I ran two ab initio 3D constructions with exactly the same parameters, but they gave me different results. I read an earlier post (Ab-initio job shows different results on repetition) which mentioned that this is caused by different random seed numbers.
This then leads me to wonder how I should know if an ab initio model generated is reliable or correct if there is no homolog structure available for me to compare to?
I would appreciate any advice/insights on this. Thank you very much!