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I set up mr-rosetta which is running over 5 days and I guess it should be keep
running for very long time (ran it on a local machine with single processor.
260 residues, 1MOL/Asy). My question is where to look for the positive sign:

So far, the LLG scores from phaser are very low: 2.31-27.1;

From rebuild:

Run_1: ROSETTA SCORE: -1273.01;
Run_2: ROSETTA SCORE: -1427.29;
Run_3: ROSETTA SCORE: -1468.84
Run_4: in running

Thanks in advance.

I need to see which functions are using the most time so I compiled with:

scons mode=profile extras=opencl bin

That was successful and I ran my program:

~/rosetta_source/bin/ragul_darc_run.opencl.macosgccprofile -database ~/rosetta_database/ -input_protein_file 2YXJ.pdb -input_ligand_file ZINC01350605_0001.fa.pdb -extra_res_fa ZINC01350605_0001.fa.params

That was successful and it created a file gmon.out.

But I'm not sure how to work with this. My understanding of gprof is that I need a command like:

gcc -g -pg executable.exe gmon.out

Hello all, I am working on using PyRosetta to improve a homology-derived protein structure, in which the disulfide bonds are not in their ideal configuration. After playing around with the refinement.py script in the tutorials, I noticed that it was leaving the disulfides untouched in the output results. I noticed in the manual (under TaskFactory) that PyRosetta/Rosetta disables cysteine repacking by default. It wasn't clear to me how to disable this behavior. I tried the following after initializing the packmover:

rr = RestrictResidueToRepacking()
rr.include_residue( 4 )

symmetric docking uses the minimal subsystem during docking. The output contains also the smallest subsystem. For example, in a C17 system (3kml), only three neighboring subunits are used in docking and the output decoys contain also only three subunits (DiMaio2011, PLoS ONE). How to reconstruct the complete system based on the output? It seems the original symmetric definition file can not be relied on any more.