Re: [ccp4bb] How to compare between electron density maps?

[00000c2488af9525-dmarc-request]

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 Cooper

On 11 May 2020 23:18, Murpholino Peligro <murpholi...@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?

Thanks

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On 11 May 2020 23:18, Murpholino Peligro <murpholi...@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?

Thanks

---

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

On 11 May 2020 23:18, Murpholino Peligro <murpholi...@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?

Thanks

---

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

On 11 May 2020 23:18, Murpholino Peligro <murpholi...@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?

Thanks

---

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

On 11 May 2020 23:18, Murpholino Peligro <murpholi...@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?

Thanks

---

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