Re: how to incorporate into MTSL into a protein?

Hi--

> 
> I go back to check my pdb file and then find possible mistakes.
> The initial structure uses two long linkers to connect three chains.
> When I prepare my pdb file, I delete these linkers without giving the
> different chain number. This may be the point. 
> 

sounds like you're making progress...

> Here, I have another question. If there is a jump on residue number due
> to the chain break, can addAtom.py read through sequence file to match
> the corresponding atoms in pdb file?
> 

For this, modify the addAtoms.py script as follows:

1) split the seq string into two, named say seq1 and seq2, broken at the
   chain break. 
2) call psfGen.seqToPSF twice: first using seq1 and startResid=1
                               second using seq2 and the appropriate startResid

hope this helps--

Charles