Python Example Scripts - Revision history

Randy: /* Anisotropy Correction */ Change example script to include the new resharpen Boolean, set by default to True

2017-12-12T10:14:47Z

‎Anisotropy Correction: Change example script to include the new resharpen Boolean, set by default to True

2016-11-25T17:26:29Z

‎Anisotropy Correction

2016-11-25T17:20:37Z

‎Reading MTZ Files for Molecular Replacement

2016-11-25T17:20:18Z

‎Automated Molecular Replacement

2016-11-25T17:14:31Z

‎Reading MTZ Files for Molecular Replacement

2015-11-04T20:38:14Z

‎Normal Mode Analysis: Fix syntax for NMA, but this still crashes because the modes and the pdb files are not in one-to-one correspondence.

2015-11-03T21:33:50Z

‎Anisotropy Correction: Change setREFL_ID to setLABI_F_SIGF

2015-11-03T21:09:51Z

‎Translational NCS Analysis: Change setREFL to setREFL_F_SIGF

2015-11-03T21:02:05Z

‎Anisotropy Correction: Change setREFL to setREFL_F_SIGF

2015-11-03T21:01:22Z

‎Reading MTZ Files for Experimental Phasing: Comment out name of script in script

@@ Line 216: / Line 216: @@
            f = r.getF()
            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())
            print "First ", nrefl , " reflections"

@@ Line 187: / Line 187: @@
 Example script script for anisotropy correction of BETA-BLIP data
        #beta_blip_ano.py
        from phaser import *
        i = InputMR_DAT()
-       HKLIn = "beta_blip.mtz"
+       HKLIn = "beta_blip_P3221.mtz"
        i.setHKLI(HKLIn)
        i.setMUTE(True)
        r = runMR_DAT(i)
@@ Line 201: / Line 197: @@
          i = InputANO()
          i.setSPAC_HALL(r.getSpaceGroupHall())
-         i.setCELL6(r.getUnitCell())
+         i.setREFL_DATA(r.getREFL_DATA())
          i.setROOT("beta_blip_ano")
          i.setMUTE(True)
@@ Line 229: / Line 222: @@
            print "First ", nrefl , " reflections"
            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):
              print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \
@@ Line 239: / Line 232: @@
          print "Job exit status FAILURE"
          print r.ErrorName(), "ERROR :", r.ErrorMessage()
 ==Cell Content Analysis==

@@ Line 13: / Line 13: @@
        from phaser import *
        i = InputMR_DAT()
-       HKLIN = "beta_blip.mtz"
+       HKLIN = "beta_blip_P3221.mtz"
        i.setHKLI(HKLIN)
        i.setMUTE(True)

@@ Line 35: / Line 35: @@
 ==Automated Molecular Replacement==
 Example script for automated structure solution of BETA-BLIP
-<pre>
        #beta_blip_auto.py
        from phaser import *
        i = InputMR_DAT()
-       i.setHKLI("beta_blip.mtz")
+       i.setHKLI("beta_blip_P3221.mtz")
        i.setHIRES(6.0)
        i.setMUTE(True)
@@ Line 46: / Line 45: @@
        if r.Success():
          i = InputMR_AUTO()
-         i.setSPAC_HALL(r.getSpaceGroupHall())
+         i.setREFL_DATA(r.getREFL_DATA())
          i.setROOT("beta_blip_auto")
          i.addENSE_PDB_ID("beta","beta.pdb",1.0)
@@ Line 72: / Line 69: @@
          print "Job exit status FAILURE"
          print r.ErrorName(), "ERROR :", r.ErrorMessage()
 ==Reading MTZ Files for Experimental Phasing==

@@ Line 9: / 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.
-<pre>
        #beta_blip_data.py
        from phaser import *
        i = InputMR_DAT()
        HKLIN = "beta_blip.mtz"
        i.setHKLI(HKLIN)
        i.setMUTE(True)
        r = runMR_DAT(i)
@@ Line 35: / Line 32: @@
          print "Job exit status FAILURE"
          print r.ErrorName(), "ERROR :", r.ErrorMessage()
 ==Automated Molecular Replacement==

@@ Line 330: / Line 330: @@
        i.setROOT("beta_nma")
        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)
-       r = runNMA(i)
+       r = runNMAXYZ(i)
        if r.Success():
          print "Normal Mode Analysis"

@@ Line 211: / Line 211: @@
          i.setCELL6(r.getUnitCell())
          i.setREFL_F_SIGF(r.getMiller(),r.getFobs(),r.getSigFobs())
-         i.setREFL_ID(F,SIGF)
+         i.setLABI_F_SIGF(F,SIGF)
          i.setHKLI(HKLIn)
          i.setROOT("beta_blip_ano")

@@ Line 302: / Line 302: @@
          i.setSPAC_HALL(r.getSpaceGroupHall())
          i.setCELL6(r.getUnitCell())
-         i.setREFL(r.getMiller(),r.getF(),r.getSIGF())
+         i.setREFL_F_SIGF(r.getMiller(),r.getF(),r.getSIGF())
          i.addCOMP_PROT_MW_NUM(28853,1)
          i.addCOMP_PROT_MW_NUM(17522,1)

@@ Line 81: / Line 81: @@
 Example script for reading SAD data from MTZ file S-insulin.mtz
 <pre>
-       insulin_data.py
+       #insulin_data.py
        from phaser import *
        i = InputEP_DAT()
@@ Line 118: / Line 118: @@
          print r.ErrorName(), "ERROR :", r.ErrorMessage()
 </pre>
 ==Automated Experimental Phasing==