Aug 4 2022 Feedback.
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
 Chemical Spreadsheets
 Chemical Search
 2D Interaction
 Convert to 3D
 Find Bioisostere
 Calculate Properties
 Standardize Table
 Align/Color by 2D Scaffold
 Formal Charges
 Enumerate Formal Charge States
 Build Prediction Model
 Generate 3D Conformers
 Generate Tautomers
 Generate Stereoisomers
 Ligand Energetics
 Cluster Set
 PCA Analysis
 Visualize Chemical Space
 Compare Two Sets
 Merge Two Sets
 Select Duplicates
 Combinatorial Chemistry
 SAR Analysis
 Chemical Superposition
 APF Superposition
 APF Tools
Learn and Predict
3D Ligand Editor
Tables and Plots
Local Databases
PrevICM User's Guide
7.12 Standardize Table

Available in the following product(s): ICM-Chemist | ICM-Chemist-Pro | ICM-VLS

NOTE: Before standardizing a chemical you may want to make a copy of the original so you do not lose any information. You can do this by right clicking on the name tab of the table and selecting clone or save as.

To remove salts, explicit hydrogens and standardize groups in a chemical table:

  • Chemistry/Standardize
  • Select the table from the drop-down list. This will also work for selections made on the table.
  • Select option - Remove Salts, Keep Salt Info in Extra Column (NOTE: option availabe in 3.7-2b and higher), Remove Explicit Hydrogens or Standardize Groups
  • Click OK.

Standardize chemical groups will apply rules from ICMHOME/ For example some chemical groups may have different representations e.g. [N+] (=O)O versus N(=O)=O

To run in batch mode:

  • Chemistry/Standardize
  • Select the Files tab
  • Enter the path and name of the sdf file you wish to standardize or use the browse button.
  • Enter the path and name of the output file or use the browse button.

To remove a salt from an individual row in a chemical table:

  • Select the row or rows.
  • Right click - Chemistry/Remove Salt (Selected Row)


Copyright© 1989-2020, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.