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.