[phenixbb] secondary structure restraints

Nathaniel Echols nechols at lbl.gov
Mon Mar 28 07:36:32 PDT 2011

On Mon, Mar 28, 2011 at 6:50 AM, Bradley Hintze <bradley.hintze at duke.edu> wrote:
> Hello PHENIX developers.
> When I run phenix.secondary_structure_restraints 1ZY7.pdb format=refmac I
> get this error:
> Traceback (most recent call last):
>   File
> "/Users/bradleyhintze/phenix/phenix-dev-699/cctbx_project/mmtbx/command_line/secondary_structure_restraints.py",
> line 6, in <module>
>     secondary_structure.run(sys.argv[1:])
>   File
> "/Users/bradleyhintze/phenix/phenix-dev-699/cctbx_project/mmtbx/secondary_structure/__init__.py",
> line 766, in run
>     if (len(proxies) == 0) :
> NameError: global name 'proxies' is not defined
> Am I missing something?

Nope, I was.  It'll be fixed tomorrow (and I'll add a regression
test).  Version 1.7 should work, although it is somewhat less smart
about extracting the hydrogen bonding atoms.

> Also, is there anything like '-h' on phenix.secondary_structure_restraints
> so that I can figure out the different options?

There was supposed to be, but I think I broke this too.  Usually if
you run one of these programs without arguments it should tell you
something informative, but in this case it just complains about a PDB
file - anyway, easily fixed.


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