Help

The sub-menu Help is shown on the left. It allows:




Content

Starts the Internet Browser on these pages

Keyboard

Info on shortcuts and mouse usage

Command line options

Possible options when Jav is started from a terminal window

About

Shows the Jav About window

Rendering info

Information about rendering



Content


Starts the Internet Browser on these pages


Keyboard


Short-cuts and mouse usage:



Command line options


The following options are available when Jav is started from a terminal window


usage: jav [options] file1 [file2 ...]


     where options represents zero or more program options


options

-------

     -h              Print this help on terminal.

     -a              Run the program in automatic mode (all defaults used).

     -b              Black background.

     -w              White background.

     -v              Verbose mode

     -s=PS           Set default PlotStyle for model(s)

     -c=CM           Set default color mode for model(s)

     -e=on/off       Draw cell edges on/off

     -l=on/off       Draw labels on/off

     -t="string"     Set string as title for main window


PS

--

     wi    Wires

     si    Simple

     bo    Bonds

     ro    Rods

     sb    Stick & Balls

     vw    Van der Waals

     bb    Backbone

     ca    C-alpha chain

     ri    Ribbons

     st    Strands

     ct    Cartoons


CM

--

     sp    By Species

     sy    By Symmetry

     re    By Residue

     ch    By Chain

     ss    By Secondary structure

     po    By position along chain


fileN

-----

     File(s) containing data for the program.

     The file content is processed according to the extension.

     Allowed file formats

        .mtz     Data in MTZ format

        .pdb     Data in PDB format

        .ent     Data in ENT format

        .cif     Data in CIF format

        .ins     Data in SHELX format

        .map     Map in CCP4 format

        .xyz     Ascii map file. Content:

                 - two optional header records

                   First record: cell parameters

                   Second record: space group symbol

                 - Following records: x, y, z, value

                   where x, y, z are grid points (integer values)

                   and value is the correspong map value.




About


Short information such as authors, contact addresses and libraries versions are supplied.




Rendering info


Some information about rendering and video card are provided




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