Unsolved

I apologize if this has been asked before, but I couldn't seem to find any information on it. Is the EnsembleDock protocol available in Rosetta3.5? I don't see a specific executable for it in the rosetta/source/bin directory. Do I just use -l <pdblist> instead of -s <pdbfile> in the normal docking protocol? And can I still use constraints in EnsembleDock?

Hi everyone,

I am using enzyme design application to mutate my enzyme. How can I extract a list of the pdb name, residues and residue number from the output generated by Rosetta.

The sequence recovery does something similar, but i need to know what residues have changed in what position. I am looking for trends hence I need to do this fo a bunch of pdbs that meet my cut off. Is there a quick way of getting a series of fastA files that I can view on any sequence alignment tool or a table ?

Thanks in advance for your help

Dear all

I been trying to perform a symmetric docking with constraints and it is not working. Reading old post residue number must be carefully set. For some reason the low-res filter is dumping all the solutions ("STRUCTURE FAILED LOW-RES FILTER"). I imagine that has to be with how I define the constraints but I even tried using AtomPair CA 52 CA 182 GAUSSIANFUNC 50.0 50.0. Please can someone have a hint of what is going on?

thanks in advance

felipet

Is the Robetta website available for hosting on your local machine for intranet access? (yes, I am trying to avoid working in a Linux terminal window at all costs ;) )