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Using MarvinJS to Draw Chemical Structures

CDD Vault provides MarvinJS from ChemAxon as a tool for entering chemical structures into your vault.  MarvinJS requires no installation and it helps you import, draw, edit, convert and save chemical structures in all of the popular chemical formats. 

The primary uses for Marvin in CDD Vault are registering molecules in the registration system and searching chemical structures over your CDD Vault Platform.  Having quick access to MarvinJS also comes in handy if you just need to draw, open or save a compound or reaction during your workday.

This guide should give you the tools you need to work with most structures but the full capabilities of Marvin are well documented in ChemAxon's MarvinJS User's Manual.

MarvinJS Structure Editor

Opening MarvinJS
The Canvas
     Editing Tools
     General Toolbar

Importing Structures
CDD Vault Structure Lookup


Marvin Structure Editor

Opening MarvinJS

Launch MarvinJS in CDD Vault by clicking on the 'Explore Data' tab and then the green 'Launch the Structure Editor' button in the structure search area.  Chemical structure search is the most easily available Marvin button (1) but you can also open the editor by clicking in the 'Molecules' tab and 'Create a new molecule' (2) or by clicking on the hexagonal benzene icon in the ELN search bar (3). 




The Canvas

On launching the structure editor you will see the MarvinJS canvas ready to paint.  Click on the black triangle in the lower right side of Marvin to resize the canvas to where you want it.  This size will be remembered as long as you are in this session on your browser.


Selecting Structures:  Once there are structures on the canvas you can perform actions on any single bond or atom by clicking on that entity.  You can select groups of entities using the Selection tool highlighted in red above.  When the selection tool is highlighted, double-clicking on a molecule will select that molecule and hitting ctrl-A will select the whole canvas at any time.

There are two modes of selecting parts of a molecule, the square frame button and the lasso button.  See examples of both tools below.


Transforming Structures:

Move a selection on the Marvin canvas by clicking on any part of the blue highlighted group and dragging the selection to where you want it.  If your selection is connected to other atoms, then the bonds will be lengthened to allow movement of the selected part. 


Rotate a selection by clicking on the blue dot outside of the selection and dragging it around the pink center of the molecule.  Note that you can also drag the center (pink spot) of the molecule to a different spot first and then rotate around that.  You can also rotate only a portion of a molecule by selecting that portion then drag it around the center spot.



You can draw from scratch or modify an imported structure in the MarvinJS window using the toolbars on the edges of the drawing canvas. Editing tools like select, erase, draw bond and text are on the left, rings are on the bottom edge and atoms are on the right. Hover your mouse pointer over any button to see what it does.  


Editing tools: 

select.png Select - See above in the 'Canvas' section an outline for using this button.

erase.png Erase - When this button is selected any atom or bond you click on in the canvas will be deleted. Clicking and dragging will create a red 'select box' and everything in the box will be deleted when the mouse button is released.

bonds.png Bonds - The bond tool from the drawing toolbar lets you specify bond types from the list. A  bond’s type is critical for defining the stereoscopic configuration of a molecule or the structure itself. Use generic ‘any’ bonds to query for any type of bond (single, double, aromatic) or wedge or straight double bonds to show stereo configurations of atoms or


To see or modify bond properties manually, select the bond or multiple bonds, right-click and select ‘bond properties’ from the context menu. Now you can set the bond type and several other properties of your bond or selected group of bonds.


- Click on the '+' or '-' buttons and then on an atom to increase or decrease the charge  on that atom.  Hydrogens will be added if possible to reconcile the valence of any atom with modified charge.


custom_group.png Custom Group - Use this button to select a group of atoms and then define their repetition  pattern and chain length.


reaction.png Reaction Symbols - Add plus signs and arrows for chemical reactions using this button.  Click to place a plus, click and drag to scribe an arrow.  For calculations, everything to the right of the arrow is considered a product of the reaction, to the left and over and under the arrow are reagents/starting materials.

text.png Text - Add text notations to the canvas by clicking here then on the canvas.  This will open a small text editor.



General Toolbar        




Clear - Click on this button to wipe your canvas clean for a fresh new start.




Import/Open - Using this button you can do either of two things, 1) browse to a file that holds a chemical structure, select it and have Marvin import the structure to your canvas or 2) Enter the text representation for a compound in the text box and have Marvin draw that structure for you.  Textual representations for structures include all popular formats like SMILES, MOL files and InChI strings.  See Importing Structures below for more detailed instructions.  


Export/Save - Save the structure you have drawn in any of the (23) most common file formats for chemical structures.


 Undo/Redo - Go back or forward through your recent edits.undo.png




 Cut/Copy/Paste - Again, just like a word processor, copy or cut the selected part of your drawing from the canvas onto your device's clipboard. 


 zoom.pngZoom All - Clicking on the triangle at the bottom of the button will give you options for zooming in '+' or out '-' or zooming so that your drawing fills the screen 'x'. 


 clean.png2-D Clean - Marvin will calculate new 2D coordinates to make your molecules appear in a more orderly, evenly spaced fashion.  Partial cleaning is possible if you select only a portion of your drawing.



 Calculate Stereo - Will calculate and label the stereochemistry of chiral centers ( R or S) or isomers of double bonds in a molecule (E or Z).



 CDD Vault Lookup (The magic blue button) - This button opens a dialog where you can enter the name of a molecule, type peptide or nucleic acid identifiers, enter a compound registration number from your Vault or any of a number of other molecule identifiers.  See CDD Structure Lookup for a more detailed explanation of the magic blue button.


 Settings - Use the settings to choose how your molecules are displayed, make implicit hydrogen choices and more. 




Atoms Toolbar


Click on the periodic table button at the top of the atoms toolbar to open the periodic table.  Clicking on any element in the periodic table will put that atom on the end of your pointer and clicking at the end of a bond will insert that element into your molecule.  Use the atom list and atom-not list buttons to multi-select elements for a list in a query structure.



Commonly used elements are the bulk of the Atoms Toolbar, these are faster than opening the periodic table.  Faster still, typing letters on the keyboard while the mouse is hovered over the end of a bond will insert the atom corresponding to that letter.


Query Atoms

Clicking the A in the Atoms Toolbar opens the query atom toolbox.   See the table below that outlines different atom types you can put into a query.

queryatom.png      queryatom2.png

Adding a hydrogen to any of the query atoms (e.g. AH) makes the query search for that ‘any’ atom OR hydrogen.  The star or asterisk button above the query atom button is a wild card exactly the same as ‘AH’, any atom including H.

Click the question mark in the query atom menu to add a pseudo-atom.  This isn’t a real atom but a user-defined entity that one could search for like ‘Resin’ or ‘Bead’

Query properties can be finely tuned for any atom.  This is a bit much to get into for this article but if you would like to learn more then try ChemAxon’s atom query properties documentation. You can view any atom’s properties by right-clicking on it and choose ‘atom properties’ from the context menu.

Templates Toolbar

The last of the toolbars is the templates one.  Clicking on any of the ring structures in the template bar will charge your pointer with that template so that future clicks on the Marvin canvas will result in a drawing of that ring.



Click on the Abbreviated Groups button (below) to open a dialog where you can look up functional groups from a list and insert those into your molecule.  You can always select and expand/contract functional groups later using the right-click context menu.  Below the user (1) clicks the Abbreviated Groups button to add a COOH group to an aryl ring and then (2) right-clicks on the new group and selects expand to draw the full carboxyllic acid.  Note that the abbreviated version of your functional group is inserted by default but check the Expand box in the dialog and the full structure of the group will be drawn immediately.



Importing Structures

To import a query structure from a saved file or string, click on the ‘open’ icon in the upper left of the MarvinJS window.  You will be presented with an import dialog where you can select a structure file or paste a text-encoded structure in the text box.  We support the import of all popular structure and chemical document formats and in the ‘Paste Source’ drop-down list you can see all of the recognized text-encoded structures. When the structure has been entered in the import dialog, click ‘Add’ to paste it into the MarvinJS canvas then click the green ‘Use this structure’ button to put this molecule or reaction into your CDD Vault page.  SSS_OpenQStruct.png


Structure Lookup (The Magic Blue Button) 

Look for the structure lookup button at the top of the MarvinJS pallet.  This button is so useful in CDD Vault that we gave it the Vault icon and affectionately call it ‘The Magic Blue Button’.  The structure lookup button will draw the structure from a normal name-to-structure lookup but it is also integrated with the compounds in your vault. 


Here are a few of the different identifiers you can put in a structure lookup in Marvin JS.