On 25/02/15 18:08, Michael Murphy wrote:
Does anyone know of a way to adjust Ramachandran angles so that they
fall within the preferred range? Either in Coot or possibly some
online server? I have been trying to do it manually without much
success, I was wondering whether there might another way to do it. -Thanks
Dear Michael,
Your question lacks the detail needed for a definitive answer, but I can
imagine that you are solving a protein structure and have been told by a
structure validation program that you have too many Ramachandran
outliers. If so, then I would say, please don't fix it by adjusting phi/psi.
When you have an occasional headache, you take an aspirin or wait for
the headache to go away, but when you have headaches every day, you go
to a medic to search for the reason and get cured.
The same is with your structure. If you have one exceptional situation,
you might decide to live with it, but when you have very many
exceptional situations in your protein, you should not try to hide the
problem by forcing some angles to fulfill our ideas about what things
should on average be, but see how you can generally adjust/improve your
refinement protocol to get a better match between the reality (measured
reflections) and the model (coordinates).
I am not a real crystallographer, and you did not provide many details,
so I cannot give any advice what you should do. But I can tell you what
you should not do. You should not try to adjust phi and psi to pull
residues into the Ramachandran plot's preferred regions.
Greetings
Gert
Ps, feel free to send me your coordinates (I promise to keep them
secret) and I will see if the latest WHAT_CHECK provides some hints for
what you can try to do.
