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Hello,

I am interested in any advice on choosing an appropriate cluster on which to run Rosetta 3.4. Most likely, I'll be using it for relaxation and high-resolution, all-atom refinement. I am just wondering about the parallel granularity -- the ratio of communication to computation (e.g. coarse vs fine grained). Is it better to go with more of a throughput cluster or a more tightly coupled, low latency cluster?

Here are my main options (pertaining to the SHARCNET systems):

Hello everyone!

I'm new in the community and I would like to know where I find information about ab initio with metalloproteins (metalloprotein abinitio relax). I just found this link in the forum that talks about docking with metal but it's not exactly what I'm looking:

http://www.rosettacommons.org/node/2259

I'm trying to generate the same results in Wang et al., 2010 (Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science)

What is the difference between "decoy" and "pose" in Rosetta?
I know conventionally "decoy" is more popular in protein docking. But it seems in Rosetta "decoy" is generalized to describe the output structure models of all Rosetta programs, not just docking results. When I read the Rosetta source code, I saw "pose" everywhere. Do they have the same concept in Rosetta?

Hi,
I have followed Rosetta Density-fitting Tutorial to try to fit a B-form DNA into a segmented cryo EM map. The result after idealize and relax using default settings gave rise to a highly distorted DNA structure, very likely due to pushing all atoms into the density. The DNA within the EM map is supposed to be only slightly bent. I wonder if there is any special functions I can use to only do a rigid body fitting of the DNA based on information like helical axis extracted from the EM density. Thanks a lot!