Re: [PyMOL] Difference between action -> align -> to molecule and using align via command line

[Thomas Holder]

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 
obvious.

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

align 4A11 & name CA & polymer, 3W15 & name CA & polymer, 
object=aln_4A11_to_3W15

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

See also:
https://pymolwiki.org/index.php/Align

Cheers,
  Thomas

> On May 18, 2017, at 12:41 PM, do r  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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[PyMOL] Difference between action -> align -> to molecule and using align via command line

[do r]

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
--
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