[phenixbb] Calculating the transformation matrix of density map alignment

Pavel Afonine pafonine at lbl.gov
Wed Dec 23 10:06:52 PST 2020

Hi Ahmad,

no, it can take maps as Fourier maps or real-space maps:

   phenix.match_maps A.pdb B.pdb A.mtz B.mtz
   phenix.match_maps A.pdb A.mtz B.pdb B.mtz
   phenix.match_maps A.pdb A.mrc B.pdb B.mrc
   phenix.match_maps A.pdb B.pdb A.mrc B.mrc

and it is general and works with any of 230 space groups and matching 
maps can be in different unit cells.


On 12/22/20 12:36, Ahmad Khalifa wrote:
> Thanks Pavel but it only takes mtz as input. I'm also only interested 
> in the transformation matrix to suppose one map onto the other in 
> their original frame of reference without superposing the maps per se.
> On Sun, Dec 20, 2020, 2:19 PM Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> wrote:
>     Hi Ahmad,
>     phenix.match_maps is the tool to superpose maps and models.
>     Pavel
>     On Sun, Dec 20, 2020, 1:38 PM Ahmad Khalifa
>     <underoath006 at gmail.com <mailto:underoath006 at gmail.com>> wrote:
>         I have two density maps that I'm trying to align, or more
>         precisely, calculate the transformation matrix (rotation and
>         translation) of their alignment (moving one map and aligning
>         it with the other map). Is there a way to accomplish that
>         using phenix or any other tool?
>         Thanks a lot and happy holidays.
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