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DockingHighResLegacy repacks all sidechains on first apply(), interface sidechains on subsequent apply()

[Using PyRosetta.ScientificLinux-r47452.64Bit]

docker = DockingHighResLegacy(jump, scoreFxn)

When I use the above in a python script, I get:

protocols.docking.DockingHighRes: in DockingHighRes.apply
protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 4141 rotamers at 256 positions.

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preparation the fragment files for mutants


I have a protein with a loop and I want to made a single mutation or small insertion in the loop.
Do I need to prepare a new fragment file for protein which has a single mutation in the loop, or can I use the fragment file from parent protein?
Is it possible to avoid regeneration of the fragment file, as it takes a lot of time?

Thank you for you help.


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Does linker modeling exist?

Hi! Is there an existing application that will model a linker (fragment based) between two protein domains, and at the same time ensure that one domain does not clash with the other one? If there is such a thing can someone provide an example/command line etc. ?

Thanks in advance,

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compiling pyrosetta with python from macports

hello, is there any possibility of getting a pyrosetta source distribution that can be compiled with a non system-supplied python (i.e. from macports) on mac osx (10.5+)? i would greatly appreciate this as i am trying to incorporate pyrosetta into a GUI that uses external modules such as OpenGL, PyQt, PyMOL etc. and to me it would seem much easier to compile pyrosetta with a macports version of python than using the system python and having to go through the seemingly painful process of installing all the other dependencies. but i might be wrong.


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Criteria on the calculation of Irmsd of the protein-protein interface

I noticed that in the paper (Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., Gray, J. J.; (2011) Benchmarking and analysis of protein docking performance in RosettaDock v3.2. PLoSONE), the one of the evaluation criteria of docking performance, I_rmsd is defined differently from the CAPRI.

It is:
The interface is defined as all residues with an intermolecular distance of at most 4.0 A.

The CAPRI definition is:
the interface residues in the target were redefined as those having at least one atom within 10 A of an atom on the other molecule.

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Cannot get PyMOL_Observer to work on MacOS

The PyMOL_Mover is working but PyMOL_Observer() complains. Hope you can help:

MacOS 10.7.3, 64 bit system

Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
Type "copyright", "credits" or "license" for more information.

IPython 0.12 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.

In [1]: from rosetta import *
In [2]: init()

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ab initio protein prediction using homologs

I have a question about the suggestion given in the documentations of ab initio modeling: "to increase your chance of sampling the correct topology, a diverse set of homologous sequences, preferably with sequence changes that may have a greater impact on sampling like deletions and differences in conserved positions, may also be run since a homologue may converge towards the native structure with significantly less sampling." After generating a number of decoys of these homologous sequences, it is recommended to map these decoys to the target sequence.

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RE: Loop Modeling and Beta-strand design


I am interested in mutating some loop residues together with the residues of the beta-strand , the loop is connected with. In such case what has to be done?.. Does fixedbb design will work in this case ??

Also , I have another query regarding Rosetta Scoring. I want to test all the 20 possibility of amino acids at two loop residues (20*20=400) of a beta hairpin . In that case will there be any large change in energies of a pair of combination of amino acids ??

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Cannot get PyMOL_mover to work on MacOS

I've trying to set up the PyRosetta PyMOL viewer on a MacOS 10.7.3, 64 bit system, but I cannot get PyRosetta to send graphics(?) to PyMOL. The current setup is:
PyRosetta 2.011 [r46035]
Python 2.7.1
PyMOL 1.5.0

I start PyMOL:
PyMOL>cd /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/
cd: now in /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit
PyMOL>run /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/
PyMOL <---> PyRosetta link started!
at port 65000

Running through the walkthrough in Baugh et al I get:

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