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Using Marvin Structure Editor for Structure Searching

The chemical structure editor provided by CDD is called Marvin Sketch JS by ChemAxon. CDD utilizes the structure editor for structure registration, drawing structures, copy/pasting structures from various representations (like SMILES), and of course structure searching.

Here are the most commonly used features of the editor with a list of common toolbar actions.

Pasting or Importing structures

     Name to structure conversion

Drawing structures

Transformations

Atom properties

General toolbar

Tools toolbar

Atoms toolbar

ChemAxon's Marvin for JavaScript User's Guide

 

Marvin JS is a version of the ChemAxon Marvin editor that does not require Java. The toolbars and menus are very similar to the full version of Marvin, however this is a lighter and faster version, so as a result some of the more advanced structure rendering and analysis tools are missing. You can of course still use the full version of the external Marvin Sketch editor if you prefer and copy/paste your structure(s) to the integrated JS window. 

 

Pasting or Importing structures

You can copy/paste structures directly into the canvas with keyboard shortcuts.

Mac: ⌘ C, V, X

Windows: Ctrl C, Ctrl V, Ctrl X

You can also import a structure from a large number of supported formats.

Press the Import button on the General toolbar to open the Import pop-up window. The dialog can also be opened by pressing the "Ctrl+O" keyboard shortcut. You can paste the structure directly into the interface, or load from file. <Auto regognize> structure format works well, but you can also select the appropriate file format from a drop-down list. Finally, press the "Import" button to load the structure on the canvas. At this point you can continue to edit the structure, then press the "Use this structure" to submit your query to CDD Vault. Use the neighboring "export" button, to copy a structure out of structure editor.

marvin_editor1.png

 

Name to structure conversion

The current version of Chemaxon's Marvin JS (version 17.15.0)  structure editor supports name-to-structure conversion for many structures. To use this functionality, open up the "import" dialog, and type in the common chemical name. When you click Import, the chemical structure of the molecule will be displayed in the canvas, if the name is recognized. If it is not, you will receive an error message. Use the "export" button to copy the structure as a MOL or SMILES representation.

name to structure.png

Drawing structures

Drawing most common bonds and atoms can be done by selecting buttons from the toolbars around the sides of the editor: bonds on the left, atoms on the right, and common substructure templates at the bottom. Combo buttons with an arrow in the lower left corner contain several selections to select from. When you make a selection, it will be remembered by the editor until you change it again.

Query atoms can be part of molecules (query structures) as well. To use these atoms, select their combo button on the Atoms toolbar. Pseudo atoms, which stand for an "Any" type query atom, can also be created through this button: click on the "question mark" in the query atom list and define the label you want to use with your pseudo atom in the dialog then close the dialog with the "OK" button and click on the atom you want to change into a pseudo atom. Note that pseudo atoms can be defined in the Atom properties dialog, too. A special class of pseudo atoms are the Homology Group, which are also available from the Atom properties dialog.

Note: if you want to perform a generic group/atom search, use the "Any" query 'A', use of '*' (asterisk) is not supported.

 

Transformations

After selecting them with the selection tool, molecules can be moved or rotated on the canvas. When you hover the cursor over the selected structure, the "move" cursor will appear indicating that the structure can be dragged on the canvas. If you select a whole molecule, it will be translated without any modifications, but when the selection contains only a fragment, the molecule will be distorted due to the changes in bond lengths and bond angles. Note that the positions of the atoms within the selected fragment are fixed, so only the bonds between the selected and non-selected part of the molecule will be distorted.

When the whole structure was been selected, it can be rotated around its center in two dimensions. The pink circle with a dot is the center of the selected area is the pivot point, around which the molecule will be rotate. Click on the green dot and drag the cursor on the canvas: you can see the angle of rotation near this green dot. When a selected part is only a fragment which connects to the rest of the molecule with one bond only, the rotation center will be that atom of the selected fragment which connects to the non-selected part of the structure.

rotate2d_1b.pngrotate2d_2b.pngrotate2d_4b.png

 

Molecules or fragments can be mirrored either horizontally or vertically using the Mirror Horizontally or Mirror Vertically options in the pop-up menu. For mirroring, you should select the molecule or fragment concerned, right-click inside the selected area, and select the appropriate menu option. Mirroring is possible only for whole, unattached molecules or for fragments which connect with no more than one bond to the unselected part of the structure. In any other case, the mirror options remain inactive.

mirror.png

Atom Properties

Currently Marvin for JavaScript supports the display of atomic charges, isotopes, and enhanced stereo specifications as atom properties. All of these attributes can be set in the Atom properties dialog window available from the pop-up menu after a right-click on the atom.

properties3.png

The dialog provides options for changing atom type, setting new atomic symbols, or defining properties of atoms. You can choose from the following atom types: Element, Query, R-group, List/NOT list, Pseudo, or Homology Group. Choosing any of these types, only the relevant property fields appear on the dialog. For example, in case of a pseudo atom, there are three properties available: pseudo, charge, and enhanced stereo. Previously defined properties can be removed by clicking on the Remove property button.

The enhanced stereo notations (Off, Absolute, And, Or) can be added to chiral atoms (marked with wedge bonds) individually in order to assign them to stereogenic groups. The default value is the "Off" identifier, while in case of "Or" and "And" groups a number should accompany the identifier. If you leave the number field empty, number 1 will be associated with the group identifier automatically. Learn more about enhanced stereo specifications in Marvin for JavaScript.

The "OK" button closes the window, and the changes appear in the structure. As a result, a charge will appear as an upper right index of the given atom, while the mass number (isotope type) will be displayed as an upper left index.

Note that atomic charges can be modified using the Increase Charge/Decrease Charge buttons on the Tools toolbar, too.

 

General Toolbar

The General toolbar at the top of the editor contains buttons for entering and exporting structures (Import, Export) and for general editing/viewing of the canvas content (Clear, Undo/Redo, Cut/Copy/Paste, Zoom, Clean, Navigate and View Settings).

clear.png

Clear

Clear the whole canvas.

import.png

Import

Load or paste an existing structure into Marvin for JavaScript. The supported structure formats include MDL Molfiles V2000 (.mol), MDL Molfiles V3000 (.mol), SMILES, CXSMILES, IUPAC, InChi

save.png

Export

Save your structures in one of a number of supported formats (see drop-down), or export as an image (PNG or JPG) with several configurable options.

zoom_all.png

Zoom All

Change the zoom ratio to the optimal value to view everything on the canvas. You can selectively zoom in (+) and out (-) using pop-up buttons. neighboring buttons. marvin_editor_zoom.png

stereo.png Calculate stereo Automatically determine R/S stereo labels for chiral atoms and E/Z labels for double bonds.
clean_2d.png Clean Clean the structure(s) on the canvas in 2D by recalculating the atomic coordinates for optimal display.
view_settings.png View Settings Set the following display properties:

Chiral flag
Valence errors
Atom Index
CPK colors
Carbon labels
Implicit Hydrogens

help.png About Marvin JS Displays information about the application (name, version) and a link to the User's Guide.

 

Tools toolbar

The Tools toolbar offers the main tools for drawing or editing structures. There are "combo" buttons on the Tools toolbar, which have a triangle in their lower right corner. When you click there, you can select a function from a list of options. Once an option is selected, the main "combo" button retains the selection.

rectangle_selection.png

Selection

Select whole structures or molecule fragments. When selection is highlighted, right-click for more options.

When a whole structure is selected, click and drag the green circle to rotate the molecule in 2D. Right click to flip the molecule vertically/horizontally.

delete.png

Delete

Erase one or more structures or molecule fragments.

single_bond.png

Bonds

Open the complete list of chemical bonds including several query bond types.

chain.png

Chain

Draw an alkyl chain of arbitrary length.

r_group.png

R-groups

"Combo" button to insert an R-group

 

r_attachment.png

R-group attachment

Add an R-group attachment point to an atom.

increase_charge.png

Increase Charge

Increase the charge of an atom with one unit (i.e. adds a positive charge to the atom).

decrease_charge.png

Decrease Charge

Decrease the charge of an atom with one unit (i.e. adds a negative charge to the atom).

 

Templates Toolbar

At the bottom of the editor, you will see six predefined generic structure templates, as well as an icon which helps you with inserting Abbreviated Groups abbrevgroup_1.png. Please note, that searching via Reaxys Groups is not supported. 

 

Atoms Toolbar

The elements of the Atoms toolbar provide tools for drawing and modifying atoms, including query atom types, too. The chosen atomic symbol appears on the tip of the cursor. After a left-click, this atom is put on the canvas. Note that you can also use keyboard shortcuts (atomic symbols) to choose any atom from the Periodic Table.

periodic_table.png

Periodic Table

A pop-up window to select an atom from the Periodic Table

You can choose any atom from the Periodic Table to put it on the canvas with a left-click. You can also define Atom Lists and NOT Lists for query structures.

Screen_Shot_2014-04-14_at_1.04.40_PM.png

Frequently used atoms

The most frequently used atoms can be reached directly from the toolbar

star_atom.png

Star atom

Draw a '*' atom (e.g., for an unspecified end group in a polymer)

any.png

Query atoms

"Combo" button to select a query atom type

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