Hello everyone,
I am trying to perform RosettaDesign, and I have a script that uses pyrosetta.rosetta.core.pack.task.parse_resfile()
In the past this worked just fine, but now with the new update it seems it doesn't work, I get this error:
RuntimeError:
File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_$ main/source/src/core/pack/task/ResfileReader.cc:1582 [ ERROR ] UtilityExitException ERROR:
I am not sure how to fix this issue, following is two codes that break:
pose = pose_from_pdb('structure.pdb')
packtask = standard_packer_task(pose)
pyrosetta.rosetta.core.pack.task.parse_resfile(pose, packtask, 'resfile')
and
resfile = rosetta.core.pack.task.operation.ReadResfile('resfile')
task = pyrosetta.rosetta.core.pack.task.TaskFactory()
task.push_back(resfile)
The contents of the resfile are as such:
NATRO
START
1 A PIKAA PGNQSTDERKH
2 A PIKAA AVILFYWQTM
3 A PIKAA QTY
I am not sure what has changed, did I compile PyRosetta incorrectly as to have missed the main/source/src/core/pack/task/ResfileReader.cc somehow?
Your help would be greatly appriciated
Category:
Post Situation:
This is not an error. This is the line that tells you you are about to be told what the error is.
The resfile is not obviously malformed (although I think start may need to be lower case). It's unlikely residues 1-3 on chain A don't exist unless your PDB starts from not-chain-A or not-1.
task.push_back(resfile) should not try to read the resfile, so if it is literally that line that is failing, something very unusual has occurred, but I think it's happening when you create a task later on.
I am having the same problem, and that is the end of the error message output (it stops right before saying anything useful).
The strangest part is that I have another copy of the same code running in a different window, just targeting pdb files that have different positions for the residues, and that part is not having this issue.
Looking at the code that throws the error message, there's a weird conditional that skips printing what the error message was if the -run:interactive flag is not set. Try adding the -run:interactive flag and see if it gives you a more informative error message.
(I'm going to take that out right now, so that future versions of Rosetta always print the error message. It's quite silly.)