ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Apr 24 2018

Contents
 
Introduction
Reference Guide
Command Line User's Guide
 ICM-shell
 ICM graphics
 Str.Analysis
 Sequence
 Molcart
 Pharmacophores
 Energy
 Molecules
 Animation
 Symmetry
 X-ray
  Structure factors
  Calculate phases
  Density correlation
 Plotting
 Docking/VLS
 Examples
 _chemSuper
 Chemical Conformation Generator
References
Glossary
 
Index
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Maps and factors
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[ Structure factors | Calculate phases | Density correlation ]

How to manipulate with structure factors


The basic description of structure factors is given in the Glossary.

How to calculate phases of reflections given a 3D model and a cell


Basic steps:
  • define crystallographic cell, map gridstep, and resolution (i.e. max h,k and l)
  • build electron density map with the specified parameters
  • calculate structure factors

Example:
 
 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 


How to automatically place a fragment into density



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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