Hi I've got provblem with Rifdocking protocol 19 when I test one of commands:
protocols.jd2.JobDistributor: [ WARNING ] mot_ferr_ems_00043_000000149_0001_58_64_E_HHHH_bc_01900_0001 reported failure and will NOT retry protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MotifGraft - motif_grafting======================= protocols.motif_grafting.movers.MotifGraftMover: Executing Motif Graft Mover protocols.motif_grafting.movers.MotifGraftMover: Target scaffold size: 65 protocols.motif_grafting.movers.MotifGraftMover: Motif size: 7 protocols.motif_grafting.movers.MotifGraftMover: contextStructure size: 211 protocols.motif_grafting.movers.MotifGraftMover: Target scaffold numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: Motif numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: contextStructure numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 7 protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment/size combination there are not fragments that match the size of your motifs. protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
File: src/protocols/motif_grafting/movers/MotifGraftMover.cc:546 For this scaffold there are not suitable scaffold grafts within your constrains protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job mot_ferr_ems_00043_000000149_0001_58_64_E_HHHH_bc_01944_0001
[ ERROR ]: Caught exception:
File: src/protocols/motif_grafting/movers/MotifGraftMover.cc:546 For this scaffold there are not suitable scaffold grafts within your constrains
I followed the protocol and my command shown below: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol /home/gaon/cao_protocol/cao_2021_protocol/paper_motif_graft.xml -beta_nov16 -in:file:silent /home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/scaffold_splits/xah.silent -keep_input_scores False -silent_read_through_errors -out:file:silent out.silent -out:file:silent_struct_type binary -mute protocols.rosetta_scripts.ParsedProtocol.REPORT -parser:script_vars CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol @/home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/grafting.flags -parser:script_vars motifpdb=/home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/motifing/motifs/mot_ferr_ems_00043_000000149_0001_58_64_E.pdb.gz hotspots=1:2:3:4:5:6:7 -out:prefix mot_ferr_ems_00043_000000149_0001_58_64_E_
Could anyone please tell me why this error happened? Could it be fixed or just because something else? I will appreciate for the help. Thank you!
"For this scaffold there are not suitable scaffold grafts within your constrains"
Not every motif will fit on every scaffold. The scaffold needs to have the correct geometry to match up with the motif you're trying to insert with the specifications you've imposed based on the parameters and settings you've specified.
The first thing I'd do is see if you can get decent results with a simpler system -- first try any examples which were provided with the protocol, to make sure they work in your hands. Then I'd try "toy" examples, like attempting to redock a known native complex, or rescaffold motifs extracted from one protein back onto the exact same protein (that is, the exact same PDB code).
If you can get the protocol to work in these simple cases, chances are that the issues you're running into are because your experimental system just won't accomodate what you're trying to do. At that point you should attempt loosening your design requirements: try adding in different scaffolds/templates. Try adjusting how many/how long of motifs you're trying to match. Look at the adjustable parameters in the protocol, and see if there's any you can tweak to make things more forgiving (e.g. if there's a geometry match threshold you can open up, or a score threshold you can loosen, or if there's an extra optimization step which takes longer but which can bring things back into alignment.) -- If there's a way you can start with a known working example and "sneak up" on the experimental conditions you're interested in, that might also help figure out where the issue lies.