIGF)
 
−
        i.setHKLI(HKLIn)
 
 
         i.setROOT("beta_blip_ano")
 
         i.setROOT("beta_blip_ano")
 
         i.setMUTE(True)
 
         i.setMUTE(True)
Line 234: Line 216:
 
           f = r.getF()
 
           f = r.getF()
 
           sigf = r.getSIGF()
 
           sigf = r.getSIGF()
−
           f_iso = r.getCorrectedF()
+
           f_iso = r.getCorrectedF(True)
−
           sigf_iso = r.getCorrectedSIGF()
+
           sigf_iso = r.getCorrectedSIGF(True)
−
           corr = r.getCorrection()
+
           corr = r.getCorrection(True)
 
           nrefl = min(10,hkl.size())
 
           nrefl = min(10,hkl.size())
 
           print "First ", nrefl , " reflections"
 
           print "First ", nrefl , " reflections"
 
           print "%4s %4s %4s %10s %10s %10s %10s %10s" % \
 
           print "%4s %4s %4s %10s %10s %10s %10s %10s" % \
−
             ("H","K","L",F,SIGF,r.getLaboutF(),r.getLaboutSIGF(),"Corr\'n")
+
             ("H","K","L","F","SIGF",r.getLaboutF(),r.getLaboutSIGF(),"Corr\'n")
 
           for i in range(0,nrefl):
 
           for i in range(0,nrefl):
 
             print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \
 
             print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \
Line 250: Line 232:
 
         print "Job exit status FAILURE"
 
         print "Job exit status FAILURE"
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
 
         print r.ErrorName(), "ERROR :", r.ErrorMessage()
−
</pre>
 
  
 
==Cell Content Analysis==
 
==Cell Content Analysis==
Line 262: Line 243:
 
       SIGF = "Sigma"
 
       SIGF = "Sigma"
 
       i.setHKLI(HKLIN)
 
       i.setHKLI(HKLIN)
−
       i.setLABI(F,SIGF)
+
       i.setLABI_F_SIGF(F,SIGF)
 
       i.setMUTE(True)
 
       i.setMUTE(True)
 
       r = runMR_DAT(i)
 
       r = runMR_DAT(i)
 
       if r.Success():
 
       if r.Success():
−
        if r.Success():
 
 
         i = InputCCA()
 
         i = InputCCA()
 
         i.setSPAC_HALL(r.getSpaceGroupHall())
 
         i.setSPAC_HALL(r.getSpaceGroupHall())
−
         i.setCELL(r.getUnitCell())
+
         i.setCELL6(r.getUnitCell())
 
         i.addCOMP_PROT_MW_NUM(28853,1)
 
         i.addCOMP_PROT_MW_NUM(28853,1)
 
         i.addCOMP_PROT_MW_NUM(17522,1)
 
         i.addCOMP_PROT_MW_NUM(17522,1)
Line 281: Line 261:
 
           print "Best VM value = " , r.getBestVM()
 
           print "Best VM value = " , r.getBestVM()
 
           print "Probability of Best VM = " , r.getBestProb()
 
           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()
 +
</pre>
 +
 +
==Translational NCS Analysis==
 +
Example script for translational NCS analysis of BETA-BLIP
 +
<pre>
 +
      #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(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_F_SIGF(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:
 
         else:
 
           print "Job exit status FAILURE"
 
           print "Job exit status FAILURE"
Line 297: Line 314:
 
       i.setROOT("beta_nma")
 
       i.setROOT("beta_nma")
 
       i.addENSE_PDB_ID("beta","beta.pdb",1.0)
 
       i.addENSE_PDB_ID("beta","beta.pdb",1.0)
−
       i.setNMAP_MODES([7,10])
+
       i.addNMA_MODE(4)
−
       i.setNMAP_FORWARD()
+
       i.setPERT_RMS_DIRE("FORWARD")
 
       i.setMUTE(True)
 
       i.setMUTE(True)
−
       r = runNMA(i)
+
       r = runNMAXYZ(i)
 
       if r.Success():
 
       if r.Success():
 
         print "Normal Mode Analysis"
 
         print "Normal Mode Analysis"
Line 323: Line 340:
 
       i = InputMR_DAT()
 
       i = InputMR_DAT()
 
       i.setHKLI("beta_blip.mtz")
 
       i.setHKLI("beta_blip.mtz")
−
       i.setLABI("Fobs","Sigma")
+
       i.setLABI_F_SIGF("Fobs","Sigma")
 
       i.setMUTE(True)
 
       i.setMUTE(True)
 
       o = Output()
 
       o = Output()

Latest revision as of 10:14, 12 December 2017

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_P3221.mtz"
     i.setHKLI(HKLIN)
     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_P3221.mtz")
     i.setHIRES(6.0)
     i.setMUTE(True)
     r = runMR_DAT(i)
     if r.Success():
       i = InputMR_AUTO()
       i.setREFL_DATA(r.getREFL_DATA())
       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_P3221.mtz"
     i.setHKLI(HKLIn)
     i.setMUTE(True)
     r = runMR_DAT(i)
     if r.Success():
       i = InputANO()
       i.setSPAC_HALL(r.getSpaceGroupHall())
       i.setREFL_DATA(r.getREFL_DATA())
       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(True)
         sigf_iso = r.getCorrectedSIGF(True)
         corr = r.getCorrection(True)
         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(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(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_F_SIGF(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.addNMA_MODE(4)
      i.setPERT_RMS_DIRE("FORWARD")
      i.setMUTE(True)
      r = runNMAXYZ(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_F_SIGF("Fobs","Sigma")
      i.setMUTE(True)
      o = Output()
      redirect_str = StringIO()
      o.setPackagePhenix(file_object=redirect_str)
      r = runMR_DAT(i,o)
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