[phenixbb] Format problem of restraint file

Nathaniel Echols nechols at lbl.gov
Sun Jun 30 14:06:37 PDT 2013

On Sun, Jun 30, 2013 at 1:51 PM, Xiang Li <li338 at purdue.edu> wrote:
> I generated the basepairing restraint file by command phenix.secondary_structure_restraints MR.1.pdb > ss.eff . Then I opened the ss.eff file with gedit and edit the basepairing information. However, after I finished editing and saved the file, the refine program can not read the file. The error is "This application does not support the file type for ss.eff (format:txt)". I have attached a copy of the eff file. Do I have a way to solve the problem?

Aside from Pavel's answer: you can also check whether it's being
parsed correctly either by going to Utilities menu->Validate parameter
file... in the GUI.  On the command line, you actually need to use
"iotbx.phil" most of the time, not "libtbx.phil" (which doesn't
understand certain parameter types like unit_cell, space_group, or


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