Crystallography‎ > ‎Molecular graphics‎ > ‎Pymol‎ > ‎

Alter (to change chain ID, secondary structures, and more)

General usage:

alter (selection),expression

To change chain ID, for example from chain A to chain B for the selection "junk":

alter (chain A) and junk, chain='B'

To change secondary structure, and manually assign them, alter can be used as follows:

alter 96-103/, ss='S'
alter 96-103/, ss='H'
alter 96-103/, ss='L'

And then, to see the effect type:


Fragment 183-189 highlighted in red:

alter 183-189/, ss='S'

I did it on purpose to show a dramatic (and non-sense) change. It is questionable whether and how to use this command, of course not to change an helix into a sheet!