[phenixbb] using reference model with polyA chain.

Francis Reyes Francis.Reyes at colorado.edu
Tue Nov 19 16:03:52 PST 2013

I'm refining a structure ( at low res ), so I trimmed off all the side chain atoms from my model while my reference model still has these chains. I'm receiving errors like...
    ----------Correcting rotamer outliers to match reference model----------   

** evaluating rotamers for working model **
  A 502  ILE is missing some sidechain atoms, **skipping**
  A 504  LYS is missing some sidechain atoms, **skipping**
  A 505  VAL is missing some sidechain atoms, **skipping**

I don't care about the side chain atoms, but I'd still like the reference model restraints to provide secondary structure. Does "**skipping**" mean  that the reference model is no longer being considered for the particular residue? Or will I still retain my secondary structure from the reference model? 



Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder

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