Garlic Features


garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software, Damir Zucic.
Features which are already implemented are marked as DONE.
Partially implemented ideas are marked PARTIAL.

DONE Garlic is free. The source code is available to everyone.
DONE With garlic, you will be able to replace residues, to create new structures and to adjust bond angles.
DONE Atoms may be drawn as spheres of different sizes. Bonds may be drawn as cylindrical sticks, conical sticks or as curved surfaces.
DONE Five types of slab are available: planar, spherical, semi-spherical, cylindrical and semi-cylindrical.
DONE The slab position and thickness are visible in a small window.
DONE Atomic bonds as well as atoms are treated as independent drawable objects.
DONE The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
DONE Garlic is capable to display stereo image.
DONE Garlic is capable to display other geometric objects, like membrane, for example.
DONE In addition to standard chemical elements, garlic allows the usage of two imaginary elements, called "jellium" (J) and "quarkonium" (Q). These elements may be used to draw some special objects. Jellium never forms any bonds, while quarkonium binds to neighboring atoms in the list (so it forms no bond, one bond or two bonds at most). Imaginary atoms may be used to adapt garlic for medical imaging, for example.
DONE Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
DONE Garlic is capable to load more than one structure.
PARTIAL It will be possible to color the residues according to hydrophobicity and other properties.
DONE Garlic is capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity, hydrophobic moment plot and sequence comparison plot.
DONE The command prompt is available at the bottom of the main window. It is capable to display one error message and one command string.