makes new.chain.store & uses instead of x$atom[,5] 

Uses new.chain.store rather than x$atom[,5] since chain ids vary too
much. Uses new technique to get these new chain ids - x$atom[,1]
contains single gaps between chains. Uses these gaps as indicators of
new chain beginning. Have had to include all variants of a protein
(eg serineA and SerineB) with rm.alt=FALSE in read.pdb function
since these were other gaps in x$atom[,1]. This should not effect 
results though since their positional data is very very similar.