Re: [modeller_usage] Partial structure alignment

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 11/17/16 5:14 PM, Parker de Waal wrote:
> Does anyone know if it is possible to perform a 3d alignment between
> two proteins while only moving the selected atoms? (i.e. leaving the
> unselected atoms for the alignment unmoved?)

Modeller's 3D alignment (superpose) does a rigid rotation and 
translation of the entire protein. It doesn't really make sense to not 
move the unselected part of the protein because that would distort the 
structure. But you could certainly do the superposition and then combine 
the moved selected atoms with the unmoved unselected atoms from the 
original PDB file, either manually or with some simple scripting.

	Ben Webb, Modeller Caretaker
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