Description

This tool is for getting validation report from OneDep validation. Only mmCIF format is supported for models and diffraction data, CCP4 format for EM maps. NMR chemical shifts and restraints are not currently supported. If validation completed successfully, validation report in pdb and xml format will appear on hard drive.

It is not possible to predict how long will it take to get the report. Therefore after several attempts (see parameters to control duration and frequency of the requests), the tool will ouput session id, which can be used later as a parameter to query RCSB again.

Note, that running this tool again with files will create a new session on validation server, not enquire about previous job.

WARNING

This tool will send your model and data to RCSB servers for processing. Please refer to their privacy policy for details:

https://www.wwpdb.org/about/privacy

Command line usage examples

% phenix.get_pdb_validation_report model.cif

% phenix.get_pdb_validation_report session_id=91c9cfa73036de43f744c7fa0f3b08c563bd9f9b

% phenix.get_pdb_validation_report model.cif structure_factors.cif

% phenix.get_pdb_validation_report model.cif map.ccp4

GUI

Graphical user interface is currently available in "PDB deposition" section. Also, GUI will remember the session id, so when the job is restored, you should be able to query RCSB to see if the results are ready. When the results are fetched resulting page will change to show them.

List of all available keywords

• timeout = 600 How long to wait for the result, in seconds
• ping_frequency = 5 how often pool PDB for the result, in seconds
• session_id = None Session ID for the job submitted previously
• output_xml = True Fetch report in XML format
• job_title = None Job title in PHENIX GUI, not used on command line
• output
  • prefix = pdb_report
  • serial = None
• guiGUI-specific parameter required for output directory
  • output_dir = None