Thanks! I have another question, I have 1000 different runs and some of them is better from others, is there a efficient way to choose only the runs with the best scores? 
and then use AnalysisReplicaExchange0 macro on a reduced list with the best scores?

On Tue, Nov 28, 2017 at 11:25 PM, Ben Webb <ben@salilab.org> wrote:
On 11/27/17 12:59 AM, מירב בריטברד wrote:
I ran modeling.py multiple times and created different output folders that each of them contain a stat file. Now I want to run clustering.py on all the stat files in the different folders, how can I do it?

Assuming you mean you want to merge multiple runs into one large ensemble and cluster the whole thing using the AnalysisReplicaExchange0 macro, just set the merge_directories argument to a list of all the directories containing your stat files (and RMF trajectories).

        Ben
--
ben@salilab.org                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
        - Sir Arthur Conan Doyle