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 Hey,

I am using Rosetta to build my protein from Ca-trace to all-atom, and then to refine this structure against cryo-em density.

However, when I use these two flags:- RBSegmentRelax::cst_wt 1.0  and -RBSegmentRelax::cst_width 4.0, I am getting the error:

Option matching -RBSegmentRelax:cst_wt not found in command line top-level context. 

When I remove these two flags, everytging works perfectly.

So, my question is: do these two flags are still used by ca_to_allatom application?

Dear structure predictors,

For extracting an alignment with the best template I used HHPred.

Which than predicted a chain of a PDB which is not the best one, because it doesn´t contain an important N-terminal part of my target. 

I would like to use another chain of this PDB but HHPred doesn´t predict it.

Is there a possibility to have a sequence structure alignment between a defined PDB and my target protein sequence with same quality HHPred does?

As I understand, the Gibbs free energy not only depends on the structure but also depends on the surrounding solution conditions. That is why under certain conditions (e.g. pH, temperature, ionic strength), the protein tends to unfold or remain native structure. So I wonder if there is a theoretical assumption to set the scoring background? For example, is it under pH 7, 25 degree C, or vacuum state? Thank you.

Hi!

I´m very new at Rosetta Commons and not an expert.

We wanted to predict comparative models using a standard protocol.

Then, we always got the Error:

unknown atom_name: CA  CB

Is this because of the Error before? :

Error: potential mismatch between sequence from alignment  and sequence from PDB! ??

This error is because no secondary structure is defined at 20 residues and therefore the coordinates for the atoms of these missing amino acids are missing.