Performs a sequence and structural alignment of two PDB entities.

struct.aln(fixed, mobile, fixed.inds=NULL, mobile.inds=NULL, 
           write.pdbs=TRUE, outpath = "fitlsq", prefix=c("fixed",
           "mobile"), max.cycles=10, cutoff=0.5, ... )



an object of class pdb as obtained from function read.pdb.


an object of class pdb as obtained from function read.pdb.


atom and xyz coordinate indices obtained from that selects the elements of fixed upon which the calculation should be based.


atom and xyz coordinate indices obtained from that selects the elements of mobile upon which the calculation should be based.


logical, if TRUE the aligned structures are written to PDB files.


character string specifing the output directory when write.pdbs is TRUE.


a character vector of length 2 containing the filename prefix in which the fitted structures should be written.


maximum number of refinement cycles.


standard deviation of the pairwise distances for aligned residues at which the fitting refinement stops.


extra arguments passed to seqaln function.


This function performs a sequence alignment followed by a structural alignment of the two PDB entities. Cycles of refinement steps of the structural alignment are performed to improve the fit by removing atoms with a high structural deviation. The primary purpose of the function is to allow rapid structural alignment (and RMSD analysis) for protein structures with unequal, but related sequences.

The function reports the residues of fixed and mobile included in the final structural alignment, as well as the related RMSD values.

This function makes use of the underlying functions seqaln, rot.lsq, and rmsd.


Returns a list with the following components:


atom and xyz indices of fixed.


atom and xyz indices of mobile.


fitted xyz coordinates of mobile.


a numeric vector of RMSD values after each cycle of refinement.


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


Lars Skjarven

See also


# \donttest{ # Needs MUSCLE installed - testing excluded if(check.utility("muscle")) { ## Stucture of PKA: a <- read.pdb("1cmk") ## Stucture of PKB: b <- read.pdb("2jdo") ## Align and fit b on to a: path = file.path(tempdir(), "struct.aln") aln <- struct.aln(a, b, outpath = path, outfile = tempfile()) ## Should be the same as aln$rmsd (when using aln$a.inds and aln$b.inds) rmsd(a$xyz, b$xyz, aln$a.inds$xyz, aln$b.inds$xyz, fit=TRUE) invisible( cat("\nSee the output files:", list.files(path, full.names = TRUE), sep="\n") ) }
#> Note: Accessing on-line PDB file #> PDB has ALT records, taking A only, rm.alt=TRUE #> Note: Accessing on-line PDB file #> #> Initial RMSD (321 atoms): 6.647 #> Cycle 1: 7 atoms rejected #> Mean: 1.3 Std: 6.1 Cut: 13.4 #> RMSD (314 of 321 atoms): 2.397 #> Cycle 2: 22 atoms rejected #> Mean: 1.2 Std: 1.7 Cut: 4.5 #> RMSD (292 of 321 atoms): 1.501 #> Cycle 3: 23 atoms rejected #> Mean: 1 Std: 0.9 Cut: 2.7 #> RMSD (269 of 321 atoms): 1.165 #> Cycle 4: 23 atoms rejected #> Mean: 0.9 Std: 0.6 Cut: 2 #> RMSD (246 of 321 atoms): 0.98 #> #> See the output files: #> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/struct.aln/fixed.pdb #> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/struct.aln/mobile_0.pdb #> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/struct.aln/mobile_1.pdb #> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/struct.aln/mobile_2.pdb #> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/struct.aln/mobile_3.pdb #> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/struct.aln/mobile_4.pdb
# } if (FALSE) { ## Align two subunits of GroEL (open and closed states) a <- read.pdb("1sx4") b <- read.pdb("1xck") ## Select chain A only a.inds <-, chain="A") b.inds <-, chain="A") ## Align and fit: aln <- struct.aln(a,b, a.inds, b.inds) }