dssp.RdSecondary structure assignment according to the method of Kabsch and Sander (DSSP) or the method of Frishman and Argos (STRIDE).
dssp(...) # S3 method for pdb dssp(pdb, exefile = "dssp", resno=TRUE, full=FALSE, verbose=FALSE, ...) # S3 method for pdbs dssp(pdbs, ...) # S3 method for xyz dssp(xyz, pdb, ...) stride(pdb, exefile = "stride", resno=TRUE) # S3 method for sse print(x, ...)
| pdb | a structure object of class |
|---|---|
| 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. |
| pdbs | a list object of class |
| xyz | a trajectory object of class |
| x | an |
| ... | additional arguments to and from functions. |
This function calls the ‘DSSP’ or ‘STRIDE’ program to define secondary structure and psi and phi torsion angles.
Returns a list with the following components:
‘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.
‘start’, ‘end’ and ‘length’ of E type sse, where start and end are residue numbers “resno”.
‘start’, ‘end’ and ‘length’ of T type sse, where start and end are residue numbers “resno”.
a numeric vector of phi angles.
a numeric vector of psi angles.
a numeric vector of solvent accessibility.
a character vector of secondary structure type per residue.
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
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.
Barry Grant, Lars Skjaerven (dssp.pdbs)
A system call is made to the ‘DSSP’ or ‘STRIDE’ program, which must be installed on your system and in the search path for executables. See http://thegrantlab.org/bio3d/tutorials/installing-bio3d for instructions of how to install these programs.
For the hbonds list component the column names can be
used as a convenient means of data access, namely:
Bridge pair 1 “BP1”,
Bridge pair 2 “BP2”,
Backbone H-bond (NH-->O) “NH-O.1”,
H-bond energy of NH-->O “E1”,
Backbone H-bond (O-->NH) “O-HN.1”,
H-bond energy of O-->NH “E2”,
Backbone H-bond (NH-->O) “NH-O.2”,
H-bond energy of NH-->O “E3”,
Backbone H-bond (O-->NH) “O-HN.2”,
H-bond energy of O-->NH “E4”.
If ‘resno=TRUE’ the following additional columns are included:
Chain ID of resno “BP1”: “ChainBP1”,
Chain ID of resno “BP2”: “ChainBP2”,
Chain ID of resno “O-HN.1”: “Chain1”,
Chain ID of resno “NH-O.2”: “Chain2”,
Chain ID of resno “O-HN.1”: “Chain3”,
Chain ID of resno “NH-O.2”: “Chain4”.
if (FALSE) { ##- PDB example # 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$calpha) * 100 ##- PDBs example aln <- read.fasta( system.file("examples/kif1a.fa",package="bio3d") ) pdbs <- read.fasta.pdb( aln ) ## Aligned PDB defined secondary structure pdbs$sse ## Aligned DSSP defined secondary structure sse <- dssp(pdbs) ##- XYZ Trajectory pdb <- read.pdb("2mda", multi=TRUE) dssp.xyz(pdb$xyz, pdb) ## Note. for large MD trajectories you may want to skip some frames, e.g. xyz <- rbind(pdb$xyz, pdb$xyz) ## dummy trajectory frames <- seq(1, to=nrow(xyz), by=4) ## frame numbers to examine ss <- dssp.xyz(xyz[frames, ], pdb) ## matrix of sse frame x residue }