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 setup_RosettaCM.py 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.
|Template fragments||352.15 KB|
|Ground truth superimposed on the template, threading should connect the fragments in a similar fashion based on the sequence,no?||177.84 KB|
|Two different threaded models, why?||375.68 KB|