Unsolved

Dear ALL,
I try to design a protein named test.pdb. Each time, the fix bb will output the result as test_0001.pdb. Is there any way to output the result as design_0001 or any name? Thank you

Hi,

I wonder if there is a way to trigger the optimization of polar hydrogens in PyRosetta just like the "-no_optH" option in Rosetta when reading structure information from PDB files into Pose. Because I found many potential hydrogen bonds in the original PDB structures were interrupted by the wrongly added hydrogens by default which result very high energy scores.

I have not found any routines to set free the movemenet of hydrogens in the MoveMap settings.

Hi,
I am trying to use rosetta3.1 cluster function to cluster 1000 pdbs of a homodimer that were created by Symmdock of rosetta3.2 and are still in centroid mode. Even if I get the pdb outputs for the clusters , I still get an output txt file that crashes at line 2,707,992 and doesn't give me the clustering information. The problem is that there are so many warning messages of the following types for each atom:
core.conformation.Conformation: [ WARNING ] missing heavyatom...
core.io.pdb.file_data: [ WARNING ] can't find atom for res 84 atom CEN...

Hi everybody,

I'm been fairly successful at creating a large list of decoys for several of my project (de novo, loop modeling, etc). My runs typically produce 30,000 to 50,000 decoy structures, which I am under the impression is a decent number.

What is the best method to determining the "most accurate" structure from these decoys? Do I cluster first, take the lowest energy (c.0.0.pdb). Or do I look at the top scoring structures from each cluster? (c.0.0.pdb, c.1.0.pdb, etc). Or do I score the entire set and take the lowest scoring structure to be the most accurate, without clustering?