The problem hasn't been solved
I'm running abinitio with AtomPair constraints and would like to assign a weight to each constraint somehow based on its reliability. I've been looking at the many constraint functions under rosetta-3.5/rosetta_source/src/core/scoring/constraints/ many of which are not documented anywhere online that I can see and also at this post
Dear Rosetta community
I'm getting some really unrealistic scores when I'm using RosettaLigand to simulate a protein - peptide/inhibitor binding.
I'm following the guide/protocol for Rosetta 3.5 from the Documentation page along with a relax protocol. The steps I run are the following:
- python clean_pdb_keep_ligand.py your_structure_original.pdb -ignorechain
- Using pymol to create the apo-protein and the ligand/peptide.
- Babel to convert to SDF, Avogadro to fix mistakes.
Ligand:
- OpeneEye - Omega with the suggested flags.
- The 'assign charges' script.
Hi,
I would like to run Rosetta for different pKa and for that I want to run modeling of
protein with different type of HIS, like canonical HIS and non canonical HIP, for different pKa (for example 7.4 and 6.0).
I would be very grateful if somebody can send me Rosetta parameter file for non canonical HIP residue,
or maybe there is some instructions how to build and implement new type of non canonical residue HIP from canonical
HIS.
Thank you for help.
I'm trying to develop a modified energy minimizer where, in addition to enforcing typical energetic interactions, I want to constrain distances between particular atoms. So I think I need to have a function associated with each constraint and I would like to use a parabolic/quadratic function to describe the behavior of the constraints. Is there a quadratic function in the constraints package of PyRosetta? I was just using the tab-autocomplete feature in iPython to look for something like this but I can't seem to find what I am looking for.
Dear rosetta_users,
I need to make same mutation at a single position in all three chains of a homotrimer by using ALLAA (all_natural_aminoacids in the resfile).
I have used the below command to run fixbb for the homotrimer with the symmetry flags, and the fixbb gave output without any error but the output had 30 chains of the monomer(outputfile=16.4MB, inputfile=845KB).
### ~/rosetta-3.4/rosetta_source/bin/fixbb.linuxgccrelease -database ~/rosetta-3.4/rosetta_database/ -s pdb.pdb -resfile resfile.resfile -symmetry:symmetry_definition pdb.symm
I get the fragment libraries from http://robetta.bakerlab.org/fragmentsubmit.jsp . But I don't know how much the sequence identity cut off. 30%? 40%? And how much the resolution and R-factor cut off? Who can tell me? Thank you!
Hi all,
I am wondering if you have any recommendations for weights on centroid disulfide energy terms:
dslfc_cen_dst, dslfc_cb_dst, dslfc_ang, dslfc_cb_dih, dslfc_bb_dih (Spencer Bliven, 2009)
or perhaps on these:
dslfc_rot, dslfc_trans, dslfc_RT (Robert Vernon, 2010)
They are not used in any scoring weights file. I am using cen_std with score4L patch.
Thanks,
Vaclav
How can I calculate the self-energies and the table of pairwise energies between rotamers of mutable (molten or changeable) residues in a redesign problem where the mutable residues can change to all amino acid types? I basically am trying to figure out how to get the tables of pairwise rotamer-to-rotamer energies between mutable residues. I want the pairwise rotamer-to-rotamer energy table between mutable residues where the residue can change to all possible amino acid types and thus all possible rotamers of all possible amino acid types.
Hi,
I have a crystal structure of rhodopsin that I would like to score, but there is a retinal molecule covalently linked to a Lys residue in that structure. How do I get PyRosetta to read in the pdb file with the retinal correctly?
How does the scoring function treat such modifications?
Thank you!
Tobias
Hi Rosetta Support group,
I was wondering if Rosetta 3.5 version has get_distances command available? I looked into rosetta source/bin/ directory to locate it but could not. Could you please suggest where to find it in Rosetta 3.5 if it is included in this version.
Thanks
Pramod