Model selection (suggestion)

[Former user]

Hi! I am working with the read.pdb&read.cif functions of the package (v2.3) and different NMR structures (e.g.2mf1 and others). My interest is to load only the second/third... model (one at a time). I've seen the "multi" argument of these functions, but after reading the data into R, all the models are concatenated. The way I solved this is cutting the input PDB file to keep only the model I want, but it would be really nice if these functions could have an additional argument to select directly the model of interest (or maybe an additional column in the object$atom records with the model number to make it easier to subset). Thanks in advance and hope this suggestion is useful to other users also!

[Lars Skjærven]

Hi, The coordinates of the different models are stored in a simple matrix where models are stored row-wise, i.e. you can obtain model 1 by accessing row 1. Quick example below:

> library(bio3d)
> pdb <- read.pdb("2mf1", multi=TRUE)
  Note: Accessing on-line PDB file

# 20 frames or models in pdb object
> dim(pdb$xyz)
[1]    20 23556

# coordinates for model 1
> pdb$xyz[1, ]

# store only model #1 in pdb object
> xyz <- pdb$xyz
> pdb$xyz <- trim(xyz, row.inds=1)

# store only model 2 in pdb object
> pdb$xyz <- trim(xyz, row.inds=2)

Hope it helps. L

[Barry Grant]

As Lars states we store coordinates for all models so you just have to use the model number you want as the row.inds for trim.pdb(), or indeed directly on the $xyz component returned from read.pdb() etc., to get the coords you are after.

marking as resolved - reopen if this is now what you intended.