Re: [PyMOL] Structural matching of Side-chain selection

[Thomas H. <tho...@sc...>]

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 <jms...@gm...> wrote:

> Dear pymol users!
> 
> I need to estimate how the side-chains dynamics are differs in MD
> compared to X-ray structure.
> 
> Assuming that I have 2 structures one from md and another from X-ray
> and I select Sidechains from the both as obj1 and obj02
> select xray &! n. n+ca+c+o
> select md &! n. n+ca+c+o
> 
> now trying to align both objects with any method I obtain error like
> 
> PyMOL>super obj01, obj02
> ExecutiveAlign: invalid selections for alignment.
> 
> How I can fix it?
> 
> James

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.