When using fixbb.static.linuxgccrelease (2018 or 2019 release) with the -auto_setup_metals option set, see cmd line below, all mutations to a residue with a link to a metal ion, are ignored in the model generated (PDB file).
Run process: /usr/local/rosetta/main/source/bin/fixbb.static.linuxgccrelease -s ../src_updated_0001.pdb -extra_res_fa ../sub.params -resfile resfile-S100.txt -nstruct 1 -ex1 -ex2 -database /usr/local/rosetta/main/database -jran 1001 -constrain_relax_to_start_coords -use_input_sc -minimize_sidechains -overwrite -auto_setup_metals
Maybe we are misunderstanding how it's intended to work but we were under the impression that you would need to add the -prevent_auto_setup_metal_bb_variants for that to happen. Just to make sure, we tried it with and without that option and the results were the same: the mutations to the residues with the links were ignored. If we don't use -auto_setup_metals then it works as expected.
Is there anything we can do for the mutations not to be ignored when using -auto_setup_metals? Is this by design or is it unintended (or maybe we are missing the obvious)?