Hi,
We have implemented a method for comparing cryoEM maps which works by scaling
the maps based on resolution dependent amplitude fall-offs. The approach is
discussed here:
Joseph AP, Lagerstedt I, Jakobi A, Burnley T, Patwardhan A, Topf M, Winn M.
Comparing Cryo-EM Reconstructions and
Well - you can see two maps overlapped in coot if the coordinates of
protein A and B can be overlapped. Read in cords a and map a, coordinated b
and map b. Then match b to a and the map b can be shifted by the same
matrix. Then you can scroll each map as you wish...
On Tue, 12 May 2020 at 07:31,
Dear Murpholino,
there is a couple of articles addressing specifically this issue :
Urzhumtsev, A., Afonine, P.V., Lunin, V.Y., Terwilliger, T.C., Adams, P.D.
(2014) " Metrics for comparison of crystallographic maps ". Acta Cryst., D70 ,
2593-2606
Urzhumtseva, L., Urzhumtsev, A. (2016)
phenix.match_maps can overlay model B and map B onto model A and map A. A
and B can be any symmetry and box (unit cell) dimensions. Model A and map A
stay in its original frame of reference. Let me know should you have
questions.
Pavel
On Mon, May 11, 2020 at 3:19 PM Murpholino Peligro
wrote:
Hello, you certainly could normalise maps (i.e. have a map of (density minus average)/rms) with mapman in the Uppsala suite and you can ask Phenix to make the electron electron density normalised when it generates a map (set "map scaling" to "sigma"). The web suggests you can do it with XDLmapman,
I want to compare electron density features of map A from protein A and
map B from protein B...
Because each map has a different rmsd level...
...what is the best way to compare electron density between maps?
Is there a way to normalize maps or something like that?
Thanks
