On Mon, Mar 28, 2011 at 6:50 AM, Bradley Hintze
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. -Nat