In order for Bench to give useful results, the input structure does need to be accurate.
- For Good Results: Crystal structures should ideally have resolution at or better than 2 Ångstroms.
- For Usable Results: Crystal structures with a resolution of approximately3.5 Ångstroms are the low end of usable results.
- Non-crystal structures (NMR models) tend to perform somewhat worse.
Additionally, if Relax models of your starting structure (generated by running Relax only, not with Prepare) are converging, then that is a good sign that you can continue with your modeling experiment.
If your crystal structure has a well-defined core but missing loops, you may wish to try the Homology Modeling tool, ensuring that your existing structure is available as one of its inputs. This may be able to re-mediate problems in the loops.
For more information on how to use the Homology Modeling tool click here.