Structure prediction

I know the full amino acid sequence for my protein. I have obtained its X-ray crystal PDB structure, as well as the mtz file from the crystallisation. There are several loops and termini not resolved. Can I ask what is the best protocol to predict the missing part? I understand it would still not be fully "true" after Rosetta's modelling. I just want to have a "mostly likely" one that can be used as the starting point for my molecular dynamic simulation.

I am exactly using the same files in the tutorial of https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling

In the "Extending the Termini" section, I use "3gbn_missing_cterm.pdb", "3gbn_missing_cterm.remodel" and "flag_missing_cterm" files as input, with a command 

$ROSETTA3/bin/remodel.linuxgccrelease @flag_missing_cterm

When reading the source code, follow the function to find the class definition, but there is no way to know which class it inherits from or whether there is a defined subclass of the class. At the same time, I don't know which file the virtual function of the virtual base class is implemented in.So I would like to ask if there is a class diagram of the code

Hi guys,

I recently downloaded and compiled Rosetta with MPI capabilities to take advantage of the 32 core processor we have on our workstation. Compilation went well, and I can call protocols - but they all seem to hang.

To help narrow things down, I am working out of the DeNovo Structure Prediction tutorial demo directory - I can call the protocol and it seems to start running as normal: