Re: [ccp4bb] How to compare between electron density maps?
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 Validating Atomic Model Fit Using Difference Maps. J Chem Inf Model. 2020 Feb 11. doi: 10.1021/acs.jcim.9b01103 The method is implemented as a task (TEMPy:Diffmap) in the CCP-EM software suite. The latests nighly builds also include options for global or local scaling of the maps. The global scaling option might be of interest to you if you are looking to scale and compare xtal maps. Regards, Agnel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] How to compare between electron density maps?
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, Alexandre Ourjoumtsev < alexander.ourjoumt...@univ-lorraine.fr> wrote: > 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 > > > - Le 12 Mai 20, à 0:18, Murpholino Peligro a > écrit : > > 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 > > -- > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] How to compare between electron density maps?
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 - Le 12 Mai 20, à 0:18, Murpholino Peligro a écrit : > 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] How to compare between electron density maps?
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: > 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 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] How to compare between electron density maps?
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, if you can get hold of it since its deprecated. I wrote a 'jiffy' to do it for ccp4 and x-plor maps but the output is x-plor format. Drop me a line if any interest (or just google for "maidaid map ucl" and the page comes up as top hit). Mapman also used to allow maps to be compared by correlation coefficient. Probably I missed the point of your question but hope some of this helps.Jon CooperOn 11 May 2020 23:18, Murpholino Peligro 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?Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 On 11 May 2020 23:18, Murpholino Peligro 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?Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 On 11 May 2020 23:18, Murpholino Peligro 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?Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 On 11 May 2020 23:18, Murpholino Peligro 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?Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 On 11 May 2020 23:18, Murpholino Peligro 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?Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] How to compare between electron density maps?
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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
