Dear Rosetta users
I have generated a model by fitting a crystal structure to electron density map using flexible fitting software (MDFF). This is a 864 aa long protein with two domains. However I am not satisfied with the fitting of a specific regions( a stretch of ~50 aa between two domains). This region contains a small helix surrounded by loops. I am trying to remodel this region using rosetta loop modeling and using electron density restraints. I am using following flags in the loop modeling protocol-
-database ~/path/to/rosetta_src_2015.39.58186_bundle/main/database (I am giving actual path in the file)
-s loop_model_input.pdb
-loops::build_attempts 10
-loop_file loop_def.txt
-loops::remodel perturb_kic
-loops::intermedrelax no
-loops::refine refine_kic
-loops::relax fastrelax
-loops::strict_loops
-relax:jump_move true
-edensity:mapfile target21.mrc
-edensity:mapreso 21.0
-edensity:grid_spacing 2.76
-edensity:realign min
-edensity:whole_structure_allatom_wt 0.05
-out::nstruct 5
-out:file:silent loopmodel.out
The loop_def.txt contains just one line
LOOP 489 541 0
When I am running this using loopmodel.linuxgccrelease, I am getting following error.
[ERROR] Exception caught by JobDistributor for job loop_model_input_0001Cannot normalize xyzVector of length() zero
protocols.jd2.JobDistributor:
protocols.jd2.JobDistributor: loop_model_input_0001 reported that its input was bad and will not retry
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: loop_model_input_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 5 jobs considered, 1 jobs attempted in 2778 seconds
caught exception 1 jobs failed; check output for error messages
I have following queries
1) Is my approach correct for doing this task? If yes how to solve this error. If no, then what should I be doing for modeling this region.
2) Is remodel a better option for such kind of modeling, If yes how should I go about using it?
Kindly let me know if anyother explanation is required.
Sorry for the long post
Thank you
Best
Ashutosh
The "Cannot normalize xyzVector of length() zero" error does happen occasionally - often it's just a fluke due to random number draws. I'd recommend re-running the protocol and see if things work better with a different random number seed.
It's only if you consistently get that error with different runs with different random number seeds would I be worried about the issue.