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Contents
 
Introduction
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Protein Structure
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Index
PrevICM User's Guide
17.9 Generate 3D Conformers
Next

To generate a series of conformers for a ligand(s):

  • Select the compounds (row(s)) you wish to generate conformers for in an ICM Molecular Table . Or to convert a whole table of compounds select Chemisty/Generate 3D Conformers menu.
  • Right click on the selected row(s) and Chemistry/Conformation Generator (selected rows) and a data entry window as shown below will be displayed.

  • Enter the maximum number of conformations you wish to generate.
  • Enter a vicinity value. For more information on vicinity please see the command language manual http://www.molsoft.com/man/reals.html#vicinity
  • Enter a thoroughness value. This relates to the length of sampling time.
  • Check boxes for Sampling Rings, Systematic Search, Cartesian Refinement (http://www.molsoft.com/man/reals.html#vicinity),Sample Cis and Trans, sample Pyramidal and Verbose (Display Warnings).
  • Click OK and the sampling will be undertaken in the background - see Windows/Background Jobs
  • Once the sampling has finished a table as shown below will be displayed. Click in the toggle boxes in the column labeled "L". To display more than one 3D structure at a time use the row selection options.


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