[phenixbb] Dots and vectors of cryo em validation in Coot

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Fri May 17 02:55:24 PDT 2019

On 15/05/2019 17:36, Ahmad Khalifa wrote:
> In the manual, it says the red dots are clashes, what about the yellow dots and the magenta dashes 
> (vectors)? I would also appreciate if you give an input on how you fix them.

The magenta dashed lines are close [1] contacts that are probably hydrogen bonds and the yellow dashed lines 
are close contacts that are not hydrogen bonds. Refinement won't necessarily remove yellow contacts from a 
rough/raw/unrefined model.


[1] "close" is a user-defined parameter.

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