Unsolved

I am considering various conformations of a given protein and I should compare their corresponding energy values. I have used Pyrosetta to compute the energies using the "scorefxn = create_score_function('standard')" command. I was under the impression that the PDB structure of a protein should have the minimum energy.

Hi around, sorry for disturbing with my problem that I haven't found posted or solved and if it has been solved I didn't find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta - docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn't work by writing:
=========
docking.py in ()
15 print "setting up docking fold tree"

Dear all,

I realized that the latest vall database that comes with Rosetta 3.2 is version 2006-05-05. Unfortunately, there is no corresponding constraint coordinate file ("vall_cst_coord.dat.") for that database. Both database files are only available for the 2001-02-02 version. Is there a way to get the constraint coordinate file also for vall 2006-05-05?
The 2001 version contains only one-third of entries in comparison to the 2006 version.

I want to use this for fragment picking using also my experimental NMR data (can't rely on Robetta).

Hello everyone,
I'm trying to refine a homotrimer by using symmetric docking in Rosetta 3.2.1. I built the symmetry definition file and ran the following command:

~/rosetta_bin/docking_protocol.linuxgccdebug -database ../rosetta_database -in:file:s INPUT.pdb -in:file:fullatom -ex1 -ex2 -symmetry:symmetry_definition symdef.txt -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8 -nstruct 1 -out:file:fullatom

Which yielded the following output

core.init: Mini-Rosetta version exported from unknown