Dots and vectors of cryo em validation in Coot
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.
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, Pavel 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.
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. Paul. [1] "close" is a user-defined parameter.
participants (3)
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Ahmad Khalifa -
Paul Emsley -
Pavel Afonine