The block alpha {...} defines the
parameters to calculate the helical content of a segment of protein
residues. The
-helical content across the
residues
to
is calculated by the formula:
List of keywords (see also for additional options):
This component returns positive values, always comprised between 0
(lowest
-helical score) and 1 (highest
-helical
score).
The block dihedralPC {...} defines the
parameters to calculate the projection of backbone dihedral angles within
a protein segment onto a dihedral principal component, following
the formalism of dihedral principal component analysis (dPCA) proposed by
Mu et al.[51] and documented in detail by Altis et
al.[52].
Given a peptide or protein segment of
residues, each with Ramachandran
angles
and
, dPCA rests on a variance/covariance analysis
of the
variables
. Note that angles
and
have little impact on chain conformation, and are therefore discarded,
following the implementation of dPCA in the analysis software Carma.[53]
For a given principal component (eigenvector) of coefficients
,
the projection of the current backbone conformation is:
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(13.12) |
dihedralPC expects the same parameters as the alpha component for defining the relevant residues (residueRange and psfSegID) in addition to the following:
List of keywords (see also for additional options):