Hi James -
For the first part, you should use split_states and super or cealign, as in my
response to one of your emails last month.
https://sourceforge.net/p/pymol/mailman/message/35156097/
Then, once you have aligned all the trajectory structures (let's say they're
called traj_01 through tra
Hi James,
The "super" method requires CA atoms in the selection because it aligns based
on the backbone trace.
You should use "rms" or "rms_cur" to get a side chain RMSD.
Cheers,
Thomas
On 12 Jul 2016, at 10:10, James Starlight wrote:
> Dear pymol users!
>
> I need to estimate how the sid
