pymol scripts

Color atoms according to the chemical shift differences between e.g. free and bound state (Downloadcsp.py (PY, 11 KB)).

The script reads the chemical shifts for the apo and bound state of the protein from the corresponding prot files. To estimate the threshold for a shift perturbations, e.g. the lower limit for a chemical shift difference to be considered, the standard deviation over all shift differences is calculated. A shift difference above low_limit * standard_dev is considered a significan chemical shift difference. The parameter low_limit can be defined in the function call.

Usage:

In pymol type:
run csp.py
csp pdbfile.pdb, shifts_apo.prot, shifts_complex.prog, nr_colors, offset, low_limit

nr_colors ... number of different colors (white ... red) to show the magnitude of the chemical shift perturbations
low_limit ... a shift difference above low_limit * standard_dev is considered significant and the corresponding atom is colored accordingly
offset ... color offset for coloring the smallest shift difference (between 0 and 1)