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I want to model a protein that has two domains. I have two separate domains modeled using Rosetta. I want to merge these two domains based on the cst file that gives inter domain distance constraints.
What are some of the best ways to model it? These domains are asymmetric. Can I use RosettaCM to do the modeling? Or should it be more like fold and dock?
Dear Rosetta users,
I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.
My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?
Thanks for help! Staszek
Hi I have not used Rosetta for a while. i wanted to relax my receptor for enzyme design and i kept on having the message
Evaluation Creator active ...
protocols.relax.FastRelax: WARNING: Pose has no residues. Doing a FastRelax would be pointless. Skipping.
protocols.jd2.JobDistributor: S_0001 reported success in 0 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs att
here is my flag file
I'm trying to use the InterfaceHoles filter and get the following error:
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER holes=======================
core.scoring.packing.compute_holes_score: compute_holes_surfs try: 1
sh: 1: alpha20_surf: not found
Any idea where alpha20_surf needs to be (or if it needs to be compiled?)
I built the last release 2017.08 recently. I have not encountered any error during the build. Here is the command I ran:
./scons.py -j8 mode=release bin extras=cxx11 extras=mpi
I have gcc version 5.4.0 so according to build tutorial this should new enough to have C++11 support.
But when I am running antibody.linuxrelease as according to the protocol on
I have recently started learning Rosetta. Now I am working on antibody modelling. I have prepared my inputs, have blast and Pro-Fit working. When I am running the antibody.py with the default preprocessing options