The questions were: "I am looking at the packing of my AMORE solutions in O and have a couple of questions :
1) why O always put symmetry_objects around the origin, instead of around my input molecule, or simply put them in the SAME unit cell?
2) how to color each of symmetry related molecules in a different color, this way any overlap would be straight forward to find? I guess I could aply one symop at a time, then naming and coloring each of them differently. There must be a macro out there to do this more efficiently."
1) why O always put symmetry_objects around the origin
2) how to color each of symmetry related molecules in a different color
You can also use PACMAN plus the file://rose.bmc.uu.se/pub/gerard/omac/auto_amore.com script to screen out poorly packing solutions.
You can also use XPAND to generate one unit cell (or asymm unit) full of atoms
Valerie Biou suggested w.r.t. the second issue: "Although you can't have different colors, it helps me to color the original object with paint_ramp using the residue ordering, so that you can at least follow the chain and often distant regions come in contact so you can distinguish them."