Auxiliary Programs Included with FIRM

• dis2con:
  Accepts input file of interproton distances (from FIRM, dis2spin, or other program) and generates constraint file for use with either DIANA or SANDER (AMBER4.x). Provisions are included for using pseudoatoms and stereo-specific assignments, and error corrections can be added to upper and lower distance constraints.
• rmix and rave:
  Supplemental program useful for FIRM refinement using multiple NOE data sets at different mixing times.
• amberdiana:
  Converts between AMBER and DIANA coordinate file formats. A data file named "diana_pdb.con" specifies the translation of atom and residue names.
• felix2noe and noe2felix:
  Converts text file of NOE volumes output from FELIX into format used by FIRM and the supporting programs, and visa versa.
• dih2con:
  Converts dihedral constraints in DIANA format into SANDER input format.
• dis2spin:
  Generates distance constraints from NOE file using the 2-spin approximation and some specified "ruler".
• equivnoe:
  Makes equivalenced protons for input into FIRM from noe file containing summed intensities.
• jnoise and shiftnoise:
  Adds random, Gaussian-distributed noise onto SANDER J-coupling and chemical shift restraint files, respectively.
• mcfirm:
  Version of FIRM for performing Monte Carlo error analysis to determine the precision of the structure determination.

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