How To Use MarvinView Features

Loading Molecules into MarvinView

MarvinView can open molecule files saved in any of the supported formats for viewing. Choose File > Open... and browse for the file in the Open file dialog.
Tick the Show preview checkbox to see the contents of the file (molecules, reactions, queries). A single item is dispalyed in the preview window; the text field at the bottom shows the index of the current structure and the number of structures in the file. When a multiple structure file is selected (e.g., MRV or SDF), the navigation buttons become active. Their functions are: go to first, go to previous, go to next, go to last. Note that the preview window allows you only to check the file content, but not to select the molecules you would like to open. For this purpose the Select textbox has to be used, where you can write the serial numbers of the molecules to open. The numbers have to be separated either by commas or by a dash. (Clicking on the Info button in this row will present tips for specifying the desired molecules.) Leaving this textbox empty means that every molecule in the file will be loaded into MarvinView. Currently this is the default behavior of file loading in Marvin.
Importing image files containing chemical structures is also possible with the help of OSRA (since version 5.3.0). Please consult this page for details. The supported image formats are: bmp, png, jpg, gif, svg, and tif. Furthermore, you can import chemical structures from ps and pdf files, too. In order to open an image file go to the File > Open... menu and select All Files from the list of Files of Type.
You can also take advantage of the Cut/Copy/Paste and Drag & Drop Functionality of Marvin to move a molecule from another chemical drawing application into MarvinView.

Saving Molecules

First and foremost, MarvinView is designed for viewing molecules and for editing them. However, you can save your molecules in any of the supported structure file formats in MarvinView, too. In case your have multiple chemical objects you would like to save, you should use the File > Save All... menu option.
In the dialog window used for saving a Saving method tab can be opened with the help of the Advanced checkbox. The first half of the tab offers the following choices:

All structures SEPARATELY: Saves all structures separately in a single file.
This is the deafult behavior of saving. Without opening the Saving method tab, this option will be applied.
Into SEPARATE FILES: Saves each structure to a separate file.
In this option the numbering of molecule files begins with the molecule in the upper left corner.

The first option remains inactive unless the chosen file type supports multimolecule files (such as MRV or SDF). Similarly, for one molecule only files these options are disabled.
When the given parameters for saving (filename, format, and route) are the same as for an already existing file, the outcome will be determined by the other two radio buttons of the dialog window. If you select the Overwrite file option, the original contents of the file will be replaced. However, selecting the Append to end of file radio button will add the new structures to the original file, so its contents will be preserved. In the first case, a new dialog window will be displayed, where you can reinforce or change your decision about overwriting the file. If the chosen file format does not support multiple structures, the Overwrite option is applied automatically.

You can create a new file from a subset of molecules selected from a larger file. Choosing the File > Save Selection... menu point opens a dialog window where you can specify the molecules you want to save in the new file. Please note that if you have selected a molecule previously in your MarvinView table, the dialog window will not appear, and only the selected molecule will be saved in the new file.

MarvinView allows you to save an image of a selected molecule in the Viewer. When you have selected a molecule, go to File > Save As Image.... You can select from JPEG, PNG, SVG, BMP, and EMF image file formats.

Printing Molecules

You can print the molecule using the Print item in either the File Menu or the Pop-up Menu.
The Print dialog box contains two sets of options: first, you choose the structures to print: all molecules, all visible molecules in the window or the selected molecule. Second, you may choose print (send to printer), print to pdf file or see the print preview.

Editing Molecules

MarvinView is intended to be used mainly to display molecules. However, there is a limited set of functionality available to edit the molecule while you view it. To make major changes to the molecule, it can be opened in either a MarvinSketch window or a Source window. In either case, the alterations made can be imported back to the Viewer.

Editing Options in MarvinView

Marvin allows you to Clean your molecule in either 2D or 3D. This will recalculate the coordinates of the atoms and bonds to the most appropriate location, based on the type of cleaning you select. You can set cleaning options via the Structure > Clean submenu or from the Pop-up Menu.
You can toggle the display of rings as aromatic using the Structure > Aromatic Form submenu.
Using the Misc submenu from the Edit Menu or from the Pop-up Menu, you can toggle the display of options such as Atomic Symbols, Map Numbers, and E/Z steroconfiguration labels.

Editing in MarvinSketch

MarvinView allows you to launch a MarvinSketch window for editing the current molecule. By selecting Edit > Structure, the molecule will be opened in MarvinSketch. While you are editing the molecule in the sketcher, you will be unable to use the viewer. When you close the sketcher or use its Transfer button, you will be able to use the viewer again and all changes you have made in the sketcher will appear in the viewer.

Editing Source

Choosing Source from the Edit menu (in the Menubar or Pop-up Menu) opens the Edit Source window. The The Edit Source window opens the file for the current molecule as text. You can view and edit the molecule file in any of the supported formats (SMILES, molfile, XYZ, etc).
You can alter a molecule by directly editing its source in the Edit Source Window. You can view and edit the source in any of the supported file formats. To change format, simply select the desired one from the Format Menu. To reload the molecule described by the text in this window into the MarvinSketch canvas (including any changes you may have made), select File > Import. This will close the Edit Source Window.

Structure Display Options

There is a wide range of functions related to the display of the molecules. These settings can be found in the View menu and in the Preferences dialog. Additionally, you can move, rotate, and zoom in/out on the structure.

Molecule Format

You can set the display format for the molecule and screen resolution using the View > Display submenu. Available molecule formats are Wireframe, Wireframe with Knobs, Sticks, Ball and Stick, and Spacefill. You can set the resolution to low or high via the Quality submenu.

Colors

The View >Colors submenu allows you to specify the color scheme of the molecules. The available options are:

Monochrome
CPK
Shapely - based on RasMol's shapely color scheme for nucleic and amino acids
Group - based on PDB residue numbers
Atom Set

Implicit/Explicit Hydrogens

Marvin has a number of options for the display of implicit and explicit hydrogens. Because Marvin is chemically intelligent, it will automatically add hydrogens as necessary within the structure. They are called implicit hydrogen atoms, are always displayed without bonds and based on the options set in the View menu. In case of Ball & Stick and Spacefill modes, the impilcit Hydrogen atoms are never displayed.

To view all hydrogen atoms explicitly, displayed as atoms with bonds connected to neighbors, chose Structure > Add > Explicit H Atoms. The Structure > Remove > Explicit H atoms will return to the previous display mode.

Marking Atoms

Hover the cursor over an atom and it will be marked by light blue circle. Clicking on it will select the atom in question and the circle will turn dark blue. At the same time, you can mark one atom, and select another one even if they are in different molecules. A property change event is sent on every atom mark. See developer guide for details.

marking atoms

Error Highlighting

Marvin can not automatically correct all valence errors or any reaction errors. Instead, these errors are highlighted and you may make the appropriate corrections yourself. This option can be enabled and disabled using the the Edit > Preferences dialog window.

Saving Display Options

Many of the display settings in Marvin are saved and reloaded the next time you start the program. Background color, molecule color scheme, and hydrogen visibility can be set from the View menu and will be saved automatically when you exit the program. Other options, including error highlighting and object visibility can be set using the Preferences dialog window from the Edit menu.

Manipulating the Molecule

You can translate, rotate, or resize the molecule on the canvas with a simple mouse drag. The View Menu and Pop-up Menu both contains a Transform submenu that allows you to set the type of motion to apply to the molecule.
By Selecting Translate or Drag, dragging the mouse across the canvas will result in a same displacement of the molecule.
Selecting Zoom allows you to resize the molecule. Dragging the mouse upward will zoom out, dragging downward will zoom in.
Selecting Rotate in 2D allows you to rotate the molecule in 2D. The center of the molecule becomes the center of rotation and the molecule will rotate around this point in the direction of the mouse drag.
Selecting Rotate in 3D allows you to rotate the molecule in 3D around a point at the 3D center of the molecule.
If you select the Zoom/Rotate option and drag the mouse on the canvas, you can zoom the content of the canvas and/or rotate it in 2D.

The View Menu and the Pop-up Menu also contains the Animation menu, which allows you to start and stop an automatic 3D rotation of the molecule.

How to Work with Multipage Molecular Document

Multipage molecular documents help to work with large drawings by dividing them into pages. To use the navigation tools of multipage molecular document doubleclick on the choosen cell.

multipage view1

A new window will open and the following controls will automatically appear on the window's interface:

Pages menu on the menubar
Navigation statusbar under the canvas
Frame of pages, margin, title and page numbers on the canvas

multipage View2

The statusbar contains information about the current page number in a textfield and the number of all pages on a label. It also contains a collection of buttons to aid your quick navigation in the document. You can go the the first, previous, next, and last page using them. Alternatively you can go directly to a specific page by entering a number in the text field and pressing enter.

Statusbar Elements
First page button	Clicking on the First page button allows you to go to the first page of multipage molecular document.
Previous page button	Clicking on the Previous page button allows you to go to the previous page of multipage molecular document.
Current page field	The Current page textfield shows you the number of current page and allows you to go to a specific page of multipage molecular document by entering a number in the text field and pressing enter.
Next page button	Clicking on the button allows you to go to the next page of multipage molecular document.
Last page button	Clicking on the Last page button allows you to go to the last page of multipage molecular document.
All pages label	The All pages label shows you the total number of pages in multipage molecular document.

Statusbar Elements

First page button

Clicking on the First page button allows you to go to the first page of multipage molecular document.

Previous page button

Clicking on the Previous page button allows you to go to the previous page of multipage molecular document.

Current page field

The Current page textfield shows you the number of current page and allows you to go to a specific page of multipage molecular document by entering a number in the text field and pressing enter.

Next page button

Clicking on the button allows you to go to the next page of multipage molecular document.

Last page button

Clicking on the Last page button allows you to go to the last page of multipage molecular document.

All pages label

The All pages label shows you the total number of pages in multipage molecular document.

All the navigation possibilities: go to first, previous, next, last, specific pages are available from the Pages menu too with some automatic page zooming functions. Pages > Fit page height adjusts the height of the current page to the height of the canvas. Pages > Fit page width adjusts the width of the current page to the width of the canvas. Pages > Fit page adjusts the current page so that the whole current page will be placed centralized within the canvas.

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