In Maestro when visualizing a structure file, you can select Tools -> Measurements -> Contacts panel in order to see Good contacts and Bad&Ugly contacts. When contacts are displayed, good contacts are green by default, bad ones are orange, and ugly ones are red. These criteria whether a contact is defined as good, bad or ugly are based on the following formula:
C = D12 / ( R1 + R2 )
where D12 is the distance between atomic centers 1 and 2, and R1 and R2 are the radii of atomic centers 1 and 2. C is defined as the "contact cutoff ratio" in Maestro and has default values of 0.85 for "Bad" contacts and 0.70 for "Ugly" contacts. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). These three values then provide 4 ranges. Distances greater than C(good) are not marked, less than C(good) but greater than C(bad) are marked as "good", etc.
This answer was provided by the Schrodinger help team.
Zoe
C = D12 / ( R1 + R2 )
where D12 is the distance between atomic centers 1 and 2, and R1 and R2 are the radii of atomic centers 1 and 2. C is defined as the "contact cutoff ratio" in Maestro and has default values of 0.85 for "Bad" contacts and 0.70 for "Ugly" contacts. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). These three values then provide 4 ranges. Distances greater than C(good) are not marked, less than C(good) but greater than C(bad) are marked as "good", etc.
This answer was provided by the Schrodinger help team.
Zoe
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