I am trying to replicate the work of the paper: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature23912.html?foxtrotcallback=true
It seems the Rosetta Script in the supplimentary meterials is old because when I try to use it I get a lot of typo errors, anyway I changed it but I could not find a way to fix this error:
Error messages were:
From line 41:
Error: Element 'CavityVolume': This element is not expected.
36: <AND filter_name="hk1"/>
37: <AND filter_name="sf1"/>
38: </CompoundStatement>
39: <ScoreType name="total_score_cen" score_type="total_score" scorefxn="SFXN2" confidence="0" threshold="0"/>
40: <PackStat name="pack" confidence="0"/>
41: <CavityVolume name="cavity" confidence="0"/>
42: <CalculatorFilter name="cavity_threshold" equation="c" threshold="1" confidence="1">
43: <VAR name="c" filter="cavity"/>
44: </CalculatorFilter>
45: <ResidueCount name="AlaCount" residue_types="ALA" max_residue_count="6" confidence="1"/>
46: <AverageDegree name="degree_core_SCN" task_operations="layer_core_SCN" confidence="1" threshold="9.4"/>
From line 63:
Error: Element 'RemoveCsts': This element is not expected.
58: </FILTERS>
59:
60: <MOVERS>
61: <Dssp name="dssp"/>
62: <SheetCstGenerator name="sheet_new1" cacb_dihedral_tolerance="0.6" blueprint="ehee.bp"/>
63: <RemoveCsts name="sheet_rm1" generator="sheet_new1"/>
64: <SetSecStructEnergies name="set_ssene1" scorefxn="SFXN1" blueprint="ehee.bp"/>
65: <BluePrintBDR name="bdr1" use_abego_bias="1" scorefxn="SFXN1" constraint_generators="sheet_new1" constraints_NtoC="-1.0" blueprint="ehee.bp"/>
66: <DumpPdb name="dump" fname="pass" tag_time="True"/>
67: <FastDesign name="fastdes" task_operations="limitchi2,layer_all" scorefxn="sfxn_std" clear_designable_residues="0" repeats="2" ramp_down_constraints="0"/>
68: <FastDesign name="fastdes4" task_operations="limitchi2,layer_all" scorefxn="sfxn_std" clear_designable_residues="0" repeats="4" ramp_down_constraints="0"/>
------------------------------------------------------------
Warning messages were:
------------------------------------------------------------
Error:
Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: structure_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5 seconds
Error: ERROR: Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages
Error:
If I remove the <CavityVolume> or the <RemoveCsts> I get errors asking for them.
Is this an update issue? or a different way to write the <CavityVolume> filter and the <RemoveCsts> mover?
Category:
Post Situation:
First off, be aware that the format of RosettaScripts changed slighlty in late 2016 (between Rosetta 3.7 and 3.8) to be more conformant with official XML syntax. Most of this change involves addition of quotes around options, and a rearrangment of some tags (like ScoreFunction tags). You can make these fixes manually, but there's also a conversion script availible at `Rosetta/tools/xsd_xrw/rewrite_rosetta_script.py` which can do it for you automatically.
Regarding CavityVolume, this is currently a devel-only filter. That is, it isn't in the released version of Rosetta. That shouldn't be the case, as it's been used in a publication, and I've prodded the appropriate people to take action to include it in a future weekly release. For the time being you'll need to remove the tag, as well as any location which uses the "cavity" filter (e.g. the "cavity_threshold" filter, etc.).
I believe the RemoveCsts mover has been renamed to "RemoveConstraints", and the interface has been changed slighlty. See the documentation (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/RemoveConstraintsMover) for details.
First off, be aware that the format of RosettaScripts changed slighlty in late 2016 (between Rosetta 3.7 and 3.8) to be more conformant with official XML syntax. Most of this change involves addition of quotes around options, and a rearrangment of some tags (like ScoreFunction tags). You can make these fixes manually, but there's also a conversion script availible at `Rosetta/tools/xsd_xrw/rewrite_rosetta_script.py` which can do it for you automatically.
Regarding CavityVolume, this is currently a devel-only filter. That is, it isn't in the released version of Rosetta. That shouldn't be the case, as it's been used in a publication, and I've prodded the appropriate people to take action to include it in a future weekly release. For the time being you'll need to remove the tag, as well as any location which uses the "cavity" filter (e.g. the "cavity_threshold" filter, etc.).
I believe the RemoveCsts mover has been renamed to "RemoveConstraints", and the interface has been changed slighlty. See the documentation (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/RemoveConstraintsMover) for details.
Hi,
Has this CavityVolume issue been solved? I see this filter published in many recent articles (as supporting info) and although it is possible to run the xml after removing the tags one wonder if the data generated is reproducible. It's very strange that such a widely used filter (an important one I assume) is still dev-only, and why nobody contacted the referenced journals to either push for the filter to be "released" or ask for a retraction/correction of the *misleading* published data.
Unfortunately, no, the CavityVolume filter is still not publically released. If you can point me to some recent papers which are using it, I can re-prod people about it, and hopefully get things moved to a public release.
De novo design of potent and selective mimics of IL-2 and IL-15
D-A Silva, S Yu, U Y. Ulge, J B. Spangler, et.al., 01/10/2019, Nature
I've opened a pull request to move the CavityVolumeFilter from devel into protocols (and into the public releases). I want to get my changes reviewed by the original author of the filter, but hopefully they'll be in the master branch of Rosetta soon.