Currently I am generating nucleic acid models using the MODELLER suite.
I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder
I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual (
http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class?