Unsolved

Hi all,

I would like to make a change to the source code of a particular application - it's a very minor, but necessary, change that should make the application more broadly applicable.

However, having made the change in the .cc file - how would I go about recompiling the code so that it links to the rest of the Rosetta package, or is the simplest way just to recompile the whole package?

Thanks in advance.

wsg

When running the Loop Modeling script on my protein of interest, the identity of the amino acids in the loop changes when it generates the full atom model from the centroid model. In other words, in the centroid model the amino acids are equivalent to the protein sequence from the original PDB, but they are "mutated" in the FA model (often to lots of G's). Is there a way to prevent this from happening?

I have run into an intermittent problem with RNA_minimizer within the rna_denovo application. I am using identical setups in different directories and shells. I have two calculations currently running without problems. When I try the same calculation in a 3rd directory, I am getting high scores for lk_nonpolar and the resulting pdb structures have steric clashes with overlap side chain atoms. There are no errors reported during the calculation, but the results are not usable.

The calculation is a simple rna hairpin using rna_helix to generate the stem.pdb file:

Dear experts,

I need the relative energy of several thousands of conformations of the same 10-residues loop including its static environment. However, I've only found the way to get the absolute energy of the complete structure. This seems a waste of time since most of the inter-residue energy terms are just the same. Is it possible to efficiently compute the energy of a small loop while taking into account its environment in PyRosetta? How?

Thanks a lot!
- Mon