Hi Dolev,

The difference is that the menu action only aligns on C-alpha atoms. Since 
PyMOL 1.8 the menu label says “align > to molecule (*/CA)” to make this more 

The exact command which is executed by the menu action is:

align 4A11 & name CA & polymer, 3W15 & name CA & polymer, 

The “polymer” selection makes sure that calcium atoms are not included, which 
also have name CA.

See also:


> On May 18, 2017, at 12:41 PM, do r <dolevra...@gmail.com> wrote:
> Hello
> I have noted that using action -> align -> to molecule via the GUI gives 
> (sometimes radically) different result then running align on the same 
> structures via command line.
> For examples, for PDB structures 4A11 and 3W15, the command
> align 4A11,3W15, aligns 1632 atoms and gives an RMSD of 7.538, whereas
> action -> align -> to molecule aligns 375 and gives an RMSD of 24.416.
> I have also seen such differences on other pairs of structures.
> Any explanation of this phenomenon will be most appreciated.
> Thanks in advance
> Dolev Rahat 

Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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