Make the addition of SEQRES residues optional

[jiayeguo]

In a recent case PDBFixer() was trying to add ~40 residues (according to SEQRES) to the end of my protein; otherwise the OXT atom that's necessary at the end of the protein wouldn't be properly added. Ways to get around this include modifying the missingResidues object to exclude residues you don't want or delete them afterwards. It would be very considerate to let the user decide whether to add the additional SEQRES residues --- after all, adding a large portion (e.g. 40 residues) per se is very likely to cause other problems.

[peastman]

Which interface are you using? In the GUI, it lists each block of missing residues and lets you select which ones to add. In the Python API, you can edit missingResidues however you want. The command line interface is less flexible. It just has a single --add-residues flag, so it's an all or nothing choice. But the command line interface is only intended for simpler cases.

[jiayeguo]

I was using the Python API interface and got around the problem by editing missingResidues. I was just hoping there is an even more explicit way to do this (maybe add an input parameter add_res = True/False to addMissingAtoms()?)

[peastman]

Modifying missingResidues is the correct way to handle this case. The manual includes example code for exactly this situation.