MarvinSpace Application

Version 5.2.1

MarvinSpace is a 3D molecular visualizer application to display macromolecules like proteins, protein-ligand complexes, RNA/DNA.
It is available as part of the Marvin Beans package.

Installation

To install the MarvinSpace application download the Marvin Beans package (that includes also MarvinSpace) and follow the platform specific installation instructions.

Usage

Command line

The MarvinSpace application can be launched from the command line (MS-DOS prompt or Command Prompt in MS-Windows). It can take input file names and optional parameters according to the scheme below:

mspace [options] [structure files]

Options:

-h, --help	print command line help
-	import structures from standard input
-v, --verbose	verbose mode
-c, --columns <number>	the number of visible columns (maximum: 5)
-r, --rows <number>	the number of visible rows (maximum: 4)
-n, --nMols <number>	the number of molecules to import (default: 1000)
--multiCell <number>	loads every input molecule to an empty cell
--singleCell <number>	loads every input molecule to the same cell
-q, --quality ( L[ow], M[ed], H[igh] ) (default: Med)	sets display quality
-p <string> <string>	display property

Multiple structure files can be passed in the command line. However, the number of molecules actually displayed is influenced by other parameters, namely -n, -c and -r. The number of cells (and thus the number of structures displayed) is the minimum of the product of row count and column count and the number of structures specified by the -n option.
Note, that the maximum number of cells is limited to 20.

Note, that Java VM options (like heap size) can be passed to JVM through the mspace command line.

Command icon

MarvinSpace can also be started by clicking the MarvinSpace application icon in the Marvin Beans installation directory. Beside of this, a shortcut for the application on the Desktop as well as in the Start menu (in Windows) is available too.

Examples

1. Display the macromolecule defined in the given PDB file:

   mspace 4DFR.pdb

2. View the first 6 structures from the given input file in a 2 rows by 3 columns table :

   mspace -r 2 -c 3 molecules.sdf

3. View upto 10 structures defined in an SDFile in the same cell:

   mspace -n 10 --singleCell ligands.sdf 

4. Show the macromolecule defined in the given PDB file with the highest display quality :

   mspace -q High 1AID.pdb

5. To display verylarge structures the heap size should be increased, in particular for surface calculations.

   mspace -Xmx256M 1FFK.pdb

MarvinSpace Parameters and Events