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Rosetta CM incorrect threading

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Rosetta CM incorrect threading

I'm trying to do density guided homology modeling using Rosetta CM. I have the following two issues:

1) I generated two threaded models, via and manual threading. They are drastically different from one another.

2) I verified that the template helices match those in the ground truth structure. I would expect from the threaded model to connect the helices in the template correctly according to the alignment between the template and ground truth sequence. As shown in the screenshot, both threaded models connect the backbone incorrectly, and I guess this is what's causing divergence in the rosetta_cm generated structures. 

I attached screenshots for the template, template aligned with the auto threaded model and the manual threaded model.

Post Situation: 
Mon, 2018-08-06 11:09

I updated the screenshots, I would appreciate your prompt input. In this google drive folder, you can find the following:

1) template.

2) manual threaded model.

3) auto threaded model.

4) template sequence. 

5) ground_truth_sequence.

6) grishin alignment file.

Tue, 2018-08-07 20:57

I just realized, some of the fragments are placed incorrectly, this is likely why the threaded model is a bit messed up. In real de novo situation, where there is no homologue, how to be able to detect this? Still, why am I getting two diffeent models from auto and manual threading? 

Fri, 2018-08-10 09:48