Nick, > There are a few commands that I've been using for which I can't seem to > find a command line equivalent:
This actions can be performed using selections with standard atom identifiers: > show/hide mainchain atoms show lines, object-name////ca+c+n+o+h hide lines, object-name////ca+c+n+o+h where object-name is the name of your object > show/hide sidechain atoms show lines, object-name and ((not name c+n+o+h) or pro/n) hide lines, object-name and ((not name c+n+o+h) or pro/n) Of course, you can substitute sticks, sphere, etc. for lines in the above. > select atoms for 'dist' command (H-bond creation) dist dist-name, selection1, selection2 i.e. dist d1, prot//N/23/CA, lig//X/1/O dist d2, prot//O/24/CA, lig//X/2/N Cheers, Warren