MarvinView Application Options

Version 5.8.1

The Marvin Beans package contains the MarvinView application.

Usage

mview [options] [structure file]

Options

-h --help	Print command line help
-	import structures from standard input
--geometry WxH+X+Y	set preferred window size (W x H) and location (X, Y)
--real-time	display input stream in real time
--spreadsheet	use spreadsheet-like viewer with one row per input record (default if the input file contains data fields)
--gridbag	use compact matrix-like viewer with more molecules in a row (default if the input file does not contain data fields)
-c <number>	maximum number of visible columns for GridBagView (default: 2)
-r <number>	maximum number of visible rows for GridBagView (default: 2)
-n <number>	maximum number of molecules to import
-S	display unique SMILES code
-f <f1>:<f2>	show specified fields (<f1>, <f2>, ...) in the given order from an SDfile. Field names are separated by colons.

Options for displaying additional atomic properties stored in SDfile:

-p <file>	palette definition property file*
-t <tagName>	name of the tag in the SDfile that contains property symbols*

* See the Property colors in MarvinView section

You can also pass options to Java VM when you run the application from command line.

Examples

1. Displaying the first 1000 structures from str.smi:

   mview str.smi

2. Viewing 500 structures starting at the 9500-th one from str.smi:

   mview -n 500 -s 9500 str.smi

3. Showing structures and 3 fields (ID, name, and stock) from stock.sdf:

   mview -f "ID:name:stock" stock.sdf

4. Display in 2 columns, show SMILES code:

   mview -Sc 2 stock.sdf

5. Search using JChem's command line search module and display the structure and the ID field from the results:

   jcsearch -q 'Clc1ccccc1' -f sdf input.sdf | mview -f ID -

6. Displaying the progress of a command line molecular dynamics simulation in real time:

   program_producing_molfiles_on_stdout | mview --real-time -

7. Atom coloring according to property symbols in SDFile:

   mview -p colors.ini -t PPL stock.sdf

Property colors in MarvinView

The property list

It is possible to color molecules in MarvinView by certain properties of their atoms. These properties are stored in an additional data field in an SDfile as a property list. The name of the data field can be specified for MarvinView by the -t parameter The property list contains one or more property symbols for each atom, by the order of the atoms. The properties of different atoms are separated by semicolon. The number of specified atoms must match the number of atoms in the molecule. If an atom has two or more properties, they are separated by slash.

An example describing the atomic properties of a molecule containing 5 atoms:

;;a;b/c;

• the first two atoms have no properties.
• the third atom has property denoted by symbol "a"
• the fourth atom has both property b and c
• the fifth atom has no properties.

The color configuration file

The color profile for each data field labels is stored in a configuration file in "symbol = value" format. The file name of the color profile is an input parameter of MarvinView (-p).

Example:

a = red
b = blue
c = green
d = black
e = navy
f = maroon
a/d = purple
b/d = lime
a/c = aqua
empty = #808080
other = fuchsia

All property symbols and their combinations (separated by slash character) can have own colors assigned. There are two special symbols: "empty" and "other". Atoms not having any property will be displayed with the color of "empty". The rest of atoms are displayed with the color of "other" (undefined combinations). MarvinView supports the 16 color names of the HTML standard (see below), but it is allowed to assign any valid RGB color value to symbols.

Supported color names:

Name	Code	Sample
Black	#000000
Green	#008000
Silver	#C0C0C0
Lime	#00FF00
Gray	#808080
Olive	#808000
White	#FFFFFF
Yellow	#FFFF00
Maroon	#808080
Navy	#000080
Red	#FF0000
Blue	#0000FF
Purple	#800080
Teal	#008080
Fuchsia	#FF00FF
Aqua	#00FFFF