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abinitio - is there a way to limit number of CPU cores the program uses?

So the lab I'm working in has access to a 16 core server but we were told to use no more than 8 cores for any one application. So I was wondering if there is a way to limit the number of cores that abinitio uses while it runs its folding simulations? I looked through the help but didn't see anything that looked like it was what I'm looking for. Thanks for the help.

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Pyrosetta energy function

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.

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'DockingProtocol' object has no attribute 'setup_foldtree'

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 -, 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:
========= in ()
15 print "setting up docking fold tree"

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Problem readin .ccp4 map file

Hi all,
I have bin trying to run the electron_density/molecular_replacement demo at step 4 and I get the following error. There is nothing wrong with the ccp4 map file (opens fine in other programs)but it appears to be looking for a MRC format map. How do I get the program to accept the ccp4 map?

core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map MR.1_2mFo-DFc.ccp4. Not loading map.

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Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation

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).

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Problem with the -dock_ppk flag

Hey everyone,

I have been running protein docking with two monomeric proteins by using Rosetta3.2. Everything seemed to be fine with the docking runs except when I added the -dock_ppk line into the flags file.

Instead of having the -dock_ppk line in the flags file, I also tried to prepack the proteins by using the command line:

/usr/local/rosetta3.2/rosetta_source/bin/docking_protocol.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ -s input1.pdb -dock_ppk

It did not work either. Here is the last portion of the log file:

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Problem with symmetric docking

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

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Symmetric docking - tetramer of trimers

I'd like to model a tetramer of trimers. In this situation I'm trying to ensure that all monomers end up on the same X-Y plane. Does anyone have any idea what my symmetry definition file should look like for this? Here's how I initially tried to do it, but I'm not getting reasonable looking structures:

symmetry_name sweeden_rules
subunits 12
number_of_interfaces 10

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