1.5 Environment Variables

Coot responds to several environment variables that modify its behaviour.

• COOT_STANDARD_RESIDUES The filename of the pdb file containing the standard amino acid residues in “standard conformation” ¹
• COOT_SCHEME_DIR The directory containing standard (part of the distribution) scheme files
• COOT_SCHEME_EXTRAS_DIR A ':'-separated list of directories containing bespoke scheme files. This variable is not set by default. If you set it, Coot will test each ':'-separated string that it points to a directory, and if it does, Coot will load all the .scm files in that directory.
• COOT_PYTHON_EXTRAS_DIR A ':'-separated list of directories containing bespoke python files. This variable is not set by default. If you set it, Coot will test each ':'-separated string that it points to a directory, and if it does, Coot will load all the .py files in that directory.
• COOT_REF_STRUCTS The directory containing a set of high resolution pdb files used as reference structures to build backbone atoms from C\alpha positions
• COOT_REF_SEC_STRUCTS The directory containing a set of high-quality structures to be used as templates for fitting beta strands. If this is not set, then the directory COOT_REF_SEC_STRUCTS will be used to find the reference pdb files.
• COOT_REFMAC_LIB_DIR Refmac's CIF directory containing the monomers and link descriptions. In the future this may simply be the same directory in which refmac looks to find the library dictionary.
• COOT_SBASE_DIR The directory to find the SBASE dictionary (often comes with CCP4).
• COOT_RESOURCES_DIR The directory that contains the splash screen image and the GTK+ application resources.
• COOT_BACKUP_DIR The directory to which backup are written (if it exists as a directory). If it is not, then backups are written to the current directory (the directory in which coot was started).

And of course extension language environment variables are used too:

• PYTHONPATH (for python modules)
• GUILE_LOAD_PATH (for guile modules)

Normally, these environment variables will be set correctly in the coot shell script.