compas (version 0.1.1)

calscco: Calculate Cartesian coordinates of side chains

Description

Rotates the free side chain dihedral angles of an amino acid to the specified values. Calculates the updated Cartesian coordinates of all the atoms of that amino acid side chain.

Usage

calscco(pdb, resno, chi)

Arguments

pdb

A PDB object

resno

The residue number of the amino acid side chain to rotate

chi

A vector of dihedral angles (in degrees), with length matching the number of free side chain dihedral angles for that amino acid type. See atomdeps for definitions.

Value

Returns a PDB object with updated coordinates of side chain atoms in "resno".

Details

Calls calCo successively for each atom in the amino acid side chain, using the bond parameters defined in atomdeps.

Examples

# NOT RUN {
## Position 10 of nat879 is ASP with 2 side chain dihedrals chi1 and chi2
nat879$atom[nat879$atom$resno==10,]
pdbn <- calscco(nat879,10,c(60.0,-80.0))
pdbn$atom[pdbn$atom$resno==10,]

# }