Re: [bug #21187] "NoneType" error message while loading side chain amide protons -- October 11, 2013 - 10:28

Hi Edward,

just in case someone has a similar problem with attaching protons and 
incorrect atom numbering, there is an incredibly easy way to fix it without 
having to write your own pdb filter, since the atoms are just numbered 
consecutively. Just use the bio3d package in R (not in CRAN) and employ the 
oneliner below:


library(bio3d)
pdb <- read.pdb("my.pdb")

pdb$atom[, "eleno"] <- 1:length( pdb$atom[, "eleno"] )

write.pdb(pdb, file="my_corrected.pdb")


That will strip the PDB file of all of its headers, but that generally should 
not be a problem.

Cheers,
Martin