Garlic at NERSC
Table of Contents
- Description
- Garlic is a free molecular viewer and editor that runs on Unix platforms.
The current default version of Garlic is 1.3 on both Seaborg and DaVinci.
- Features
-
Garlic is a highly portable molecular viewer/editor: the only libraries
it requires are the standard C library (libc), the standard math library
(libm), and the standard X library (libX11). All other molecular
visualization programs require additional libraries.
- Accessing Garlic
-
Garlic is available on Seaborg
via the modules facility.
- Documentation
-
Links to online local documentation (pdf/html format) .
- Additional Resources
-
Links to the Garlic distribution site, supplemental information, a FAQ
page.
Sample Screen Shots
Description
-
Garlic is a free molecular viewer and editor written for unix and unix clones.
Features
- Garlic is free. The source code is available to everyone.
- With garlic, you will be able to replace residues, to create new
structures and to adjust bond angles.
- Atoms may be drawn as spheres of different sizes. Bonds may be drawn as
cylindrical sticks, conical sticks or as curved surfaces.
- Five types of slab are available: planar, spherical, semi-spherical,
cylindrical and semi-cylindrical.
- The slab position and thickness are visible in a small window.
- Atomic bonds as well as atoms are treated as independent
drawable objects.
- The atomic and bond colors depend on position. Five mapping modes are
available (as for slab).
- Garlic is capable of displaying stereo images.
- Garlic is capable of displaying other geometric objects,
e.g., membranes.
- 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.
- Atomic information is available for an atom covered by the mouse pointer.
No clicks are required, simply move the mouse pointer over the structure!
- Garlic is capable of loading more than one structure.
- It will be possible to color the residues according to hydrophobicity
and other properties.
- Garlic is capable of drawing a Ramachandran plot, helical wheel,
Venn diagram, averaged hydrophobicity, hydrophobic moment plot and a
sequence comparison plot.
- The command prompt is available at the bottom of the main window. It
is capable of displaying one error message and one command string.
- More information can be found at the
vendor's web site.
The default web site may change or move in the future:
http://garlic.mefos.hr is referenced.
Accessing Garlic
- On NERSC machines (Seaborg), use the modules facility as follows:
% module load garlic
Documentation
Pdf/postscript Documentation
Local Documentation Downloads: (Use shift left-mouse to download files)
Additional Resources
Sample Screen Shots
