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I am trying to use loopmodel to fold a linear peptide of 216 standard aa (obtained from the only existing data: fasta file, by using either the BuildPeptide or FragmentPicker executables of rosetta3.3).

I first tried "loopmodel.mpi.linuxgccrelease" (in my Open MPI compilation :scons bin mode=release cxx=gcc cxx_ver=4.6" ALL executables are both ".mpi." and non-mpi, which is strange as not all are parallelized) according to the command line:

Hi,

I have a question about output file test_loop_output.fasc in
an example of Cyclic Coordinate Descent loop closure - loop_modeling.py.
Here we have rmsd and Lrmsd, what is the difference?
In manual you can find that Lrmsd is the rmsd of all loops in the reference
frame of the fixed protein structure.
What does it means? What is rmsd?
How to find rmsd for all loop backbone atoms?

Thank you,

Victor

Hi,

Just curious if there is or there will be a flag to use Roland's 2010 Rotamer library within Rosetta. We have been replacing the 2008 binaries with data using the 2010 library and then using the 2008 flag, which works well enough. I'm still learning C++, or I would try and implement it myself.

Also, if it does already work within Rosetta, where would I find it within the code, and which level of smoothing was used? (optim, 5%, 20%)? We have been using optim (with the neighbor-dependent ramachandran flag) across most of Rosetta's apps and it seems to work well.

hi,

is it possible to restrict a space in Rosetta Design... like use some dummies guaranteeing that positions in this area are not to large thus blocking space... or do I have to restrict the surrounding amino acids going for small ones and just hope that´s enough.
Thanx!