Commonly used UNIX variables for directories

The following directory environment variables are defined within Xplor-NIH.

C13SHIFTS

Used to set up Carbon Chemical Shift restraints (Section 23). Contains $^{13}$C random coil shifts and correlation of secondary shifts with angles.

DNA_DNA_PAIRS

Contains oriented pairs files for the DNA-DNA positional/orientational database potential (Section 29).

GAUSSIANS

Contains dihedral angle correlations for use with dihedral angle database restraints (Section 25). These files are for the Gaussian representations of the potentials of mean force.

HBDB

Contains databases for use with Hydrogen Bond Database Restraints (Section 36).

PROTSHIFTS

Contatins setup files for proton chemical shift restraints (Section 24).

QUARTS

Contains dihedral angle correlations for use with dihedral angle database restraints (Section 25). These files are for the quartic representations of the potentials of mean force.

RNA_RNA_PAIRS

Contains oriented pairs files for the RNA-RNA positional/orientational database potential (Section 29).

SAXS

Contains setup files for the SAXS potential term. This is covered in Grishaev et al. (2005), and needs an entry in this manual.

SYMMETRY

Contains data files for crystallographic refinement (Section 14).

TOPPAR

Contains topology and parameter files.

TOPPAR_C22

Contains topology and parameter based on the Charmm22 set.

XPLOR_DIR

Root directory of the Xplor-NIH distribution.