Using Bio3D to convert 3 letter amino acid to 1 letter

Bio3D is a package written for the R platform. Details are in thegrantlab.org/bio3d/index.php


library(bio3d, lib.loc = "~/R")

pdb < - read.pdb("File.pdb")

atom.select(pdb,"calpha")$atom   ---- Gives the atom index of all alpha carbons

pdb$atom$resid    -- Gives the residue ID of all atoms

pdb$atom$resid(atom.select(pdb,"calpha")$atom)  --- Combines the two

Scanning speed using Airport vs CUPS Driver

Just found out - the really painful way - that the Brother MFC L2700DW CUPS driver makes scanning documents 10-15 times faster than the default Airport driver that Apple automagically installs to make your life "simple". Guess it works great till you get into heavy usage. Haven't been able to set up the duplex scanning though. It was really the duplex scanning that took me to Brother's website which lists their CUPS driver for Macs.