[phenixbb] Dots and vectors of cryo em validation in Coot
pafonine at lbl.gov
Wed May 15 14:18:52 PDT 2019
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
All the best,
On 5/15/19 19:36, 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.
> Best regards.
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