bio3d (version 2.1-2)

dssp: Secondary Structure Analysis with DSSP or STRIDE

Description

Secondary structure assignment according to the method of Kabsch and Sander (DSSP) or the method of Frishman and Argos (STRIDE).

Usage

dssp(pdb, exefile = "dssp", resno=TRUE, full=FALSE, verbose=FALSE)
stride(pdb, exefile = "stride", resno=TRUE)
## S3 method for class 'sse':
print(x, \dots)

Arguments

pdb

a structure object of class "pdb", obtained from read.pdb.

exefile

file path to the DSSP or STRIDE program on your system (i.e. how is DSSP or STRIDE invoked).

resno

logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence).

full

logical, if TRUE bridge pairs and hbonds columns are parsed.

verbose

logical, if TRUE DSSP warning and error messages are printed.

x

an sse object obtained from dssp or stride.

...

additional arguments to print.

Value

• Returns a list with the following components:
• helix
  start, end, length, chain and type of helix, where start and end are residue numbers or residue index positions depending on the value of resno input argument.
• sheet
  start, end and length of E type sse, where start and end are residue numbers resno.
• turn
  start, end and length of T type sse, where start and end are residue numbers resno.
• phi
  a numeric vector of phi angles.
• psi
  a numeric vector of psi angles.
• acc
  a numeric vector of solvent accessibility.
• sse
  a character vector of secondary structure type per residue.
• hbonds
  a 10 or 16 column matrix containing the bridge pair records as well as backbone NH-->O and O-->NH H-bond records. (Only available for dssp

Details

This function calls the DSSP or STRIDE program to define secondary structure and psi and phi torsion angles.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

DSSP is the work of Kabsch and Sander: Kabsch and Sander (1983) Biopolymers. 12, 2577--2637.

For information on obtaining DSSP, see: http://swift.cmbi.ru.nl/gv/dssp/.

STRIDE is the work of Frishman and Argos: Frishman and Argos (1995) Proteins. 3, 566--579.

For information on obtaining the STRIDE program, see: http://webclu.bio.wzw.tum.de/stride/, or copy it from an installation of VMD.

See Also

read.pdb, torsion.pdb, torsion.xyz, plot.bio3d

Examples

# Read a PDB file
pdb <- read.pdb("1bg2")
sse <- dssp(pdb)
sse2 <- stride(pdb)

## Short summary
sse
sse2

# Helix data
sse$helix

# Precent SSE content
sum(sse$helix$length)/sum(pdb$calpha) * 100
sum(sse$sheet$length)/sum(pdb$calpha) * 100