Custom settings and aliases for UCSF Chimera. Those listed below are ones I frequently use, but there are many others (inspect the script for more details)
Put chimera_aliases.com somehere on your system and specify it as a file to read at startup (Favorites...Preferences...Command Line).
Adds a bunch of extra commands of variable utility (read the script to see them all).
I like symclip - to symmetrically clip with respect to the center of rotation, cootmode to make a Coot-like density representation for the specified volume, and cofron to make moving/rotating more Coot-like, and centersel, which moves the center of rotation to the current selection.
local_diff_map calulates a difference map by locally aligning and then subtracting density within a specified distance of the selected atoms.
local_fitmap (usage: local_fitmap #mapid1 #mapid2 raidus) aligns map 1 to a sphere of density of the specified radius centered on the current center of rotation extracted from map 2. Useful for locally comparing 3D classes.
display_only (usage: display_only #modelid) will display only the indicated model and hide everything else.
display_all will display all models
activate_only (usage: activate_only modelid) will activate indicated model for motion and deactivate everything else. Absence of "#" before modelid is intended.
activate_all will activate all models for motion.
toggle_display (usage: toggle_display #modelid1 #modelid2) will switch between showing model 1 and model 2 a set number of times. Useful for comparing aligned maps, e.g. different 3D classes.
cootmode_wire (usage: cootmode_wire #mapid) will change the indicated map to a blue mesh with meshlighting off, depth cueing adjusted, and surface caps off; it will also change all models to yellow colorbyhet wire representation, to mimick Coot for easier visual inspection of map/model fit.