Element ‘trRosettaProtocol’: This element is not expected.

[Anonymous]

Hi,

I want to run the given protocol for trRosettaProtocol mover described in the website (https://new.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/trRosettaProtocol). However, when I tried to run the Example script, I got following errors. I used the newest version of weekly release of rosetta which is rosetta_bin_linux_2021.07.61567_bundle, and compiled with tensorflow_gpu as described in the protocol. Then I run the rosetta script using the command in below. Besides, in the tutorial, there is a folder name “Rosetta/main/source/src/protocols/trRosetta” containing input files for protocol, but my downloaded version that folder is not exist. My question is that did I download the wrong version of rosetta to use trRosettaProtocol or rosetta_script is not the right command to be used for.

Thanks in advance,

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My commands:

ROSETTA/main/source/bin/rosetta_scripts.tensorflow_gpu.linuxgccrelease

-parser:protocol trRosetta_protocol.xml

-database $ROSETTA/main/database/

-input_empty_pose true   ### NOTE: I used this one after this ERROR: Attempting to initiate job distribution for input job ‘S’, but the generated pose has no residues.make sure you specified a valid input PDB, silent file or database. If this is intended, use the flag ‘-input_empty_pose true’ (we check this to quickly curb silly mistakes, such as accidentally providing pdb (or other input) files with no atoms)

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Error messages were:

From line 21:

Error: Element ‘trRosettaProtocol’: This element is not expected. Expected is one of ( AbscriptLoopCloserCM, AbscriptMover, AcceptToBestMover, AddChain, AddChainBreak, AddCompositionConstraintMover, AddConstraints, AddConstraintsToCurrentConformationMover, AddHelixSequenceConstraints, AddHydrogens ).

16:     </FILTERS>

17:     <MOVERS>

18:         <trRosettaProtocol name=”predict_struct” msa_file=”hhblits_full_1544230.a3m”

19:             sequence=”GAMDPRTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAF”

20:             mutate_gly_to_ala=”false” backbone_randomization_mode=”ramachandran”

21:         />

22:     </MOVERS>

23:     <PROTOCOLS>

24:         <Add mover=”predict_struct” />

25:     </PROTOCOLS>

26:     <OUTPUT scorefxn=”r15″ />

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Warning messages were:

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[Anonymous]

I haven’t verified this carefully but “2021.07” should mean “the 7th week of 2021”, which is in February; the trrosetta C++ didn’t go online until a few weeks ago (so probably early April?) – I think it’s just not there yet in the released code.

[Anonymous]

In the download page, release date is given as Thursday, March 4, 2021 for “2021.07″. That is why, I thought that it may be in this released version.

[Author]

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