[phenixbb] simulated annealing

Nathaniel Echols nechols at lbl.gov
Fri Jun 18 18:13:06 PDT 2010

On Fri, Jun 18, 2010 at 5:05 PM, jp d <yoyoq at 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
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.

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