Re: global and internal motion of protein

From: Nicholas M Glykos (
Date: Wed Oct 27 2010 - 04:43:08 CDT

> I want to know how can I remove the global motion of protein in order to
> get the internal motion of protein?

carma -v -fit -atmid ALLID -segid A my.dcd my.psf

will give you a new .dcd file (carma.fitted.dcd) containing coordinates
for your protein segment A, with the overall rotations/translations
removed using Kabsch's algorithm, as applied to all protein atoms (ALLID).

You'll also get a file containing the value of RMSD vs
frame number, plus 12 numbers corresponding to the 3x3 rotation matrices
and the corresponding translation vectors.

          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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