On Fri, Jun 18, 2010 at 5:05 PM, jp d <yoyoq@yahoo.com> wrote:
hi,
using supplied phenix examples  1rxf.mtz  and  1rxf_randomise.pdb
i can run the following command and it fails
in phenix1.6.2  but not in phenix1.5-2

the error is: 
RuntimeError: Bond distance > max_reasonable_bond_distance: 52.1931 > 50

This is telling you that one of the bonds in the model is longer than the limit we've set - a simple sanity check that warns you there is something seriously wrong with the PDB file.  This parameter appears to have been added since 1.5-2.  It's possible that it's really a bug in the restraints generation, but usually these types of errors indicate corrupted coordinates.  (For instance, in certain circumstances CNS sometimes outputs atoms at 999.99,999.99,999.99, which would probably trigger this error.)

You should still use 1.6.2.  You can, if you'd like, add the parameter max_reasonable_bond_distance=None to force it to accept absurd bond lengths, but this is probably just going to mask a problem with either your PDB file or our code.  We need to see the PDB file to tell for sure.

-Nat