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Sep 22 2022
The basic description of structure factors is given in the Glossary.
read pdb "1igd" # use your PDB name here myCell = Cell(a_1.) gridstep = 0.5 # map dimensions maxHKL = Iarray(0.45 * myCell[1:3]/gridstep) defSymGroup = 19 # P212121 group make map gridstep make factor maxHKL "mySF" fcalc = Sqrt( mySF.ac * mySF.ac + mySF.bc * mySF.bc ) phase = Atan2(mySF.bc , mySF.ac) group table mySF phase show mySF
In order to compare calculated phases I would recommend using the same factor table when calculating the _second_ set of phases. Then "ac" and "bc" columns will be simply replaced by the new calculated data, and new "phase2" column would be right next to the "phase" column, relating to the original object. In addition to the previous script:
read pdb "1igd" # use your PDB name here myCell = Cell(a_1.) gridstep = 0.5 maxHKL = Iarray(0.45 * myCell[1:3]/gridstep) defSymGroup = 19 # Symgroup("P 21 21 21") make map "myMap" gridstep make factor maxHKL "mySF" phase = Atan2(mySF.bc , mySF.ac) # ... now the 2nd object ... read pdb "1crn" # the second PDB, not 1crn, of course superimpose a_1. a_2. # you may need an alignment, see superimpose make map cell "myMap" gridstep myCell # to have the same cell! make factor maxHKL "mySF" phase2 = Atan2(mySF.bc , mySF.ac) delta = Remainder(phase2-phase , 360.0) group table mySF phase phase2 delta # maybe something else show mySF
This section needs to be written. Make maps, set GRID.margin to about the size of the ligand and run montecarlo.
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