Free protein structure software for linux

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. Jmol is cross-platform, running on Linux/Unix, Mac OS X, and Windows systems.
- The JmolApplet is a web browser applet that can be integrated into web pages.
- The Jmol application is a standalone Java application that runs on the desktop.
- The JmolViewer is a development tool kit that can be integrated into other Java applications.
Main features:
- Free, open-source software licensed under the GNU Lesser General Public License
- Applet, Application, and Systems Integration Component
- Cross-platform
- Supports all major web browsers
- High-performance 3D rendering with no hardware requirements
- File formats
- Animations
- Vibrations
- basic unit-cell support
- schematic shapes for secondary structures
- measurements
- RasMol/Chime scripting language support
- JavaScript support library
- Exports to .jpg, .pdf, and PovRay
Jmol v10 is a complete rearchitecture and rewrite of Jmol, undertaken in the Spring of 2003, with the specific goal of developing Jmol into a replacement for the Chime Plug-in.
Jmol v10 retains most of the features and functionality of the previous Jmol releases while offering significant enhancments in the following areas:
- true 3D graphics engine that requires no special hardware
- 24 bit color with accurate lighting and shading
- substantially higher rendering performance
- handles large macromolecules with excellent performance
- protein/nucleic acid secondary structure graphics
- RasMol/Chime script compatibility
Enhancements:
- bug fix: isosurface color -- not operating for some isosurface types
- bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
- bug fix: gamess reader MO fix
- bug fix: state save of STRUCTURE misplaced

StressFreeZone RPG project is a massive multiplatform RPG system.

StressFreeZone RPG is a multiplatform RPG system which runs on Linux and Windows (other systems are possible). The client is based on the SDL libraries and uses OpenGL.

The structure is server/client oriented, but the server will probably only run under Linux.

Common Music (CM) is an object-oriented music composition environment.

Common Music produces sound by transforming a high-level representation of musical structure into a variety of control protocols for sound synthesis and display.

tracx project reads and stores any kind of XML data using a dedicated programming language. Read XML structure can be traced and changed.

Unix Shell and JDBC database escapes allows you to retrieve data and store it into the XML structure. Implementations based on C++ and Java are available.

GLib is the low-level core library that forms the basis for projects
such as GTK+ and GNOME.

GLib2 provides data structure handling for C, portability wrappers, and interfaces for such runtime functionality as an event loop, threads, dynamic loading, and an object system.

TextSearch is a program that helps you search through a set of text files which are in a hierarchical structure, i.e. a directory structure. Each document is searched using a regular expression and an overview of the results is shown as a tree structure. By clicking on a file, it can be viewed, with matches being highlighted.

As opposed to other programs out there, focus is not so much on statistics, i.e. how often a word would occur in an entire corpus of files, but rather on occurrences in single files.

TextSearch is published as open source under the GPL.

Why do I need it?

a) Youre writing your diploma thesis about the occurences of certain terms in publications by various political parties, and you need a way to quickly look for a certain term in many files.
b) Youre a programmer, you have a large code tree, and youd just like to know where youve used sprintf() instead of snprintf().

Bio::Graphics::Glyph::cds module contains the "cds" glyph.

SYNOPSIS

See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >.

This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the frame in which the translation occurs. At low magnifications, draws the amino acid sequence of the resulting protein. Amino acids that are created by a splice are optionally shown in a distinctive color.

OPTIONS

The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.

Option Description Default
------ ----------- -------

-fgcolor Foreground color black

-outlinecolor Synonym for -fgcolor

-bgcolor Background color turquoise

-fillcolor Synonym for -bgcolor

-linewidth Line width 1

-height Height of glyph 10

-font Glyph font gdSmallFont

-connector Connector type 0 (false)

-connector_color
Connector color black

-label Whether to draw a label 0 (false)

-description Whether to draw a description 0 (false)

-strand_arrow Whether to indicate 0 (false)
strandedness

-hilite Highlight color undef (no color)
In addition, the alignment glyph recognizes the following glyph-specific options:
Option Description Default
------ ----------- -------

-frame0f Color for first (+) frame background color

-frame1f Color for second (+) frame background color

-frame2f Color for third (+) frame background color

-frame0r Color for first (-) frame background color

-frame1r Color for second (-) frame background color

-frame2r Color for third (-) frame background color

-gridcolor Color for the "staff" lightslategray

-sixframe Draw a six-frame staff 0 (false; usually draws 3 frame)

-require_subparts
Dont draw the reading frame 0 (false)
unless it is a feature
subpart.

-codontable Codon table to use 1 (see Bio::Tools::CodonTable)

The -require_subparts option is suggested when rendering spliced transcripts which contain multiple CDS subparts. Otherwise, the glyph will hickup when zoomed way down onto an intron between two CDSs (a phantom reading frame will appear). For unspliced sequences, do *not* use -require_subparts.