The problem hasn't been solved
I am a beginner to rosetta, and I was wondering if there is a way to truncate/ get rid of a specific part of a sequence and create a stable protein? I have the PDB of the protein and the specific parts of the sequence I need to truncate. It is to get rid of loops at the terminus. Do I just input a sequence to rosetta with the unwanted parts deleted and have it model the protein ?
Sequence :
G-SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN-TSN
I am running loop model with the remodel protocol (remodel.static.linuxgccrelease). It succesfully can model despite ligands in the file using -ignore_unrecognized_res when a single structure is required with -nstruct 1 however as soo as I try to increase it to -nstruct 2 I get a segmentation fault. Anyone experience this before?
Hi all
I'm trying to dock the ligand into receptor with rosetta ligand docking with following command line
mpirun -np 20 rosetta_scripts.mpi.linuxgccrelease @options
where options file looks like this
Hi all,
I am new to Rosetta and FARFAR2. I have attempted modelling the structure of PDB:1KXK using the following command line:
rna_denovo -sequence gucuaccuaucgggcuaaggagccguaugcgaugaaagucgcacguacgguucuaugcccgggggaaaac -cycles 20000 -nstruct 3 -bps_moves false -minimize_rna true -secstruct ".....(((.((((((...(((((((((((((((....))))))..)))))))))..)))))))))....."
Now I want to compare the obtained structure to the original PDB and to calculate the RMSD. I ran the following:
Hello all,
I'm interested in applying RMSD constraints to a pose using pyrosetta.
I currenly have a native pose which is deformed manually, such the the backbone RMSD with respect to the native is 1 Angstroms.
pose.residue(r).set_xyz(a, py.rosetta.numeric.xyzVector_double_t(new_coords[0], new_coords[1], new_coords[2]))
However, when I relax (cartesian), I notice the structure relaxing back to the native, ie the RMSD decreases to ~0 Angstroms.
HI everyone, I want to RosettaMatch to introduce a ligand into a scaffold protein, but the ligand contains uncommon metals like Rh, I am afraid Rh is not recognizable like Fe by Rosetta.
So I want to ask about how to add a new metal element to Rosetta, and how many files should I edit to make sure it's done? As far as I know, maybe I have to edit atom_type_sets and residue_types sets under database/chemical/, but more specifically, I have no idea.
Any suggestions would help! And thanks for you time and effort.
I recently download the rosetta 2022.46 source code and rosetta 2022.46 ubuntu binanry. Then I'm confused how to install them. I try to unpack the binary file into my home directory, but then it seems nothing has been installed. for examle, "no module called pyrosetta" or "no module called pyrosetta.toolbox" or "init is not defined".
And I also complie the source code using scons , but it seems just create a bin folder contained release in some specific folder, but not installed in the system.
Who can help me to solve this problem?
Hi, everyone!
I am performing protein-protein docking with AtomPairConstaint (the experiment shows the distance between two ligands) and I have some questions:
a. Whether the ref2015 or ref2015_cst function considers the ligand (with params file)?
b. If I use ref2015_cst in the docking_protocol, does the score function consider the constraint weight in both low- and high-resolution stages?
