[phenixbb] How to compare between electron density maps?

Alexandre OURJOUMTSEV sacha at igbmc.fr
Mon May 11 23:39:50 PDT 2020

Dear all,
I repeat my mail sent previously to ccp4bb on the same request:

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) "COMPaRS: stand-alone program for map comparison using quantile rang scaling". J. Appl.Cryst., 49, 2270-2275.

Best regards,

Sacha Urzhumtsev

De : phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> de la part de Tom Terwilliger <tterwilliger at newmexicoconsortium.org>
Envoyé : mardi 12 mai 2020 01:00
À : Murpholino Peligro
Cc : phenixbb at phenix-online.org
Objet : Re: [phenixbb] How to compare between electron density maps?

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 map1.ccp4.

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; http://scripts.iucr.org/cgi-bin/paper?S2059798318009324

All the best,
Tom T

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

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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<mailto:tterwilliger at newmexicoconsortium.org>
Tel: 505-431-0010

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