FlexPepDock in RosettaScripts keeps running
Submitted by gw on Tue, 2012-08-21 12:31
You are here
Unsolved
The problem hasn't been solved
enzdes error
Submitted by bo on Tue, 2012-08-21 09:12
I'm trying to learn enzdes using tutorials in demo and in the paper "de novo enzyme design using rosetta3". The first several steps went well, but when I tried the actual design step, I got this error: ERROR: Illegal value for real option -enzdes:cut1 specified: 6.0. This does not make sense at all. Anyone can help with this? Thanks.
Post Situation:
Forums:
packstat in InterfaceAnalyzer
Submitted by Anonymous on Mon, 2012-08-20 03:19
InterfaceAnalyzer manual refers to RosettaHoles (version 1, ProteinSci2009) for details about the metric packstat. But is the RosettaHoles score calculated by InterfaceAnalyzer only for the interface, or for the whole complex? (Current holes application is version 2, thus can not test it myself.) If it is calculated only using the interface residues, could it include the voids not at the interface by accident (voids formed by interface residue side chains otherwise would have been filled by residue not included in the calculation)?
TIA!
Post Situation:
Forums:
rs filter for terms in .sc files
Submitted by gw on Sat, 2012-08-18 16:20
I would like to apply a filter in rosetta scripts that checks for specific "score terms", ie numbers that are output to .sc files in various protocols. For instance, I would like to get these terms that are normally output from movers like FlexPepDock (pep_sc or I_sc) and InterfaceAnalyzerMover (dG_separated/dSASAx100, dSASA_int).
I figured out how to use the filter EnergyPerResidue to get term in the score function of my choice:
Post Situation:
Forums:
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:
Forums:
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:
Forums:
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:
Forums:
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:
Forums:
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:
Forums:
Score Function weights
Submitted by thorx020 on Sun, 2012-08-12 13:59