I am trying to use the LoopModelerMover to relax a couple of loops in a protein complex. I would like to let Rosetta select cutpoints automatically so I leave the cutpoints set to 0. An example script is attached as a text file. I have tried specifying the loops as loop subtags and as a loops file, and in both cases I get this error.
ERROR: Can't build a fold tree from a loop with an unspecified cut point.
I have also tried omitting the cutpoint subtag and the cutpoint column in the loops file, and I still get this error. However, the script runs fine when I manually specify cutpoints in in the loop subtags or in the loops file. This has happened with the 3.12 numbered release as well as the 2020.50 and 2021.38 weekly releases. This seems to be the same problem reported in these threads https://www.rosettacommons.org/node/10856 and https://www.rosettacommons.org/node/10677, but unfortunately no solutions have been posted to either.
Interestingly, I do not get this error when use the loopmodel application from terminal, but I do get this message:
[ WARNING ] The LoopRelaxMover is no longer maintained. Please use the LoopModeler mover as replacement.
I'd really just to like to get this over with. Is it fine to use the loopmodel application even with the warning? If not, is there an older version of Rosetta I should use where the LoopModelerMover definitely works?
Response from Cody Krivacic in the Kortemme lab:
"KIC will automatically set the cut points for you based on the pivot residues it chooses, so while it may be confusing from an end-user perspective, it’s perfectly fine to manually choose the initial cut points. I looked through old protocols and this is how I’ve set it up in the past, but just to be sure I did a little digging, and the PivotPicker class returns a new loop for the ClosureProblem/KICMover classes to work with that already has pivot 2 set as the cut point. Sorry for the confusion, I’ll make sure this is reflected in the documentation."