You are here

Home

Unsolved

The problem hasn't been solved

fixbb design using damped LJ

Submitted by Anonymous on Fri, 2012-08-17 03:51

I used fixbb in Rosetta 3.4 to perform fixed BB design using damped LJ potential (by specifying parameter -soft_rep_design). But I noticed that the final score reported by fixbb seemed to be calculated using default weights. (I got to know this by using score_jd2 to recalc the score for deboys using default weights and damped weights and compare them to the score reported by fixbb.) Does this mean my design was really done using damped LJ?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Potentially incorrect heavyAtoms_end() iterator in core/conformation/Residue.hh

Submitted by tsjain on Wed, 2012-08-15 12:20

The following is the definition of heavyAtoms_end in Residue.hh

Atoms::const_iterator heavyAtoms_end() const
{
return atoms_.begin() + nheavyatoms() - 1;
}

With this definition, any loop of the form for( conformation::Atoms::const_iterator blah = res.sidechainAtoms_begin(); blah != res.heavyAtoms_end(); ++blah), will SKIP iterating over the LAST heavyatom in the residue. From my understanding of the iterator concept, the end iterator should always point to one past the last element to be accessed.

Is this a bug or am I missing something here?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Rotate MOVER

Submitted by gw on Wed, 2012-08-15 12:09

I'm trying to use the docking .xml scipts mentioned in the paper "RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite" under the heading "Ligand docking and design". It is also mentioned in a book chapter "Rosetta Ligand docking with flexible XML protocols."

I modified it for my purposes (chain name, start from other coordinates). I can produce docked structures, but only if I don't include the rotate mover by removing it from the low_res_dock mover:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

How to generate a symmetry definition file for octahedral symmetry?

Submitted by Anonymous on Wed, 2012-08-15 05:20

I would like to generate a symm def file with octahedral symmetry, based on a PDB file, for use with fixbb. According to the PLoS paper by DiMaio et al http://dx.doi.org/10.1371/journal.pone.0020450 tetrahedral, octahedral and icosahedral point symmetries are not properly supported by make_symmdef_file.pl. The instructions for making a symm def file http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/symm... also note, that these symmetries are not fully supported.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Using MoveMap within Relax Application?

Submitted by m_grisewood on Mon, 2012-08-13 12:21

Hi. I am trying to fix atoms (or residues) in place during the relax application. After searching through the forum, I saw that MoveMap could be used to accomplish this for the FastRelax application. I assume this is the same thing as the "fast" option for relax in the newest version of Rosetta. The old post I am referring to can be found here http://www.rosettacommons.org/content/frelax-relaxation-constrains. However, I am unsure how the commands listed at the end of the post can be applied.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Making mutations in PyRosetta?

Submitted by thorx020 on Thu, 2012-08-09 09:24

Hi all,

I'm new to PyRosetta and just had a quick question. Is there a way to make mutations to an existing protein structure using PyRosetta? I'm currently doing all the mutations in PyMOL then saving the mutants as new pdb's and calling them into PyRosetta for analysis. If I could just write a short script to mutate the structure using PyRosetta, it would save me a lot of time. Thanks!

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

ndruns and nstruct in fixbb

Submitted by Anonymous on Tue, 2012-08-07 01:52

In manual for fixbb in Rosetta 2.x, ndruns is used to specify the number of iterations. In the manual for fixbb in Rosetta 3.x, the parameter ndruns is not introduced anymore. Rather, nstruct is used to specify "The number of iterations to perform per input structure". Does it mean nstruct has replaced ndruns? Or is ndruns the same as nstruct but only one decoy (the best scoring decoy) is returned?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

RNA Denovo RMSD data

Submitted by eremma on Thu, 2012-08-02 01:40

Hi,
I am new to the Rosetta software and I would really appreciate some help from someone with experience in RNA Denovo. I am using the rna_denovo application on a cluster with Rosetta 3.3 and I want to predict 3D structures for a large number of RNA molecules.
Initially I predict 3D structures for which there is NMR data available so that I can determine how well the algorithm works. I am supplying the NMR structure as the native structure in order to plot RMSD vs. energy (score).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Unsolved