| dssp {bio3d} | R Documentation |
Secondary structure assignment according to the method of Kabsch and Sander.
dssp(pdb, exepath = "", resno=TRUE)
pdb |
a structure object of class "pdb", obtained from
read.pdb. |
exepath |
path to the ‘DSSP’ program on your system (i.e. the directory where ‘DSSP’ is stored). |
resno |
logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence). |
This function calls the ‘DSSP’ program to define secondary structure and psi and phi torsion angles.
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. |
A system call is made to the ‘DSSP’ program, which must be installed on your system and in the search path for executables.
Barry Grant
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/.
read.pdb, stride,
torsion.pdb, torsion.xyz,
plot.bio3d
## Not run:
# Read a PDB file
pdb <- read.pdb(system.file("examples/d1bg2__.ent", package="bio3d"))
sse <- dssp(pdb)
# Helix data
sse$helix
# Precent SSE content
sum(sse$helix$length)/sum(pdb$calpha) * 100
sum(sse$sheet$length)/sum(pdb$calpha) * 100
## End(Not run)