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I'm getting an unusal error when using SPLINE EPR_DISTANCE constraints with the score.linuxgccrelease function. I generated some structures ab initio using SPLINE EPR_DISTANCE constraints with rosetta_scripts.linuxgccrelease and I wanted to rescore the binary output file with some different constraint weights using score.linuxgccrelease. However, if my input constraint file (cst_fa_file) to the score.linuxgccrelease release function contains any SPLINE EPR_DISTANCE constraints, I get:
I have a protein structure solved by iTasser against a distant relative. But it has a loop that was not solved correctly and it has two cysteines that probably form a disulfide, so I want to remodel the loop with a disulfide (Rosetta Remodel 3.9 on Linux).
I want to keep the sequences as is, so the disulfide scanner is not for me.
I tried with a PDB template with the following lines:
I am trying to read a pdb file that has a chloride anion important for its structure. The error is that it is not recognized by rosetta, as sometimes happily happen with other small ions. Looking through the database file I found a params file for a chloride ion model, located at: $ROSETTA_HOME/main/database/chemical/residue_type_sets/fa_standard/residue_types/anions/CL.params. The file reads:
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 have checked the D070_Refinement.py* script provided by the Graylab, and I would like to make my own little refinement script based on it and the other guides and tutorials available.
I have, however, run into problems as the ‘MinMover’ method is not available under pyrosetta.rosetta.protocols.simple_moves which prevents me from using the approach outlined in D070_refinement.py to minimize the pose score.
I'm having trouble relaxing multiple PDB files via MPI and a pdblist on the TACC Stampede2 cluster. Apparently, only the first file in the pdblist is relaxed, regardless of which PBD file is first in the list. My pdblist has Unix EOL breaks, so that should be good. Do I need to add some flag to relax multiple files in batch using MPI? What am I missing?
Here's the SLURM file I'm using:
I my attempt to get a working RosettaDesign protocol, I have come across the RemodelMover() class.
From the Rosetta C++ documentation, the RemodelMover should take a blueprint file in order to specify which residues to remodel. but the RemodelMover() class in PyRosetta has no method to input a blueprint file nor a resfile.
on its own the RemodelMover works without any errors, but would remodel the entire structure.