How to locate gaps in a protein chain and cap them.

[Andrew Orry]

Q. How to locate gaps in a protein chain and then cap them with "acet" at the N-terminal and  "conh" at the C-terminal.

A. 

This script reads in the PDB structure 1xbb, identifies gaps in the protein chain and determines their N- and C-terminal residue numbers. It then  processes the termini by adding an acetyl (Acet) group to the N-terminal residues and a CONH group to the C-terminal residues. 

Please feel free to adapt it to your needs or suggest improvements.

# read in PDB 1xbb as an example

read pdb "1xbb"

# find N- and C- residue numbers for the gaps in the protein chain
r_ = Res( Select( a_ delete ) )
for i=1,Nof(r_)
  r_[i]
endfor
NandC = Iarray(r_ number)
split molecule segment a_
convertObject a_ no yes yes no

#add acet group to N-terminal
for j=2,Nof(NandC),2
 myRes = NandC [j]
 modify a_/$myRes "acet"
 delete myRes
endfor

#add conh to C-terminal
for k=1,Nof(NandC),2
 myRes = NandC [k]
 modify a_/$myRes "conh"
 delete myRes
endfor

[Ruben]

That works. Indeed, Select( a_A delete ). (or Select(a_A error )) function selects the boundary atoms, and Res( Select( a_A delete )) selects the residues.