[Chimera-users] How to show local agreement between cryo-EM map and model

Tom Goddard goddard at sonic.net
Mon Apr 17 10:33:29 PDT 2017


HI Tofayel,

  The Chimera command to measure the local correlation between two maps using a sliding window is “vop localCorrelation”.  Here is a past mailing list post about its use

	http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-October/008076.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-October/008076.html>

Basically you make a map from your atomic model using the Chimera molmap command then correlation over a small box centered at each point of the map grid and color using that correlation value.  Here is the documentation on vop localCorrelation

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#localCorrelation

  Tom

> On Apr 16, 2017, at 6:36 AM, #AHMED TOFAYEL# wrote:
> 
> Dear developers and users,
> 
> Is it possible to generate/color a cryo-EM map to show local agreement between the map and the model generated using the same map? If I am not wrong, the following figure had accomplished the job but I don't understand how to generate a similar figure for my project:
> 
> http://d2ni3bh4dzb2ig.cloudfront.net/content/embojnl/28/6/755/DC7/embed/inline-supplementary-material-7.jpg?download=true <http://d2ni3bh4dzb2ig.cloudfront.net/content/embojnl/28/6/755/DC7/embed/inline-supplementary-material-7.jpg?download=true>
> 
> Best regards,
> Tofayel
> NTU Singapore
>    
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