[phenixbb] close contact and torsion angle

Pavel Afonine pafonine at lbl.gov
Thu Oct 11 22:08:27 PDT 2012


> There are some close contacts (hydrogen bonds) in my refined model. Can I just ignore it, delete it or what?  I added hydrogen for refinement since the resolution is 1.47 A.  Should I remove all these added hydrogens and refine again?

I guess "no atom - no problem" is not so good approach, so I would 
simply resolve the clash, re-run refinement and see what happens.

> Second question is there are several outilers of torsion angles (6 from Ramachandran plot in coot ). But 16 are outside expected Ramachandran regions from the validation report from PDB bank(ADIT) . What is the cause?  And should I re-refine to correct them? Or just go ahead to deposit it?

If it's not that rare case of a valid outlier, rebuild that place such 
that it does not have geometry outliers and also is supported by the 
density map. Then re-run refinement and see what happens.

That's all I can tell given the amount of information you provided -;)

Good luck,

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