I'm currently visualizing a mutation in UCSF chimera. The mutation has been confirmed, I'm looking at the moment how it may destabilize protein.
I can easily see clashes with nearby atoms in UCSF chimera when I replace WT AA with MUT AA. My question is what is the point of minimization ?
I tried it and it took till the end of the default steps (100) to remove all clashes, and number of contacts to zero. Does number of steps to minimize structure has any significance ? Also, max rotamer probability is .12,with next .09 and .08 and so on.