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



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