Jun 28 2018 Feedback.
Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
 Read
 Save
 Chemical Spreadsheets
  Read and Display
  Chemical Spreadsheet Template
  Display
  Calculate Chemical Properties
  Sort
  Copy-Paste
  Add New Data to Spreadsheet
  Hide
  SDF
  Excel
  Print
  Filter
  Find/Replace
  Mark Row
  Hyperlink
  Copy chemical
  Edit
  Standardize
  Properties
  InChi
  Duplicates
  Compare
  Merge
  Convert
  Copy
  Edit
  Color Column
  Chemical View
  Side-by-Side
  Zoom and Translate
  3D Browse
  Find and Replace
  Fragments
  Rotate Chemical
  Color Chemical
 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
10.3 Working with Chemical Spreadsheets.
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[ Read and Display | Chemical Spreadsheet Template | Display | Calculate Chemical Properties | Sort | Copy-Paste | Add New Data to Spreadsheet | Hide | SDF | Excel | Print | Filter | Find/Replace | Mark Row | Hyperlink | Copy chemical | Edit | Standardize | Properties | InChi | Duplicates | Compare | Merge | Convert | Copy | Edit | Color Column | Chemical View | Side-by-Side | Zoom and Translate | 3D Browse | Find and Replace | Fragments | Rotate Chemical | Color Chemical ]

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

When an sdf file is read into ICM it is displayed as a chemical spreadsheet. Many of the operations you can perform on chemical spreadsheets (Molecular Tables) are described in the table section of this manual. Some useful chemical-only options are described in this section.

An example of an ICM molecular table:

10.3.1 Read and Display Chemical Spreadsheet


When an sdf file is read (File/Open SDF) into ICM it is displayed as a chemical spreadsheet.

10.3.2 Chemical Spreadsheet Template


| Video |

To create a chemical spreadsheet table template:

  • Chemistry/Create Empty Chemical Table
  • Enter a name for the table.
  • Choose whether you wish to add an ICM column and the prefix.
  • Enter the number of empty roads you would like to insert.
  • Click Next to select property columns.
  • You can add plots and histograms to the template.

You can apply the template to new data by:

  • Cut and paste or append the new data into the template or double click in a cell and edit the chemical. The chemical properties will be automatically calculated and the plots/histograms populated with data.

You can save a template by:

  • Right click on the template listed in the ICM workspace (left hand side).
  • Select Save As.. and choose Save as type ICM binary .icb

You can open a template by:

  • File/Open file type ICM Binary .icb.

10.3.3 Molecular Table Display


| Video |

There are three built-in table views.

  • Table View (Default)
  • Grid View - select the columns you wish to display in a grid.
  • Form View

You can toggle between each view using the buttons on the right hand side of the table shown below.

10.3.4 How to add Property Columns into a Chemical Spreadsheet.


| Video |

To add chemical properties (e.g. MW, LogP, PSA etc...):

10.3.5 How to sort a column(s) in a chemical spreadsheet.


10.3.6 How to copy, cut and paste columns and rows in a chemical spreadsheet.


For large data it is recomended to use Tools/Table/Append rows.

10.3.7 Add New Data to Chemical Spreadsheet


[ Hightlight New Data ]

To add new data to a chemical spreadsheet:

10.3.7.1 Highlight New Data


To highlight new data added to chemical spreadsheet.

10.3.8 How to show and hide columns and rows in a chemical spreadsheet.


10.3.9 How to save a chemical spreadsheet in sdf format.


10.3.10 How to export your chemical spreadsheet into Excel.


10.3.11 How to print a chemical spreadsheet.


10.3.12 How to filter columns in a chemical spreadsheet.


NOTE: You can also use the filter slide bars in the table tools panel. | Video |

10.3.13 How to use find and replace in a chemical spreadsheet.


10.3.14 How to mark and label rows in a chemical spreadsheet.


10.3.15 How to insert hyperlinks to the PDB, PubMed, and Uniprot.


10.3.16 How to copy and paste 2D chemicals.


10.3.17 How to edit data inside a chemical spreadsheet.


10.3.18 How to remove salts, explicit hydrogens and standardize chemical groups.


10.3.19 How to calculate chemical properties in a chemical spreadsheet.


10.3.20 InChi


To convert a column containing an InChi key to 2D structure or vice-versa 2D structure to InChi key:

  • Right click on a column and select Insert Column
  • Choose Function -> Chemical -> Select 2DfromInChi or Inchi

10.3.21 How to identify duplicate chemicals in a chemical spreadsheet.


10.3.22 How to compare two chemical spreadsheets.


10.3.23 How to merge two chemical spreadsheets.


10.3.24 Display and Convert Molecule


To display and convert a molecule from a molecular table in the 3D graphics display window:

  • Select the molecule image or images in the molecular table.
  • Right click and select the Chemistry/ Convert to 3D option.

10.3.25 Copy Molecule


To copy a molecule to paste into another application or into the ICM Molecular Editor:

  • Right click on the molecule and a menu will be displayed.
  • Select the option "Copy Molecule"

To copy a molecule or image to paste into another row within an ICM table or into the ICM Molecular editor:

  • Right click on the molecule and a menu will be displayed.
  • Select the option "Copy Molecule"
  • Right click in the cell into which you wish to paste the molecule.
  • Select the option "Paste Molecule"

NOTE: To learn how to insert a row read the insert row section.

Molecules drawn in ICM can be cut and pasted into ISIS-Draw and molecules from ISIS-Draw can be cut and pasted into ICM.

To perform thes functions the correct settings need to be turned on in ISIS-Draw so that the compound drawing is saved in the clipboard.

IN ISIS-DRAW - Go to Options/Settings/General/Copy Mol Rxn file to the clipboard.

Compounds drawn in ISIS Draw can be cut and pasted into the ICM Molecular Editor and into ICM tables. Compounds can be copied in ICM by:

  • Right click on the compound in the chemical table and select Copy Molecule.

10.3.26 Edit Molecule


To edit a molecule:

  • Right click on the molecule and a menu will be displayed.
  • Select the option Edit Molecule and the ICM Molecular Editor will be displayed.
  • Edit the molecule.
  • Click Exit in the ICM molecular editor.

10.3.27 Color Table Column


You can color your table based on values within a column by: You can also color the compound according to specific values see Color Chemical Structure.

  • Selecting the column.
  • Right click on the column header and a menu will be displayed.
  • Select the option "Color By"

NOTE: You can remove the color from the table by right clicking on the column header selecting Clear Selection Color.

Links to other coloring options:

  • Rows can be colored by marking them as described here.
  • A 2D chemical sketch can be colored according to specific values (e.g. pharmacophore features) see Color Chemical Structure.

10.3.28 Chemical View Options


Different chemical view options in the ICM molecular table can be set.

  • Right click on the "mol" column header.
  • Select Chemical view options... and the following data entry box will be displayed

Options can be changed by checking the appropriate boxes or by entering the desired font and size.

10.3.29 Chemical Table Side-by-Side View


Chemical tables can be visually compared by placing them side-by-side. This can be done by:

  • Double click on the table header for side-by-side view.
  • Double click on the table header again to remove side-by-side view.

10.3.30 Zoom, Translate and Z-rotate a Chemical in a table.


Sometimes you may want to get a better view of a chemical in a an ICM molecular table you can do this inside the chemical table by:

  • Double clicking on the chemical drawing and the background will turn yellow.

NOTE: You can also browse your structures in 3D. See section entitled "Set Chemical Table 3D Browse Mode".

10.3.31 Set Chemical Table 3D Browse Mode


To browse the chemicals contained within a Chemical Spreadsheet in the graphical display:

  • Right click on the "mol" column header.
  • Select the option "Set 3D Browse Mode".
  • Use the box in the column "L" to toggle the 3D display on and off.
  • Multiple chemicals can be displayed by selecting the rows and then checking the box.

To remove 3D browse:

  • Right click on the "mol" column header.
  • Select UnSet 3D Browse Mode.

10.3.32 Chemical Find and Replace


Chemical Find&Replace tool allows you to find an arbitrary chemical fragment with one or more attachment point(s) and replace it with another fragment with the same number of attachment points.

To find a substructure and replace it with something else:

  • Select the column in which the molecular structures are displayed. The column is usually called "mol".
  • Right click on the "mol" column header and select Find and Replace. A data entry box as shown below will be displayed.

  • Click on the Molecular Editor button at the end of the Find What: data entry box.
  • The ICM Molecular Editor will be displayed. Draw the substructure you wish to search for and replaced.
  • Draw the pattern and mark attachment points with R1,R2.... R-groups can be added by right clicking at the attachment point and selecting the R-group from the drop down options.
  • Close the ICM Molecular Editor and the string will be displayed.
  • Repeat with the "Replace With:" data entry box. Make sure the same number of R1,R2... labels are drawn.
  • Click the Find Next button and then Replace or Replace All. When a substructure to replace is identified it will be colored red.

NOTE: There are a number of keyboard shortcuts which can be used to draw chemicals. Also please note that an aromatic bond in the source molecule will not match a double bond in the replacement pattern.

Here is an example:

10.3.33 Split Chemical(s) into Fragments


Chemicals displayed in an ICM Molecular Table can be split into fragments. This is useful for generating a series of R-groups to be added to a scaffold (See section describing reactions.

To generate fragments:

  • Select the column or row(s) you wish to generate the fragment from.
  • Right click on the "mol" column header and select "Split Into Fragments".
  • A new table of chemical fragments will be displayed. Each fragment is assigned an attachment point which is flagged with an asterisk (*).

10.3.34 Rotate Chemical for Best-Fit


To improve the display of a chemical within an ICM molecular table you can choose an option called "Rotate for best fit".

This option can be found by:

  • Right click on the "mol" column header.
  • Select "Rotate for Best Fit"

10.3.35 Color Chemical Structure


To color the structure of a chemical in an ICM molecular table by fragment of pharmacophore frequency:

  • Right click on the "mol" column header.
  • Select Color Structure By
  • Select "By Fragment Frequence" or "By Pharmacophore Features"

NOTE: The coloring can be controled using the "Edit Rainbow" option and the coloring can be removed using the "Off" option


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