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I was using a script i wrote last year regarding motif grafting, but it no longer works, i suspect a pyrosetta update issue.
anyway, i am looking through the errors and it seemed the pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover's init_parameters() have some additional arguments that is must have.
my code is as follows:
Does anyone have experience adding custom atom types to Pyrosetta? I have tried creating my own `atom_properties.txt` file, shown below.
NAME ATOM LJ_RADIUS LJ_WDEPTH LK_DGFREE LK_LAMBDA LK_VOLUME
A1 X 2.0000 0.0486 1.0000 3.5000 23.7000
A2 X 2.0000 0.2000 1.0000 5.0000 23.7000
VIRT VIRT 0.0000 0.0000 0.0000 3.5000 0.0000 VIRTUAL
recently, i doing the Exercises of workshop6, but i found i was confused about the packing and design in rosetta...
Anybody can help to figure out why the two setting method of PACK （def pack1 and def pack2) return different energy？it should be the same as i think！
if i run pack1 followed by pack2, then it return the same(lower) energy. it seens that the design energy is not optimized. so should i set another packing after the design?
thanks if anyone can help.
Good morning everyone~
Recently, I had read the paper entitled "De novo design of potent and selective mimics of IL-2 and IL-15”
And I am very interesting in it, and I want to learning how to performing it in using pyrosetta.
However, in the Code availability section, I can not find any information about the submodule
I have GLIBC issue with the compiled PyRosetta4.Release.python35.linux.release-191 on a Suse Linux cluster. So I would like to compile it from the source but I cannot find the download link and cannot download it from github using my login details. Kindly suggest the link to download the source code for PyRosetta4.
I work with a protein where the crystal structure does not include the first 14 amino acids, which are intrinsically disordered.
I would like to add the missing 14 residues using PyRosetta, and I have therefore looked into the FAQ and tried to find the relevant methods in the documentation. After some considerations I have come up with strategy:
I am using FastRelax from PyRosetta. When I run it from PyRosetta, the number of rotamers built are way more than the number of rotamers when I run it with C++ relax binary. For instance: I use the following to relax a pdb with movemap in PyRosetta as follows:
def relax_pdb_with_movemap(self, pose, movemap):
relax = FastRelax()
In C++ I give the following command: