struct.aln. bio3d 2.3-0

Usage

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, ... )

Arguments

fixed: an object of class pdb as obtained from function read.pdb.
mobile: an object of class pdb as obtained from function read.pdb.
fixed.inds: atom and xyz coordinate indices obtained from atom.select that selects the elements of fixed upon which the calculation should be based.
mobile.inds: atom and xyz coordinate indices obtained from atom.select that selects the elements of mobile upon which the calculation should be based.
write.pdbs: logical, if TRUE the aligned structures are written to PDB files.
outpath: character string specifing the output directory when write.pdbs is TRUE.
prefix: a character vector of length 2 containing the filename prefix in which the fitted structures should be written.
max.cycles: maximum number of refinement cycles.
cutoff: standard deviation of the pairwise distances for aligned residues at which the fitting refinement stops.
...: extra arguments passed to seqaln function.

Description

Performs a sequence and structural alignment of two PDB entities.

Details

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.

Value

a.inds: atom and xyz indices of fixed.
b.inds: atom and xyz indices of mobile.
xyz: fitted xyz coordinates of mobile.
rmsd: a numeric vector of RMSD values after each cycle of refinement.

References

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

Examples


# Needs MUSCLE installed - testing excluded


     ## Stucture of PKA:
     a <- read.pdb("1cmk")

  Note: Accessing on-line PDB file
   PDB has ALT records, taking A only, rm.alt=TRUE


     ## Stucture of PKB:
     b <- read.pdb("2jdo")

  Note: Accessing on-line PDB file


     ## Align and fit b on to a:
     path = file.path(tempdir(), "struct.aln")
     aln <- struct.aln(a, b, outpath = path, outfile = tempfile())


 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

     
     ## 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)

[1] 0.98

     
     invisible( cat("\nSee the output files:", list.files(path, full.names = TRUE), sep="\n") )


See the output files:
/tmp/RtmpTDihxb/struct.aln/fixed.pdb
/tmp/RtmpTDihxb/struct.aln/mobile_0.pdb
/tmp/RtmpTDihxb/struct.aln/mobile_1.pdb
/tmp/RtmpTDihxb/struct.aln/mobile_2.pdb
/tmp/RtmpTDihxb/struct.aln/mobile_3.pdb
/tmp/RtmpTDihxb/struct.aln/mobile_4.pdb



     ## Align two subunits of GroEL (open and closed states)
     a <- read.pdb("1sx4")

  Note: Accessing on-line PDB file

     b <- read.pdb("1xck")

  Note: Accessing on-line PDB file


     ## Select chain A only
     a.inds <- atom.select(a, chain="A")
     b.inds <- atom.select(b, chain="A")

     ## Align and fit:
     aln <- struct.aln(a,b, a.inds, b.inds)


 Initial RMSD (524 atoms): 12.062
 Cycle 1: 42 atoms rejected
  Mean: 8.1 Std: 6.6 Cut: 21.4
  RMSD (482 of 524 atoms): 9.736
 Cycle 2: 46 atoms rejected
  Mean: 6 Std: 5.6 Cut: 17.2
  RMSD (436 of 524 atoms): 7.242
 Cycle 3: 39 atoms rejected
  Mean: 4 Std: 4.4 Cut: 12.8
  RMSD (397 of 524 atoms): 5.193
 Cycle 4: 36 atoms rejected
  Mean: 3.1 Std: 3.2 Cut: 9.4
  RMSD (361 of 524 atoms): 3.678
 Cycle 5: 31 atoms rejected
  Mean: 2.3 Std: 2.2 Cut: 6.7
  RMSD (330 of 524 atoms): 2.697
 Cycle 6: 33 atoms rejected
  Mean: 1.7 Std: 1.5 Cut: 4.8
  RMSD (297 of 524 atoms): 2.019
 Cycle 7: 32 atoms rejected
  Mean: 1.4 Std: 1.1 Cut: 3.6
  RMSD (265 of 524 atoms): 1.475
 Cycle 8: 22 atoms rejected
  Mean: 1 Std: 0.9 Cut: 2.7
  RMSD (243 of 524 atoms): 0.976

Author

Lars Skjarven

Structure Alignment Of Two PDB Files