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garlic, free molecular visualization program, protein structure, DNA
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structure, PDB, molecular rendering, biological macromolecule, unix, linux,
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free software download, open source software, Damir Zucic.
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Garlic is the most portable molecular visualization program in the unix
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world, because the only libraries required by this program are the standard
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C library (libc), the standard math library (libm) and the standard X
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library (libX11). All other molecular visualization programs require some
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Before starting the installation, you might be interested to check the
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technical requirements . Most contemporary unix and unix-like systems (like
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linux) meet these requirements without need to change the configuration, so
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you can skip this text if you are impatient.
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To compile and install garlic, follow these instructions:
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(1) Put garlic package (garlic-1.1.tar.gz) into some empty directory.
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Uncompress and unpack the package:
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(2) gzip -d garlic-1.1.tar.gz
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(3) Change your working directory:
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Check which C compiler is available on your system.
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(4) If you don't know how to find this information, try this:
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to obtain the list of available compilers.
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If gcc (GNU C) compiler is not available on your system,
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use your favorite editor to edit Makefile. Replace gcc in:
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line with the name of your compiler (this may be cc, for example).
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If gcc is available on your system, do not change the CC line.
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Find a directory which contains the Xlib library. Try this:
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Check where is the file libX11.so (sharable library - prefered)
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or libX11.a (static library - reserve option).
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(6) If your directory is different from /usr/X11R6/lib, modify the line:
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LIBPATH = -L/usr/X11R6/lib
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in Makefile. For example, if libX11.so is stored in /usr/shlib
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directory on your system, the LIBPATH should be changed to:
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LIBPATH = -L/usr/shlib
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Compile the package - just type:
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If everything worked fine, copy the executable to a choosen
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/usr/local/bin may be a good choice. This job should be done by root
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(8) (system administrator):
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cp garlic /usr/local/bin
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If you don't have root privileges, ask your local administrator to
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garlic, or just leave it in one of your directories.
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Now the .garlicrc configuration file should be copyed to a directory
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where it will be accessible to everyone as the public configuration
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script. If this is not done, garlic will work anyway, using
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(9) defaults. The recommended directory is /usr/local/lib/garlic
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but if /usr/local/lib does not exist on your system, /usr/lib/garlic
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may be used. This should be done by root (system administrator):
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mkdir /usr/local/lib/garlic
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cp .garlicrc /usr/local/lib/garlic
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It may be good idea to copy the configuration file to your home
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If you do this, you can personalize your garlic sessions, because
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private configuration file overrides the system-wide defaults.
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Of course, you don't need root privileges for this:
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It is recommended to set the environment variable MOL_PATH, so
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(11) will search all directories listed in this variable to find the
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file. Click here for detailed instructions.
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Clean up the mess (sources and .o files). Be sure to leave
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(12) trp.pdb for later practice (this is the only PDB file
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included in the original garlic package). Do not delete files
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with extension .script (tutorial scripts).
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If garlic refuses to work because it fails to get the TrueColor visual,
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try to execute xdpyinfo and xwininfo (click into root window);
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check the list of supported visuals and the current color depth.
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Choose the color depth for which the TrueColor visual is available!
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Protein and DNA coordinates may be found at The Protein Data Bank .
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If you can't compile, install or run garlic, write to me (Damir Zucic),
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my address is zucic@pref.etfos.hr .
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