Website Help System

Structure Search User Manual

Quick Start

Basic Search Instructions

Basic Search Intructions

  1. Choose an editor
  2. Draw or paste a structure (paste feature works in Marvin and ChemDraw)
  3. Press the search button (scroll down to view results)
  4. Advanced search options view
  5. Save and Load (registered Users Only)

For detailed instructions, please refer to Structure Search Help.
 

Advanced Search Instructions

Advanced Search Instructions

  1. Search options
  2. Choosing an editor
  3. Draw or paste a structure (paste feature only works in Marvin and ChemDraw)
  4. Press the search button (scroll down to view results)
  5. Less search options view
  6. Save and Load (registered users only)

For detailed instructions, please refer to Structure Search Help.
 

Search Result Instructions

  1. Re-sort search results
  2. View next page of results
  3. Select products to purchase (registered users only)
  4. Add products to Quick Order (registered users only)
  5. Export search results as SD File

Structure Search Help

Getting Started

Structure Search is used to find Sigma-Aldrich® products by chemical structure powered by the CambridgeSoft Enterprise Search Cartridge.

Go to Structure Search

Search Options

Search options can only be selected in the advanced search mode (More Options)

Supported Search Types

  • Substructure - Search for structures that contain the query structure
  • Exact - Search for structures identical to the query structure (excluding stereochemistry and salt form)
  • Similarity - Search for structures that are similar to the query structure – default setting is 70%
  • Identity - Search for structures identical to the query structure (including stereochemistry)
  • Fragment - Search for structures with multiple components (i.e. salts)

Search Options

  • Stereo - Search for structures containing identical stereochemistry to the query structure
  • Tautomer - Tautomer searches include lactim-lactam, keto-enol, imine-enamine, and other common proton-shift tautomerisms.
  • Total Hits - The default total hits value is 100, but can be set to 100, 250, 500, 1000, or 2000. Increasing the total hits will cause slower search times.

Display Settings

  • Items per Page - The default results shown per page value is 10, but can be set to 5, 10, 25, or 50.

Additional Criteria

The name and physical property criteria can be used in addition to the query structure to narrow the search.

  • Name - Use an IUPAC name or common name fragment
  • Physical Properties - Select an operator from the drop-down list and enter the property values
  • MW — Molecular Weight, MP — Melting Point, BP — Boiling Point

(Example – Draw Indole in the structure editor, type "fluoro" in the Name field then click search – all fluoro substituted Indoles will be found.)

Choosing an Editor

Java Molecular Editor

Java Molecular Editor (JME) is a simple editor for quickly drawing chemical structures. This editor has been provided by Peter Ertl from Novartis.

JME supports:

  • Basic query atom features (select 'More Options')
  • Substituent groups from the provided list
  • Paste as SMILES and convert structure

MarvinSketch

MarvinSketch is a rich structure editing applet provided by ChemAxon.

MarvinSketch supports:

  • Advanced query atom features (select 'More Options')
  • Paste from ChemDraw or IsisDraw
  • Load structures from disk (mol, mol2, sdf, smlies, smarts, inchi, cml, pdb)

ChemDraw

ChemDraw Plugin is a rich structure editing plugin provided by CambridgeSoft. It is required that you have ChemDraw installed on your computer for this plugin to work. See troubleshooting section for help with ChemDraw plugin.

ChemDraw supports:

  • Advanced query atom features (select 'More Options')
  • Chemical Shorthand
  • Paste from ChemDraw or IsisDraw
  • Load structures from disk (mol, mol2, sdf, smlies, smarts, inchi, cml, pdb)

Sorting Search Results

The default search results sort is by similarity, but can be resorted by the following values:

  • Similarity — This is a similarity score based on tanimoto coefficient
  • Name — The common name of the molecule
  • IUPAC — Systematic name according to naming rules defined by the International Union of Pure and Applied Chemistry
  • CAS # — Registration number assigned by Chemical Abstract Services
  • MW — Molecular Weight
  • MDL # — Registration number assigned by MDL Information Systems

Exporting Search Results

The search result list and all associated names, physical properties, registry numbers, and products can be exported in standard structure-data file (SDFile; SDF) format according to MDL Information Systems CTFile specifications. Use the 'Export' link on the substructure search results page. The SDF can be imported into standard structure management systems for additional searching within your own environment.

Verifiable customers of Sigma-Aldrich Corp. may receive an SDF of our entire structure archive upon execution of a data-license agreement. Please email Sigma-AldrichDataSharing@sial.com to initiate your request.

Search Preferences

Saving Search Criteria

You will need to login to our site to save Search Criteria. Click the Save Search Criteria button on the Substructure Search page. Fill in the required fields and choose to save your search criteria.

Loading Search Criteria

You will need to login to our site to load Saved Search Criteria. Click the Load Structure button on the Substructure Search page and a page will appear displaying the following information:

  • The Search Criteria Name
  • Search Criteria Comments
  • The date the Search Criteria was saved
  • Action: View, Load, Delete

To load your Search Criteria, click on the Action 'Load'. This will load the Search Criteria in the Search Criteria page. Once the page is displayed, click 'Search' to submit the Substructure Search.

Troubleshooting

Browser Support

Microsoft Internet Explorer 6.0+

Operating System Support

All operating systems that support Java.

Java Support

Browser must have Java and Javascript enabled. If you are experiencing problems with any of the Editors, please ensure that your Java is up to date. To check your Java version use the Oracle Java Checker.

ChemDraw Support

The Sigma-Aldrich structure search is compatible with the ChemDraw Standard, Pro, and Ultra. We are currently unable to support the free ChemDraw .NET plugin.

To determine which version of the plugin your browser is using, right click in the canvas and select Help > About ChemDraw Plugin. The 'Level' will indicate which version is being used. For further support with your ChemDraw plugin, please contact CambridgeSoft support.

User Manual for Java Molecular Editor (JME)

Use the Java Molecular Editor (JME) to draw the query structure. JME is a Java applet and Java must be enabled on your browser for it to function properly. Sigma-Aldrich is using JME with permission from Peter Ertl of Novartis Pharma AG.

 

Display the SMILES string for the drawn molecule
  Clears the drawn molecule
  Creates a new fragment to draw an additional molecule (i.e. specific salt form)
  Delete a specified fragment
  Create a query (select “More Options”)
  Change a selected atom into an ion
  Undo the previous action
  Draw a new bond or change an existing bond as specified
  Draw a hydrocarbon chain
  Draw a hydrocarbon ring
  Draw a standard atom or change an existing atom as specified
  Draw a non-standard atom or change an existing atom by typing the symbol

 

Copy and Paste into JME

(Only available through the More Options view)Copy and paste from your desktop structure drawing tool is only supported with the use of SMILES. A structure can be drawn on your desktop, copied as SMILES, and pasted into the SMILES search field of our search engine. After pasting the SMILES, press the Convert button and the structure will be drawn on the canvas. Please refer to Daylight Chemical Information Systems for a list of structure editors that support SMILES.

Drawing Hydrogens

Please note that hydrogens added to atoms while drawing, (displayed in color), are there for visualization purposes only. They will not prevent the system from replacing the hydrogen with another atom. To fix the atom as hydrogen, you must add a bond and then add a hydrogen using the X atom function.

Isotopes

Isotope searches are possible, but cannot be drawn in the JME structure editor. To conduct an isotope search, please use MarvinSketch or ChemDraw.

Drag and Rotate

Drag — Left click on the canvas to drag the structure
Rotate — Right click on the canvas to rotate the structure

User Manual for MarvinSketch

Use MarvinSketch (Marvin) to draw the query structure. Marvin is a Java applet and Java must be enabled on your browser for it to function properly. Sigma-Aldrich is using Marvin with permission from ChemAxon.

Overview

  • Copy and paste between different editors
  • Advanced query features (generic atoms and bonds, atom lists/not lists, query properties, pseudo atoms, multiple groups, Link nodes, etc (select 'More Options'))
  • Wide range of file types supported: MOL, MOL2, SDF, RXN, RDF (V2000/V3000), SMILES, SMARTS/SMIRKS (recursive), MRV, InChi, CML, PDB, etc
  • Abbreviated groups
  • Pre-loaded structure templates and 'My Templates'
  • 3D editing
  • 3D geometry and conformer generation
  • 2D cleaning and conformer generation
  • Drawing and formatting shapes, arrows and text boxes
  • User definable customizable styles (colors, structure representations, etc)

Visit the ChemAxon Animation library for MarvinSketch demonstrations

The default layout of the MarvinSketch user interface is shown in the following picture:

It consists of the following primary components:

  • Menu Bar: It is located at the top of the main frame, containing menu titles that describe the content of each menu.
  • Canvas: This is the main area where chemical structures, queries and reactions are drawn.
  • General Toolbar: This toolbar contains buttons for freqently used commands.
  • Tools Toolbar: Contains basic elements for stucture drawing like bond, chain, reaction arrow, graphics, etc.
  • Atoms Toolbar: Location of the most freqent atom types and the Periodic System button.
  • Advanced Templates Toolbar: This special toolbar is a container of structure templates. The templates are rotatable by pressing and holding down the left mouse button while dragging.
  • Status Bar: Shows file status, contains navigation buttons and the dimension button. The Status Bar appears at the bottom of the main frame, and unlike toolbars, it cannot be customized or moved. Some buttons of the Status Bar appear dynamically when you invoke the corresponding command, like enabling multipage molecular documents.

Basic MarvinSketch Functions

User Manual for ChemDraw

The ChemDraw plugin is installed during the normal ChemDraw/ChemBioDraw installation process – our website uses the plugin that is already installed on your computer. Please refer to the help file associated with your ChemDraw installation.

ChemDraw Plugin Support

The Sigma-Aldrich structure search is compatible with the ChemDraw Standard, Pro, and Ultra plugin. We are currently unable to support the free ChemDraw .NET plugin available from the CambridgeSoft website.

To determine which version of the plugin your browser is using, right click in the canvas and select Help > About ChemDraw Plugin. The "Level" will indicate which version is being used.

For further support with your ChemDraw plugin please contact CambridgeSoft support.

Use ChemDraw to draw the query structure. Sigma-Aldrich supports the ChemDraw plugin with permission from CambridgeSoft.

Download the Guide to ChemDraw Manuals (PDF)

Where did my toolbar go?

The ChemDraw toolbar frequently gets hidden. To restore your toolbar, right-click in the canvas then select View > Show Main Toolbar. If you are using a dual-monitor configuration, the toolbar may be located on a different screen that your browser and can be moved.

How do I load a structure from my computer?

It is possible to open a file from your computer inside the ChemDraw Plugin. Right click on the ChemDraw canvas and select File > Open and select a file from your computer.

Paste a structure from a different editor?

It is possible to Copy from ChemDraw, IsisDraw or Symyx draw and paste directly into the ChemDraw plugin.

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