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

Pavel Afonine pafonine at lbl.gov
Wed May 15 14:18:52 PDT 2019

Hi Ahmad,

this is not really my area of expertise so I can be wrong and I hope 
someone from MolProbity team clarifies this..

Meanwhile, I think the color of dots reflects the severity of the clash, 
with red being the worst. Also, I depending on what mode you are using, 
it may also show some favorable non-covalent interactions that are not 
really clashes (=not to worry about), I'm recalling they are green..

As to fixing, exercise your best model building / rebuilding skills as 
well as use an appropriate refinement strategy, such as do refinement 
with H atoms added to the model, for example -- this typically helps to 
alleviate clashes.

All the best,

On 5/15/19 19:36, Ahmad Khalifa wrote:
> Hello,
> 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.
> Best regards.

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