Hello group. I am trying to change a residue (e.g., LYS) to CYS-MTSL. This was previously discussed; however, what should I do if the pdb (X-ray structure downloaded from pdb.org) does not have the CYS present already? Is executing the addAtoms.py script supposed to work in this case? The output generated from addAtoms.py and addAtoms2.py (this fixes covalent geometry) from Xplor v. 2.22 is an incorrectly folded structure. The demo works, so it must be my input info. I also tried adding protocol.genExtendedStructure(sel="not known") or (sel="resid xx"). Unfortunately, the tertiary structure is still incorrect.
I have not done any modifications to the downloaded pdb; could this be the problem? Thanks, Valerie
