[ccp4bb] skewness in a good EM map?

[Robert Oeffner]

Hi,

In crystallography one of the features of a good map is that the histogram of 
map values has skewness. Does this also apply to EM maps? Whereas X-ray maps 
depicts the electron density EM maps depicts the electrostatic potential as I 
understand it. Any pointers about skewness or not in EM maps is greatly 
appreciated.

thanks,

Rob



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Re: [ccp4bb] skewness in a good EM map?

[Guillaume Gaullier]

Hello,


This was discussed on the CCPEM list recently, see this discussion: 
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCPEM;dda7f5e8.2310 (you can 
navigate to the answers with the "By topic: Next" link at the top).


I hope this helps,


Guillaume



From: CCP4 bulletin board  on behalf of Robert Oeffner 

Sent: Tuesday, November 7, 2023 2:56:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] skewness in a good EM map?

Hi,

In crystallography one of the features of a good map is that the histogram of 
map values has skewness. Does this also apply to EM maps? Whereas X-ray maps 
depicts the electron density EM maps depicts the electrostatic potential as I 
understand it. Any pointers about skewness or not in EM maps is greatly 
appreciated.

thanks,

Rob



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Re: [ccp4bb] skewness in a good EM map?

[Pavel Afonine]

Hi Rob,
the fundamental property of crystallographic or cryo-em maps -- the
presence of high density points -- is what skewness depicts. So I can't see
why the idea of using skewness to quantify maps would be any different for
x-ray vs cryo-em. I've just downloaded a cryo-EM map for this (PDB: 8d3y,
EMDB: 27168) entry. The histogram (and its log for easier plotting) is:

-0.0816 16 1.204119983
-0.0707 107 2.029383778
-0.0597 458 2.660865478
-0.0488 1643 3.215637563
-0.0378 4954 3.694956002
-0.0269 21438 4.331184267
-0.0159 819411 5.91350179
-0.005 9110776 6.959555369
0.006 569464 5.755466274
0.0169 73635 4.867084291
0.0279 22271 4.347739718
0.0388 10113 4.004880007
0.0498 5938 3.773640193
0.0607 3752 3.57426283
0.0717 2189 3.340245762
0.0826 1106 3.043755127
0.0936 471 2.673020907
0.1045 185 2.267171728
0.1155 61 1.785329835
0.1264 12 1.079181246

The skew is 4.2 which is well far from zero and positive!

More on map histograms in the context of cryo-EM :
https://www.nature.com/articles/s41592-020-0914-9
and references therein.

Good luck!
Pavel


On Tue, Nov 7, 2023 at 6:07 AM Robert Oeffner  wrote:

> Hi,
>
> In crystallography one of the features of a good map is that the histogram
> of map values has skewness. Does this also apply to EM maps? Whereas X-ray
> maps depicts the electron density EM maps depicts the electrostatic
> potential as I understand it. Any pointers about skewness or not in EM maps
> is greatly appreciated.
>
> thanks,
>
> Rob
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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Re: [ccp4bb] skewness in a good EM map?

[Robert Daniel Oeffner]

Thanks for the replies and the links with more information.

Robert



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