[Chimera-users] Depicting entropy and mobility in pdb files

[George Tzotzos]

Hi everybody,

I’ve generated two pdb files which are of identical coordinates. Their only difference is that the b-factor column has been replaced with data indicating residue conservation (structure 1) and residue intrinsic mobility from normal mode analysis (structure 2).

Below are indicative atomic coordinates.

Structure 1
ATOM     24  NH1 ARG A   5       5.258 -15.260 -22.393  1.00  2.87           N
ATOM     25  NH2 ARG A   5       6.717 -16.030 -20.793  1.00  2.87           N
ATOM     26  N   ARG A   6        3.934 -11.168 -16.245  1.00  2.84           N
ATOM     27  CA  ARG A   6       5.160 -10.666 -15.652  1.00  2.84           C

Structure 2
ATOM     24  NH1 ARG A   5       5.258 -15.260 -22.393  1.00  1.35           N
ATOM     25  NH2 ARG A   5       6.717 -16.030 -20.793  1.00  1.35           N
ATOM     26  N    ARG A   6       3.934 -11.168 -16.245  1.00  1.73           N
ATOM     27  CA  ARG A   6       5.160 -10.666 -15.652  1.00  1.73           C

Is there a way to visualise these differences (e.g. by different thickness of ribbons or any other means e.g. colour of spheres).

Thank in advance for any suggestions

George