Plot RMSF in b factor column

[jhold]

I would like to write out a pdb that has the RMSF in the b factor column. Currently I get the error message below:

Error in write.pdb(pdb = NULL, xyz = pdb$xyz, file = "RMSF.pdb", : write.pdb: the lengths of all input vectors != 'length(xyz)/3'.

When I check the following I get the same #

nrow(pdb$atom) [1] 9741 length(pdb$xyz)/3 [1] 9741

Below is the script I am currently using. Any suggestions would be appreciated.

library(bio3d)

mydcdfile <- "MD.dcd" mypdbfile <- "MD.pdb"

dcd <- read.dcd(mydcdfile) pdb <- read.pdb(mypdbfile)

align trajectory and store new coordinates as xyz

ca.inds <- atom.select(pdb, elety="CA") xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=ca.inds$xyz, mobile.inds=ca.inds$xyz) dim(xyz) == dim(dcd)

#RMSF rf <- rmsf(xyz[,ca.inds$xyz]) rf <- rmsf(xyz) plot(rf, ylab="RMSF", xlab="Residue Position", typ="l") write.pdb(pdb=NULL, xyz=pdb$xyz, file="RMSF.pdb", b=rf)

[Barry Grant]

Looks like you have Calpha atom RMSF values but are trying to write an all atom PDB hence the error message...

Make your PDB match your RMSF vector or vice-versa.

For example something like this...

ca.pdb <- trim.pdb(pdb, "calpha")
write.pdb(ca.pdb, b=rf, file="rmsf.pdb")