From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
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 carma.fit-rms.dat 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, http://utopia.duth.gr/~glykos/
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