Format problem of restraint file
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Hi everyone, 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? Thanks for your help! Sincerely, Xiang
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Hi Xiang, libtbx.phil ss12.eff tells: (...) Syntax error: no matching "}" for "{" at file "ss12.eff", line 769 You need to have "}" after line 1284. Perhaps the same for next nucleic_acids block, etc.. You need to make sure all { and } match. I quickly edited your file so it at least passes libtbx.phil (attached). Pavel On 6/30/13 1:51 PM, Xiang Li wrote:
Hi everyone,
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?
Thanks for your help!
Sincerely, Xiang
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On Sun, Jun 30, 2013 at 1:51 PM, Xiang Li
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 atom_selection). -Nat
participants (3)
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Nathaniel Echols
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Pavel Afonine
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Xiang Li