Sep 13 2018 Feedback.
Contents
 
Introduction
Help Videos
Reference Guide
 Graphics Reference Guide
 ICM-Browser-Pro Guide
 ActiveICM Guide
 ICM-Chemist Guide
 ICM-Chemist-Pro Guide
  3D Ligand Editor
  Convert to 3D
  Ligand Energetics
  Superimpose Chemicals
  QSAR
 Menu Option Guide
 Tab Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
3.5 ICM-Chemist-Pro Reference Guide
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[ 3D Ligand Editor | Convert to 3D | Ligand Energetics | Superimpose Chemicals | QSAR ]

3.5.1 How to use the ICM 3D Ligand Editor


ICM Chemist-Pro Contains All the Tools in ICM-Chemist ICM-Chemist Reference Guide
ICM 3D Ligand Editor: Setup
How to setup the ligand in the ICM 3D Ligand Editor. HTML GUI Manual video
How to setup the receptor in the ICM 3D Ligand Editor. HTML GUI Manual video
How to change the 3D Ligand Editor preferences. HTML GUI Manual video
ICM 3D Ligand Editor: Display
How to display and undisplay the ligand surface representation in the ICM 3D Ligand Editor. HTML GUI Manual video
How to display hydrogen bonds in the ICM 3D ligand editor. HTML GUI Manual video
How to display energy atomic circles in the ICM 3D Ligand Editor. HTML GUI Manual video
How to display and undisplay hydrogen atoms in the ICM 3D Ligand Editor. HTML GUI Manual video
How to display unsatisfied hydrogen bonds in the ICM 3D Ligand Editor. HTML GUI Manual video
How to center on a ligand in the ICM 3D Ligand Editor. HTML GUI Manual video
ICM 3D Ligand Editor: Edit Ligand
How to begin editing your ligand in the ICM 3D Ligand Editor. HTML GUI Manual video
How to undo and redo changes in the ICM 3D Ligand Editor. HTML GUI Manual video
How to add and sample new substiutents to your ligand in the ICM 3D Ligand Editor. HTML GUI Manual video
How to sample more than one substituent at a time in the ICM 3D Ligand Editor. HTML GUI Manual video
How to edit the ligand in 2D in the ICM 3D Ligand Editor. HTML GUI Manual video
How to evaluate the SCORE and ligand strain. HTML GUI Manual video
How to add an edited ligand to a chemical spreadsheet (table). HTML GUI Manual video
How to change the size of the ligand binding pocket - change purple box size. HTML GUI Manual video
ICM 3D Ligand Editor: Docking and Minimization
How to perform ligand minimization in the ICM 3D Ligand Editor. HTML GUI Manual video
How to re-dock a ligand in the ICM 3D Ligand Editor. HTML GUI Manual video
How to restrain (tether) atoms during docking. HTML GUI Manual video
How to screen databases of chemical substituents. HTML GUI Manual video
How to sample linkers between two chemical fragments. HTML GUI Manual video

3.5.2 How to Convert Chemicals to 3D


Convert Chemicals to 3D
How to convert 2D chemical sketches to 3D. HTML GUI Manual video
How to convert 3D chemicals to 2D. HTML GUI Manual video
How to generate 3D ligand conformers. HTML GUI Manual video

3.5.3 Ligand Energetics


Ligand Energetics
How to calculate conformation entropy. HTML GUI Manual video
How to calculate conformational strain. HTML GUI Manual video

3.5.4 How to Superimpose Chemicals


How to Superimpose Chemicals
How to Perform Rigid Chemical Substructure Superposition. HTML GUI Manual video
How to Perform Flexible Chemical Substructure Superposition. HTML GUI Manual video
How to use Atomic Property Fields for Chemical Superposition HTML GUI Manual video

3.5.5 How to Perform QSAR


QSAR
How to build a QSAR prediction model. HTML GUI Manual video
How to apply a QSAR prediction model. HTML GUI Manual video


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