ptm (version 0.2.2)

ball: Search for Atoms Close to a Given Atom

Description

Finds the atoms within a sphere with the indicated center and radius

Usage

ball(pdb, chain, res, r, backbone = FALSE)

Arguments

pdb

is either a PDB id, or the path to a pdb file.

chain

a character indicating the chain to which the residue belongs

res

position in the primary structure of the residue of interest, which will be use as center of the sphere.

r

radius in <U+00E5>ngstr<U+00F6>ms of the sphere.

backbone

logical, when TRUE it means that we include those atoms belonging to the main chain (CA, N, O and C) beside all the side chain atoms.

Value

A dataframe with the atoms identification and their distances to the central atom.

Details

The position indicated by res must be occupied by one of the following amino acids (otherwise the function will return an error message): Met (SD atom), Cys (SG atom), Glu (centroid of OE1 and OE2 atoms), Asp (centroid of OD1 and OD2 atoms), His (centroid of ND1 and NE2 atoms), Lys (NZ atom), Arg (centroid of NE, NH1 and NH2 atoms), Phe (centroid of CG, CD1, CD2, CE1, CE2 and CZ atoms), Tyr (centroid of CG, CD1, CD2, CE1, CE2 and CZ atoms), Trp (centroid of the indol rings, ring-1: CG, CD1, CD2, NE1, CE2; ring-2: CD2, CE3, CZ2, CZ3, CE2). All the atoms belonging to the central residue are excluded from the results.

See Also

res.dist(), pairwise.dist(), dist2closest()

Examples

# NOT RUN {
ball(pdb = '6e7f', chain = 'A', res = 181, r = 6, backbone = TRUE)
# }