Help

Previous

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


Shorts-cuts and mouse usage:



Command line options


The following options are available when Jav is started from 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.


Created with the Personal Edition of HelpNDoc: Full featured Documentation generator