# Structure prediction

## Centroid mode minimization

Category:
Structure prediction

Hi everyone,

I was wondering if there is something like the Relax Application but to use it directly in centroid mode. I know AbInitio uses fragment insertion to start building structures in centroid mode that are later fed to the All-Atom relax application, but is there something that can do a montecarlo local exploration without leaving centroid representation?

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## Error of compiling AbrelaxApplication.cc

Category:
Structure prediction

Hi,I want to use ResolutionSwitcher in Montecarlo.cc to relax pdb after stage1-4,when i add "#include<protocols/abinitio/ResolutionSwitcher.hh> in MonteCarlo.cc",it turn to be a error"Resolution switcher was not declared in this scope".

I included all the header files but still not working.

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## What is the best protocol to predict the missing residues in X-ray crystallisation?

Category:
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.

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## Remodel: the pose does not have residue with chain=H, PDBnum=114

Category:
Structure prediction

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

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## AbInitioRelax.mpi Hangs - Waiting for Job Request

Category:
Structure prediction

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:

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