Jun 5 2018 Feedback.
Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
 Read
  Extract from PDB
  Large SDF Files
  Extract 3D
 Save
 Chemical Spreadsheets
 Editor
 Chemical Search
 2D Interaction
 Convert to 3D
 Fragments
 Find Bioisostere
 Molcart
 Calculate Properties
 Standardize Table
 Annotate
 Align/Color by 2D Scaffold
 Formal Charges
 Enumerate Formal Charge States
 Convert
 Build Prediction Model
 Predict
 Generate 3D Conformers
 Generate Tautomers
 Generate Stereoisomers
 Prodrug
 Ligand Energetics
 Cluster Set
 PCA Analysis
 Visualize Chemical Space
 Compare Two Sets
 Merge Two Sets
 Select Duplicates
 MPO
 Combinatorial Chemistry
 SAR Analysis
 Chemical Superposition
 APF Superposition
 APF Tools
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
10.1 Read Chemical Structures
Next

[ Extract from PDB | Large SDF Files | Extract 3D ]

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

| Video

Chemical structures can be read into ICM from MOL/MOL2, SMILES, and SDF files or you can construct your own structures by drawing them in the ICM Molecular Editor. Chemicals can also be searched and downloaded via the Search Tab using the PDB Chemical Substructure Search, search by PDB Ligand Code, or by searching DrugBank, ChEMBL, SureChEMBL or PubChem.

To read a chemical format file:

  • Select File/Open.
  • Select the chemical structure file you wish to open: MOL, MOL2 or SDF.
  • Once selected the file will be displayed as a chemical table (See ICM molecular tables section).

If you know the chemical smiles string for the compound you can build the 2D molecule by:

  • Select File/New.
  • Click the Compound tab at the top of the window.
  • Enter a name for the compound.
  • Type in the Smiles String in the Smiles String data entry box. Remember to delete the previous string.
  • Check the boxes Display Molecule Delete Other Objects according to your preference.
  • Click the OK button.

Smiles can be read from a text file into a chemical table by:

  • File/Open and select Files of type: Smiles format
  • Then you can convert SMILES to 2D sketch using Chemistry/Convert.

Smiles can be read directly into the ICM Molecular Editor:

Multi mol2 3D files can be read by:

  • File/Open and select Files of type: mol2 format.

Chemicals can be read directly from ChEMBL, SureCHEMBL, PubChem, and DrugBank

  • Click on the search tab and find the database you wish to search in the drop down dialog box.

10.1.1 Extract 2D structure from PDB Chemical


To extract a 2D chemical representation from a PDB file into a chemical spreadsheet.

  • Read the PDB file.
  • Right click on the ligand and choose Extract Ligand.
  • Choose whether you want to extract the 3D coordinates.
  • Choose whether you want to append to an existing table (chemical spreadsheet).

10.1.2 Read Large SDF Files


The ability to read large SDF files (e.g. >100K chemicals) depends on the memory of your computer. A work around for this is available in ICM.

  • File/Open and in the Filter Section choose "MDL sdf format as SMILES"
  • The table header will contain an "S" symbol representing that the table contains a SMILES column rather than mol. Each cell will also be labeled "Smiles".

10.1.3 Extract 3D coordinates from 3D Chemical.


To extract the 3D coordinates of a chemical into a chemical spreadsheet e.g for 3D QSAR or after chemical superposition.

  • Select the 3D chemicals in the ICM workspace. One or more can be selected by clicking holding the CTRL key and clicking. A range of chemicals can be selected by holding the keyboard tab and clicking.
  • Right click on any of the selected chemicals in the ICM workspace and choose Extract Ligand.
  • Select "keep 3D coordinates.
  • Append to an existing table if needed.


Prev
Cheminformatics
Home
Up
Next
Save

Copyright© 1989-2018, 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.