Resfile Error

[Anonymous]

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

[Anonymous]

File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_$ main/source/src/core/pack/task/ResfileReader.cc:1582 [ ERROR ] UtilityExitException ERROR:

 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.

[Anonymous]

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.

[Anonymous]

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.)

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