[phenixbb] How to compare between electron density maps?

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Mon May 11 16:00:10 PDT 2020

Hi Murpholino,

You can use phenix.map_comparison map1.ccp4 map2.ccp4 contour_to_match=1.035

This will identify the contour in map2.ccp4 that encloses a volume equal to
that enclosed by the contour at 1.035 (absolute, not sigma value) in

The method is described in Afonine, P.V., Klaholz, B.P., Moriarty, N.W.,
Poon, B.K., Sobolev, O.V., Terwilliger, T.C., Adams, P.D, Urzhumtsev, A.
(2018). New tools for the analysis and validation of Cryo-EM maps and
atomic models. <https://doi.org/10.1107/S2059798318009324> Acta Cryst. D74,
814-840. bioRxiv 279844;

All the best,
Tom T

On Mon, May 11, 2020 at 4:19 PM Murpholino Peligro <murpholinox at gmail.com>

> 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
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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