[phenixbb] secondary restraints

Nathaniel Echols nechols at lbl.gov
Mon Jun 21 12:16:00 PDT 2010

On Mon, Jun 21, 2010 at 11:55 AM, Jianghai Zhu <jzhu at idi.harvard.edu> wrote:

> I am using secondary restraints in the phenix.refine. I got the following
> error message.
> hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
>  "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name H"
> => 0 donors
>  "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name O"
> => 3 acceptors
> . . .

Traceback (most recent call last):
> . . .

> "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py",
> line 652, in _donors_and_acceptors
>    donor_isel.insert(k, n_atoms)
> IndexError: Index out of range.

The code will try to switch intelligently between restraining H-O and N-O
distances, depending on whether or not hydrogen atoms are present in the PDB
file - but it does so globally, and *any* hydrogen atoms are enough to
trigger use of the H-O restraints.  The warning messages are telling you
that hydrogens are missing on those residues; this could happen if you added
residues in Coot, but didn't re-run phenix.ready_set to fully hydrogenate
them.  The IndexError is just a bug, probably due to some special case
present in your model.

If you intended to refine with hydrogens, you should run phenix.ready_set
first; if not, I'd recommend deleting whatever hydrogen atoms are present
now, and/or add this parameter:


which will tell it to only restrain N-O distances.  I'd still like to figure
out why it crashes, however - could you please send me the PDB file
privately?  (I don't need data for this, just the model.)

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