Mapping from alignment positions to PDB atomic indices

Find the best alignment between a PDB structure and an existing alignment. Then, given a set of column indices of the original alignment, returns atom selections of equivalent C-alpha atoms in the PDB structure.

pdb2aln.ind(aln, pdb, inds = NULL, ...)

Arguments

aln	an alignment list object with `id` and `ali` components, similar to that generated by `read.fasta`, `read.fasta.pdb`, `pdbaln`, and `seqaln`.
pdb	the PDB object to be aligned to `aln`.
inds	a numeric vector containing a subset of column indices of `aln`. If NULL, non-gap positions of `aln$ali` are used.
...	additional arguments passed to `pdb2aln`.

Details

Call pdb2aln to align the sequence of pdb to aln. Then, find the atomic indices of C-alpha atoms in pdb that are equivalent to inds, the subset of column indices of aln$ali.

The function is a rountine utility in a combined analysis of molecular dynamics (MD) simulation trajectories and crystallographic structures. For example, a typical post-analysis of MD simulation is to compare the principal components (PCs) derived from simulation trajectories with those derived from crystallographic structures. The C-alpha atoms used to fit trajectories and do PCA must be the same (or equivalent) to those used in the analysis of crystallographic structures, e.g. the 'non-gap' alignment positions. Call pdb2aln.ind with providing relevant alignment positions, one can easily get equivalent atom selections ('select' class objects) for the simulation topology (PDB) file and then do proper trajectory analysis.

Value

Returns a list containing two "select" objects:

atom and xyz indices for the alignment.

atom and xyz indices for the PDB.

Note that if any element of inds has no corresponding CA atom in the PDB, the output a$atom and b$atom will be shorter than inds, i.e. only indices having equivalent CA atoms are returned.

References

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

Author

Xin-Qiu Yao, Lars Skjaerven & Barry Grant

Examples

if (FALSE) {
##--- Read aligned PDB coordinates (CA only)
aln  <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))
pdbs <- read.fasta.pdb(aln)

##--- Read the topology file of MD simulations
##--- For illustration, here we read another pdb file (all atoms)
pdb <- read.pdb("2kin")

#--- Map the non-gap positions to PDB C-alpha atoms
#pc.inds <- gap.inspect(pdbs$ali)
#npc.inds <- pdb2aln.ind(aln=pdbs, pdb=pdb, inds=pc.inds$f.inds)

#npc.inds$a
#npc.inds$b

#--- Or, map the non-gap positions with a known close sequence in the alignment
#npc.inds <- pdb2aln.ind(aln=pdbs, pdb=pdb, aln.id="1bg2", inds=pc.inds$f.inds)

#--- Map core positions
core <- core.find(pdbs)
core.inds <- pdb2aln.ind(aln=pdbs, pdb=pdb, inds = core$c1A.atom)

core.inds$a
core.inds$b

##--- Fit simulation trajectories to one of the X-ray structures based on
##--- core positions
#xyz <- fit.xyz(pdbs$xyz[1,], pdb$xyz, core.inds$a$xyz, core.inds$b$xyz)

##--- Do PCA of trajectories based on non-gap positions
#pc.traj <- pca(xyz[, npc.inds$b$xyz])

}