Reply To: all-atom refinement with Relax application

[Anonymous]

Brian

1) the relax::min_tolerance is used in gradient based minimization – its default value should be fine for almost all cases – i don’t think a paper has been published on relax mode from Rosetta3.0

2)
all stages do repacking and minimization and have the following moveset
stage 1 moveset – small/shear – lots of minimization
stage 2 moveset – small/shear – optionally wobblemover
stage 3 moveset – small/shear – lots of minimization

how you increase the number of cycles really depends on your desired effect, if you just want a lower score then increasing only stage3 should be fine but if you want more conformational sampling, I would do stage2 and stage3. In general though, I would recommend increasing nstruct and making more models – instead of doing longer runs, are you familiar with fast relax or with sequence relax, you might find that those provide the functionality you are looking for. If you explain your system a little bit, I will be able to provide a better answer.