Retrieving complete model from points on a trajectory

[J Newc]

I used the bio3d package to carry out some normal mode analysis on a membrane protein, with the aim in mind to detect likely pore opening motions. I then created a trajectories of the low frequency modes:

#install.packages("bio3d") library(bio3d)

pdb <- read.pdb("path/to/file.pdb")

modes <- nma(pdb) print(modes) dssp(pdb) plot(modes, sse=pdb)

outfile = ('path/to/outfile') mktrj(modes, mode=7, file=outfile)

I would like to compare the extremes of one of the motions, however all of the residues have been reassigned to Alanine and only C-alpha atoms are present in the pdb file. Is there a way in which I could retreive a full model of the protein from different stages along the trajectory?

Thanks in advance

[Lars Skjærven]

Hi, You need to add info from the pdb object to the mktrj function. e.g.

mktrj(modes, mode=7, file=outfile, resid=pdb$atom$resid[pdb$calpha], resno=pdb$atom$resno[pdb$calpha])

# or:
pdb.ca <- trim(pdb, "calpha")
mktrj(modes, mode=7, file=outfile, resid=pdb.ca$atom$resid, resno=pdb.ca$atom$resno)

[J Newc]

Thanks very much that totally sorts out my issue!