Use pdbfit() to an specific range of residues.

[Victor Fica]

Hi, I am recently using bio3d, i want to use pdbfit to an specific range of residues. I have a list of class "pdbs" obtained by pdbaln(files), the average sequence lenght is 216, but i want to fit only the first 110 residues of all pdbs.

Anny help would be great :)

[Lars Skjærven]

Hi Victor, Use the inds argument for this. Note that inds refers to the columns of the pdbs$xyz matrix, and thus not the residue numbers of the PDB files. Note also gaps here. See attached example:

> attach(transducin)

# check for gaps
> print(pdbs, alignment=F)

Call:
  pdbaln(files = files, fit = TRUE, ncore = 8)

Class:
  pdbs, fasta

Alignment dimensions:
  53 sequence rows; 354 position columns (305 non-gap, 49 gap) 

+ attr: xyz, resno, b, chain, id, ali, resid, sse, call

> plot(pdbs)
> gaps.pos = gap.inspect(pdbs$xyz)
> gaps.res = gap.inspect(pdbs$ali)

> length(gaps.pos$f.inds)
[1] 915
> length(gaps.res$f.inds)
[1] 305

# fit on all non-gap containing columns
> pdbfit(pdbs, inds=gaps.pos$f.inds) #, outpath="fit1")

# fit on the first 60 columns
> pdbfit(pdbs, inds=gaps.pos$f.inds[1:60]) #, outpath="fit2")

# this corresponds to residues 31-50
> pdbs$resno[1:5, gaps.res$f.inds[1:20]]
       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
1TND_A   31   32   33   34   35   36   37   38   39    40    41    42    43
1TND_B   31   32   33   34   35   36   37   38   39    40    41    42    43
1TND_C   31   32   33   34   35   36   37   38   39    40    41    42    43
1TAD_A   31   32   33   34   35   36   37   38   39    40    41    42    43
1TAD_B   31   32   33   34   35   36   37   38   39    40    41    42    43
       [,14] [,15] [,16] [,17] [,18] [,19] [,20]
1TND_A    44    45    46    47    48    49    50
1TND_B    44    45    46    47    48    49    50
1TND_C    44    45    46    47    48    49    50
1TAD_A    44    45    46    47    48    49    50
1TAD_B    44    45    46    47    48    49    50

# superimpose on core atoms
> core <- core.find(pdbs)
> pdbfit(pdbs, core)