FastModelFree

Optimizing PDB Coordinates before using Fast Model Free

PDB Inertia

This program calculates the principal moments of inertia for the atoms in a standard pdb file.. By default the program writes the moments of inertia to standard output. Optionally, the program can output a new pdb file in which the molecule is translated so that its center of mass is located at the origin and rotated so that the moments of inertia are aligned with the Cartesian axes. At present, the program only reads lines starting with the 'ATOM' keyword and only recognizes the atoms H, C, N, O, P, S.

• Type the following command in the directory containing your pdb file
  • pdbinertial -r infile.pdb outfile.pdb

• This will output a translated and rotated pdb file.

R2R1 Diffusion

The program (r2r1_diffusion) uses the apprach of Tjandra, et al. [J. Am. Chem. Soc. 117:12562-12566 (1995)] to determine the diffusion tensors for spherical, and axially-symmetric motional models from experimental nitrogen-15 spin relaxation data.

• You will need to calculate the R2/R1 ratios and R2/R1 uncertainity ratios. This can be done with any program such as excel, kaleidograph, origin, etc. Save the file as a tab deliminated text file.

Example File
{{# residue R2/R1 dR2/R1}}