You are here

Home » Forums » Rosetta 3 » Rosetta 3 - Applications

Rosetta ScriptsFeatures Reporter issue

6 posts / 0 new
Log in or register to post comments
Last post
Rosetta ScriptsFeatures Reporter issue
#1
Top

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:

AttachmentSize
complex.pdb230.43 KB
Category: 
Structure prediction
Post Situation: 
Unsolved
Sun, 2017-03-12 08:19
David Weis
Top

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.

Mon, 2017-03-13 08:10
smlewis
Top

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

Mon, 2017-03-13 10:03
David Weis
Top

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>

 

 

Mon, 2017-03-13 10:22
rmoretti
(Reply to #5)
Top

RESOLVED. This goes in 3.8.

    <MOVERS>

        <ReportToDB name="X" database_name="X.db3">

                <TotalScoreFeatures scorefxn="t14"/>

                <ResidueFeatures/>

                <InterfaceFeatures scorefxn="t14" />

        </ReportToDB>

    </MOVERS>

Mon, 2017-03-13 10:52
David Weis
Top

Are these dependancies documented somewhere?

Mon, 2017-03-13 10:59
David Weis