The problem hasn't been solved
(I would appreciate it if any of the following can be commented)
Dear friends,
I am trying to use "ddg_monomer.linuxgccrelease" by following "High Resolution Protocol" in
https://www.rosettacommons.org/docs/latest/ddg-monomer.html
1. To pre-minimize, the command line is
Is it perhaps possible to get a list of all torsion angles in the pose? I’m using the pyrosetta with the CHARMM force filed to do some monte-carlo simulations of spin-label rotamers. This works very well, except that it turns out I need to apply the CMAP correction as well. This correction is basically a 24x24 lookup table for the energy between two dihedral angles.
Parsing and loading the CMAP from the parameter file is (almost) trivial in python. But now I have to map the mm_atom_name(s) to the correct two torsions.
For example I have to map
Is there any support in rosetta for writing out a PDB file with multiple configurations of the side-chains? I have a set of side-chain hypotheses at each residue along a fixed backbone and would like to visualize this as an ensemble. This is analogous to dumping a PDB file with a side-chain at every rotamer location in the Dunbrack rotamer set.
I think I know how to implement this from scratch, but if there is any built-in support along these lines that would be great.
Thanks,
Jason
I've been working on a homology model of a spanning helical membrane protein. The options I'm using seem to work for a somewhat similar protein, so I can't figure out what the problem is. Essentially, the problem with the decoys is two fold:
Hi,
I have a couple of questions regarding Rosetta clustering and Calibur and I wasn't able to find an answer to them on the site
Which type of clustering algorithm is used in Rosetta clustering? EDIT:I meant to ask- when calculating the RMSD is the superimposing done pairwise in Rosetta clustering?
Hello,
I'm attempting a complete build with intel/14.0.1.106 + mvapich2/2.0b compiler and MPI libraries. I'd like to be able to compile and run the unit tests as well as the integration tests to serve as a base level benchmark for performance improvements on our system.
#### Part of my configuration file ############################
cat > site.settings.stampede <<EOF
...snip
import os
Hello ~
I'm interested in Pyrosetta
and learning the tutorial
Workshop #4: PyRosetta Folding
page 4
11. Create a new subroutine in your folding code for an alternate random move based upon a “fragment insertion”. A fragment insertion is the replacement of the torsion angles for a set of consecutive residues with new torsion angles pulled at random from a fragment library file. Prior to calling the subroutine, load the set of fragments from the fragment file:
fragset = ConstantLengthFragSet(3)
Is there perhaps a (python) script lying around somewhere in the src distribution to convert charmm parameter files (.prm) into mm_torsion_params.txt and mm_atom_properties.txt (in the database directory database\chemical\mm_atom_type_sets\fa_standard)?
I have added the MM parameters for R1A and now I naturally have a lot of missing types for the mm_* score terms. I’m thinking the easiest way to sort this out is just to regenerate the mm_torsion_params.txt and mm_atom_properties.txt from my working charmm parameter files?
Dear friends,
When I tried to run "remove_loop_coords.py", I was told "ImportError: No module named Bio.PDB":
Hello ~
I'm interested in Pyrosetta
and learning the tutorial
Workshop #4: PyRosetta Folding
page 4
11. Create a new subroutine in your folding code for an alternate random move based upon a “fragment insertion”. A fragment insertion is the replacement of the torsion angles for a set of consecutive residues with new torsion angles pulled at random from a fragment library file. Prior to calling the subroutine, load the set of fragments from the fragment file:
fragset = ConstantLengthFragSet(3)