Icm Chemist Tutorial

8/14/2019 Icm Chemist Tutorial

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ICM-Chemist

How-To Guide

Version 3.6-1g

Last Updated 12/01/2009


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HOW TO IMPORT, SKETCHAND EDIT CHEMICALS

ICM-Chemist


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How to access the ICM Molecular Editor

1. Click here

2. Start sketching


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How to sketch chemicals in the ICM Molecular

ct atoms and bonds here

2. Click on the canvas to start sketching

.1b Select rings here

.c Click Templates menu for even more templates


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How to save a 2D sketch into a chemical spr

.pted the name of spreadsheet and chemical name

.2 New chemical spreadheet


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Edit Add Smile

How to use SMILES strings to sketch a ch

= =Example of a SMILES string C1C CC CC


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, ,How to load a mol sdf or mol2 file. /1 File Open

.2 Locate file

SDF and mol files will open in chemical spreadshee .Mol2 will open up in the graphical display

f


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How to extract a 2D sketch of a ligand in complex wi

.1 Click here to search the PDB

.2 Right click on the ligand in the ICM workspace

.ompound and the ICM Molecular Editor will be displayed


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WORKING WITHCHEMICAL

SPREADHSHEETS

ICM-Chemist

H dd l i h i l


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How to add columns into a chemical sprea

.on a column header and select insert column

. . . .ment you want to add E g mol for chemical functions

. 3 Press the Add To List button

. ( )4 Select the argument s


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H t h th i f h i l d h t f


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How to change the view of a chemical spreadsheet f

( -n the column header to select click and hold CTRL key for non contiguous select

. 2a Right click anywhere on the spreadsheet and select Table View

.2b Or you can use the butt

H t t d t l d i h


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. ( -e header click and hold CTRL key for non contiguous selections or SHIFT key for

. , ( )a To copy cut and paste rows right click here on a selected row s

. , 2b To copy cut and paste rows right click here on a selected colum

, ,How to copy cut and paste columns and rows in a che

H t hid i h i l d


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- )CTRL key for non contiguous selections or SHIFT key for range

. 2 Right click here and select Hide Rows

How to hide rows in a chemical spreads

H t hid lumn in h mi l pr d


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How to hide columns in a chemical spread- )ld CTRL key for non contiguous selections or SHIFT key for range

. ( )2 Right click here and select Hide Column s

How to save a chemical spreadsheet in sdf


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ck on the spreadsheet header tab

. ..2 Select Save As

How to save a chemical spreadsheet in sdf

How to export a chemical spreadsheet into


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. 2 Select Export To Excel

How to export a chemical spreadsheet into

How to print a chemical spreadsheet


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. 2 Select Print Table

How to print a chemical spreadsheet

How to filter columns in a chemical spread


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t click on the column header you wish to filter

. 2 Select Filter Custom or From List



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.1 Enter filters

. This symbol indicates the column is filtered

To remove a filter right click on the column that is filtere

How to use find and replace in a chemical sp


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How to use find and replace in a chemical sp

t click on the mol column

t Chemical Find and Replace

.3 Use the editor to sketch the group you want to

.4 Use the editor to sketch the group you want to repl

You can also do text find and replace by right clicking anywhere on th

How to mark and label rows in a chemical sp


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How to mark and label rows in a chemical sp

. -ow number Click and hold CTRL key for non contiguous selections or SHIFT key fo

. 2 Right click on the selected row and choose Mark Selected Rows

. ( ) .3 You can select marked labeled rows here

How to insert hyperlinks


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. 1 Right click on the column header and select Format

.How to insert hyperlinks

.2 Choose hyperlink type here

.3 Click OK and the hyperlink will be generated

How to copy and paste 2D chemicals


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.How to copy and paste 2D chemicals

.t click on the 2D chemical

. 2 Select Copy 2D Molecule

How to edit data inside a chemical sprea


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How to edit data inside a chemical sprea

.1 Click here

. .2 Edit data by double clicking on the data

How to remove salts explicit hydrogens and standardi


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,How to remove salts explicit hydrogens and standardi

. /1 Chemistry Standardize

.2 Select here

.3 Select Files tab for batch mode

How to calculate chemical properties in a sp


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How to calculate chemical properties in a sp

. /1 Chemistry Calculate Properties

.2 Select properties

.3 Properties will be displayed in new colu

How to identify duplicate chemicals in a sp


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. / 1 Chemistry Select Duplicates

. /2 Enter table spreadsheet name

How to identify duplicate chemicals in a sp

.3 Duplicate compounds will be selected and highlighted in


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How to merge two chemical spreadshee


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g p

. / 1 Chemistry Merge Two Sets

se the tables you want to compare

.3 Select the way you want to merge


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HOW TO PERFORMCHEMICAL SEARCHING

ICM-Chemist

.How to setup a chemical search


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.p

.1 Click here

al search window will be displayed

How to draw a chemical search query


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,oms and templates to sketch

. ,2 Right click on an atom to select filters such as ring membership co

How to add conditions to your chemical s


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. 1 Right click here and select Add condition

e click and use drop down arrows to enter condition

,How to search chemical spreadsheets local databa


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,

.1 Select what you want to search here

.2 Select your query optio

How to send a chemical search query


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.1 Select how you want to display the results

.2 Press Search


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HOW TO WORK WITHPHARMACOPHORES

ICM-Chemist

.How to search a 2D pharmacophore


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.1 Click on chemical search button and sketch

Distance bond

Pharmacophore types

.2 Select query options and search

How to extract a 3D pharmacophore from a 3


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. /1 File Open 3D ligand or read in PDB

on 3D ligand and select Extract pharmacophore

isplay and undisplay pharmacophore types

.How to edit a 3D pharmacophore


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a pharmacophore point and select the Pharmacophore menu

Use connect to move a point

Edit move and clone


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How color a 2D chemical sketch by pharmacopho


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.1 Right click on column header

. /2 Select Color Structure By By Pharmacophore Features


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HOW TO PERFORMCHEMICAL CLUSTERING

ICM-Chemist

.

How to perform chemical clustering


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. 1 Click on the Run Clustering button

How to select representative centers from


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Right click in white space for all centers or on a node for centers

-How to re order branches and change distanc


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- To re order branches right click in white space

To change distance click and drag here


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HOW TO GENERATESTEREOISOMERS AND

TAUTOMERS

ICM-Chemist

.How to generate stereoisomers


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. /1 Chemistry Generate Stereoisomers

ter name of chemical table

Choose Files for batch mode

.How to generate tautomers


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. /1 Chemistry Generate Tautomers

ter name of chemical table

Choose Files for batch mode


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HOW TO GENERATECOMBINATORIAL

LIBRARIES

ICM-Chemist


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Documents

Icm Chemist Tutorial