Error in Loop modeling and other queries

[Anonymous]

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

 

 

 

[Anonymous]

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.

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