On 12/7/16 11:44 AM, Mahesh Velusamy wrote: > I have been doing separate optimization steps on selected region where i > experienced that certain residue(ARG,LYS,TYR) atoms get distorted (like > bonds between two atoms were distorted). So is their anyway to control the > random deviation of certain residues atoms.

You can't control how they are moved during optimization (since that's a function of the first derivatives) but you can certainly control how much they're initially randomized by. Just make separate selections and randomize them differently (or not at all, potentially).

For example:

# all atoms for optimization all_sel = selection(...)

# subset of these atoms in 'certain residues' badres = all_sel.only_residue_types('ARG LYS TYR')

# remaining subset goodres = all_sel - badres

# randomize bad residues less than good ones goodres.randomize_xyz(deviation=10.0) badres.randomize_xyz(deviation=1.0)

Note that randomize_xyz() already does something similar for residues containing rings to avoid this issue: https://salilab.org/modeller/9.17/manual/node251.html Ben Webb, Modeller Caretaker