Dear Sir or Madam,
Hello,
I am trying to run the docking protocol for a high resolution local refinement, but I get a Segmentation fault error. The command is
docking_protocol.linuxgccrelease -partners A_B -docking_local_refine -database $ROSETTA_DB -in:file:l list.txt -ex1 -ex2aro -use_input_sc -out:file:silent decoys_high_res_refinement.silent -out:file:silent_struct_type binary -out:path:score score_high_res_refinement.sc -out:prefix high_res_ref_ -out:nstruct 100
Hello,
I have a problem with cleaning my protein before ligand docking. I use the command clean_pdb.py 1i09 A to download and clean GSK-3, but the final structure has some missing residues, even more than the initial structure in the protein data bank. There is no gap in the AA sequence when open the structure as a text file, but using PyMol, there are dotted lines instead of solid lines in some areas of the structure. I have uploaded the initial and the cleaned PDB files for your consideration.
import subprocess
def minimize(working_directory):
subprocess.run([rosetta/main/source/bin/rosetta_scripts.static.linuxgccrelease,
f"@{flags_relax.txt}",
f"-parser:protocol",
f"{dock_relax.xml}"',
"-database","rosetta/main/database/],
cwd=str(working_directory))
The above is the program I used.When I use rosetta_scripts.static.linuxgccrelease command to minimize pdb, but the following warning appears and the program cannot be stopped:
hello,
I was performing protein protein advanced docking from tutorials and I did docking_analyser.xml protocol and got docking_analysis.csv with all scorings and now I have trouble making plots in R with provided script sc_vs_rmsd.R . I have tried Rscript sc_vs_rmsd.R docking_analysis.csv total_score but it outputs error "Must request at least one colour from a hue palette." I would appreciate very much if some one could help me. thank you
jovana
Hello,
I am calculating the Pnear for the Rosetta ligand docking outputs to evaluate the funnel-likeness of energy vs RMSD by treating the lowest energy model as the native structure. Is it right to use binding energy and ligand RMSD (no superposition) as E and RMSD in Pnear formula? I see in the papers it is used for de novo designs and they use the total energy and general RMSD.
I really appreciate your help.
I'm trying to seperate a protein-protein complex, apply residue labels based on core/surface/boundary layer definitions, and then reset the protein-protein complex for design. My first thought was to use the RigidBodyTransMover, however, I cannot perform the reverse rigid body translation to recombine the protein-protein complex; the ouput file has the proteins out of contact. I'm unfamiliar with the coordinates, but am noticing that the end coordinate differs after back transformation:
