The problem hasn't been solved
I have used backrub (Rosetta3.5) and it calculates scores for decoys.
When I recalculate scores using score.linuxgccrelease from the same rosetta version, different values (30% difference) are generated.
Both used score12 and and dun02. Why are the values so different?
Hi all,
I have a pdb files with coordinates of a residue conformations interacting with a organic molecule. I want to score this conformations with score.linuxrelease app. The program crash when reading the coordinates of the ligand can not identify the name of the ligand (LIG).
There is a way to overcome this? Is necesary some kind of parametrization?
Thanks in advance
Yasser
Dear all,
I have been trying to extract PDBs from silent file and keep getting this error:
core.init: command: /opt/rosetta3.3/rosetta_source/bin/extract_pdbs.linuxgccrelease -in:file:silent silent.out -database /opt/rosetta3.3/rosetta_database/
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-20988320 seed_offset=0 real_seed=-20988320
core.init.random: RandomGenerator:init: Normal mode, seed=-20988320 RG_type=mt19937
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types
In a pose, how can I replace the rotamer of a particular residue? I know I can use the pose.replace_residue function to change the amino acid type at the residue at seqpos in the pose sequence.
replace_residue (Size const seqpos, Residue const &new_rsd_in, bool const orient_backbone)
Replaces the residue at with
Hello everyone,
I am using rosetta scripts (Version 3.5) to redesign a protein-protein interface. I use the following taskoperation to restrict the redesign with 8 ang CB distance cutoff from the interface,
RestrictToInterfaceVector name=vector jump=1 CB_dist_cutoff=10.0 nearby_atom_cutoff=8 vector_angle_cutoff=75.0 vector_dist_cutoff=9.0
I would like to see the residues selected by the program that are within 8 ang cutoff distance. Is this information written somewhere in the outfile?
Hello, I have been trying to validate interface energies computed using Rosetta 2.3, but have been having some difficulty obtaining agreement between two expressions that should be equivalent.
I start with a protein with two chains in a single PDB file, ab.pdb.
Then I run Rosetta++ with the following flags:
-interface -ddg_bind_only -s ab.pdb -intout ab.txt -output_structure -Wpack_only -relax_unbound false
This gives me three files:
ab_nat_0001.pdb (A chain only)
ab_nat_0002.pdb (B chain only)
ab_nat_0003.pdb (A+B chains together)
along with the following energies:
Hi folks--
Help! I am trying to energy minimize a protein with distance restraints in cartesian space. Instead of making nice regular bonds and bond angles, I get an arginine side chain that looks like a pitchfork and a phenylalanine ring that looks like somebody stepped on it. After having tried different weight sets and minimizers (FastRelax, MinMover), I am frustrated and need some advice. Has anyone successfully regularized a distorted structure in pyRosetta with the setting MinMover.cartesian(True) ? I don't see any bond length or bond angle weights in any of the wts files.
Hi, everbody,
I'm using enzyme design to redesign a enzyme, and encountering a tough problem for me.
In the catalytic site, there is a protonated ASP, and a .cst file need to be given to constraint -OH of ASP and ligand.
Although I find the parameters of protonation state of ASP (ASP_P1.params or ASP_P2.params file) in the installation directory(.../rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states),
the 3 letter abbreviation of protonated ASP is also ASP, so I don't know how to inform the rosetta to recognize the ASPH.
HI,
I downloaded PyRosetta.MacOSX.Lion-r56325.64Bit, and put in my home folder/opt in my Mac. Unfortunately, ./iPyRosetta doesn't work. The following error message showed
In [1]: import rosetta
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
in ()
----> 1 import rosetta
/Users/rliang/opt/PyRosetta.MacOSX.Lion-r56325.64Bit/rosetta/__init__.py in ()
28
29 # Double-checked right order...
---> 30 import utility
Hi, everbody,
I'm using enzyme design to redesign a enzyme, and encountering a tough problem for me.
In the catalytic site, there is a protonated ASP, and a .cst file need to be given to constraint -OH of ASP and ligand.
Although I find the parameters of protonation state of ASP (ASP_P1.params or ASP_P2.params file) in the installation directory(.../rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states),
the 3 letter abbreviation of protonated ASP is also ASP, so I don't know how to inform the rosetta to recognize the ASPH.