Rosetta ScriptsFeatures Reporter issue

This topic has 15 replies, 3 voices, and was last updated 7 years, 10 months ago by Anonymous.

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- March 12, 2017 at 3:19 pm #2613
  Anonymous
  I am attempting to use the Fetures Reporter InterfaceFeatures on MacOS with Rosetta 3.8, but I get an error back. If I comment out InterfaceFeatures, the script runs fine. The PDB file is clean, just two proteins (attached). Do I have some misunderstanding about the nature of the InterfaceFeatures reporter?
  
  My script is
  
  <ROSETTASCRIPTS>
  
  <SCOREFXNS>
  
  <ScoreFunction name=”t14″ weights=”talaris2014″ />
  
  </SCOREFXNS>
  
  <RESIDUE_SELECTORS>
  
  </RESIDUE_SELECTORS>
  
  <TASKOPERATIONS>
  
  </TASKOPERATIONS>
  
  <FILTERS>
  
  </FILTERS>
  
  <MOVERS>
  
  <ReportToDB name=”X” database_name=”X.db3″>
  
  <TotalScoreFeatures scorefxn=”t14″/>
  
  <InterfaceFeatures scorefxn=”t14″ />
  
  </ReportToDB>
  
  </MOVERS>
  
  <APPLY_TO_POSE>
  
  </APPLY_TO_POSE>
  
  <PROTOCOLS>
  
  <Add mover_name=”X”/>
  
  </PROTOCOLS>
  
  </ROSETTASCRIPTS>
  
  Executed on command line as
  
  rosetta_scripts.macosclangrelease -s complex.pdb -parser:protocol test.xml -overwrite
  
  Returns these errors in trace
  
  protocols.features.ReportToDB: Tag with name ‘InterfaceFeatures’ is invalid
  
  Error: ERROR: Exception caught by rosetta_scripts application:
- March 13, 2017 at 3:10 pm #12217
  Anonymous
  It’s not your PDB that’s the problem, there is an error of some sort in your XML.
  
  First fix: try running it through the XML fixer: https://www.rosettacommons.org/docs/latest/Release-Notes#rosetta-3-8_new-rosettascripts-xml . If that doesn’t change the XML / work, we’ll try debugging the XML further.
- March 13, 2017 at 3:10 pm #12738
  Anonymous
  It’s not your PDB that’s the problem, there is an error of some sort in your XML.
  
  First fix: try running it through the XML fixer: https://www.rosettacommons.org/docs/latest/Release-Notes#rosetta-3-8_new-rosettascripts-xml . If that doesn’t change the XML / work, we’ll try debugging the XML further.
- March 13, 2017 at 3:10 pm #13259
  Anonymous
  It’s not your PDB that’s the problem, there is an error of some sort in your XML.
  
  First fix: try running it through the XML fixer: https://www.rosettacommons.org/docs/latest/Release-Notes#rosetta-3-8_new-rosettascripts-xml . If that doesn’t change the XML / work, we’ll try debugging the XML further.
- March 13, 2017 at 5:03 pm #12220
  Anonymous
  Maybe not executing the XML fixer correctly?
  
  /Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py –input old_test.xml –output new_test.xml
  
  Traceback (most recent call last):
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 1391, in <module>
  
  new_version = rewrite_xml_rosetta_script_lines( lines )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 1360, in rewrite_xml_rosetta_script_lines
  
  toks = modfunc( element_root, toks )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 792, in rename_report_to_db_children
  
  rename_report_to_db_children( elem, tokens )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 792, in rename_report_to_db_children
  
  rename_report_to_db_children( elem, tokens )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 782, in rename_report_to_db_children
  
  assert( attr )
  
  AssertionError
- March 13, 2017 at 5:03 pm #12741
  Anonymous
  Maybe not executing the XML fixer correctly?
  
  /Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py –input old_test.xml –output new_test.xml
  
  Traceback (most recent call last):
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 1391, in <module>
  
  new_version = rewrite_xml_rosetta_script_lines( lines )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 1360, in rewrite_xml_rosetta_script_lines
  
  toks = modfunc( element_root, toks )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 792, in rename_report_to_db_children
  
  rename_report_to_db_children( elem, tokens )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 792, in rename_report_to_db_children
  
  rename_report_to_db_children( elem, tokens )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 782, in rename_report_to_db_children
  
  assert( attr )
  
  AssertionError
- March 13, 2017 at 5:03 pm #13262
  Anonymous
  Maybe not executing the XML fixer correctly?
  
  /Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py –input old_test.xml –output new_test.xml
  
  Traceback (most recent call last):
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 1391, in <module>
  
  new_version = rewrite_xml_rosetta_script_lines( lines )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 1360, in rewrite_xml_rosetta_script_lines
  
  toks = modfunc( element_root, toks )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 792, in rename_report_to_db_children
  
  rename_report_to_db_children( elem, tokens )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 792, in rename_report_to_db_children
  
  rename_report_to_db_children( elem, tokens )
  
  File “/Users/dweis/apps/rosetta/3.8/tools/xsd_xrw/rewrite_rosetta_script.py”, line 782, in rename_report_to_db_children
  
  assert( attr )
  
  AssertionError
- March 13, 2017 at 5:22 pm #12221
  Anonymous
  I’m able to get your script to work on the most recent version of Rosetta (Rosetta 3.8, more or less) by adding the ResidueFeatures reporter to the list (the InterfaceFeatures reporter has a dependency on the ResidueFeatures reporter, and will not work if you don’t also include it.)
  
  Your script, however, won’t work with Rosetta 3.7 because it’s in the new RosettaScripts format. If you do want to use it with Rosetta 3.7 or before, you need to use the old format:
```
        <ReportToDB name="X" database_name="X.db3">



<feature name="TotalScoreFeatures" scorefxn="t14"/>



<feature name="ResidueFeatures" name="feature" />

<feature name="InterfaceFeatures" name="feature" scorefxn="t14" />



</ReportToDB>
```
- March 13, 2017 at 5:22 pm #12742
  Anonymous
  I’m able to get your script to work on the most recent version of Rosetta (Rosetta 3.8, more or less) by adding the ResidueFeatures reporter to the list (the InterfaceFeatures reporter has a dependency on the ResidueFeatures reporter, and will not work if you don’t also include it.)
  
  Your script, however, won’t work with Rosetta 3.7 because it’s in the new RosettaScripts format. If you do want to use it with Rosetta 3.7 or before, you need to use the old format:
```
        <ReportToDB name="X" database_name="X.db3">



<feature name="TotalScoreFeatures" scorefxn="t14"/>



<feature name="ResidueFeatures" name="feature" />

<feature name="InterfaceFeatures" name="feature" scorefxn="t14" />



</ReportToDB>
```
- March 13, 2017 at 5:22 pm #13263
  Anonymous
  I’m able to get your script to work on the most recent version of Rosetta (Rosetta 3.8, more or less) by adding the ResidueFeatures reporter to the list (the InterfaceFeatures reporter has a dependency on the ResidueFeatures reporter, and will not work if you don’t also include it.)
  
  Your script, however, won’t work with Rosetta 3.7 because it’s in the new RosettaScripts format. If you do want to use it with Rosetta 3.7 or before, you need to use the old format:
```
        <ReportToDB name="X" database_name="X.db3">



<feature name="TotalScoreFeatures" scorefxn="t14"/>



<feature name="ResidueFeatures" name="feature" />

<feature name="InterfaceFeatures" name="feature" scorefxn="t14" />



</ReportToDB>
```
- March 13, 2017 at 5:59 pm #12224
  Anonymous
  Are these dependancies documented somewhere?
- March 13, 2017 at 5:59 pm #12745
  Anonymous
  Are these dependancies documented somewhere?
- March 13, 2017 at 5:59 pm #13266
  Anonymous
  Are these dependancies documented somewhere?
- March 13, 2017 at 5:52 pm #12223
  Anonymous
  RESOLVED. This goes in 3.8.
  
  <MOVERS>
  
  <ReportToDB name=”X” database_name=”X.db3″>
  
  <TotalScoreFeatures scorefxn=”t14″/>
  
  <ResidueFeatures/>
  
  <InterfaceFeatures scorefxn=”t14″ />
  
  </ReportToDB>
  
  </MOVERS>
- March 13, 2017 at 5:52 pm #12744
  Anonymous
  RESOLVED. This goes in 3.8.
  
  <MOVERS>
  
  <ReportToDB name=”X” database_name=”X.db3″>
  
  <TotalScoreFeatures scorefxn=”t14″/>
  
  <ResidueFeatures/>
  
  <InterfaceFeatures scorefxn=”t14″ />
  
  </ReportToDB>
  
  </MOVERS>
- March 13, 2017 at 5:52 pm #13265
  Anonymous
  RESOLVED. This goes in 3.8.
  
  <MOVERS>
  
  <ReportToDB name=”X” database_name=”X.db3″>
  
  <TotalScoreFeatures scorefxn=”t14″/>
  
  <ResidueFeatures/>
  
  <InterfaceFeatures scorefxn=”t14″ />
  
  </ReportToDB>
  
  </MOVERS>
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