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Rosetta score vs Experiment

Submitted by thorx020 on Tue, 2012-09-04 12:38

Hi all,

I understand that the best way to interpret Rosetta scores is "lower=better". However, there are many papers that use Rosetta to design/enhance a protein then experimentally verify their structure/stability in the lab. Since the "lower=better" metric is so general, how can one be confident that the Rosetta-predicted structure/stability will match experimental values?

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PyRosetta - General

How to remove clashes in peptide bonds and proline residue?

Submitted by Anatol on Fri, 2012-08-31 09:26

Hi all:

I have got a protein model with clashes in several peptide bonds between O and N atoms, proline residues and some side chanis. The "relax" app removed clashes in the side-chain, but was not able to correct the peptide bonds and proline residues. The following are the options that I used in both fast and throrough runs of the app:

relax.linuxgccrelease -database /home2/rosetta_database -in:file:s 8nC.pdb -relax:fast(thorough) -score:weights score12_full -ex1 -ex2 -nstruct 10

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Rosetta 3 - General

make fragment

Submitted by zadie1118 on Thu, 2012-08-30 07:45

Hi

I'm trying to use the make_fragments.pl script but i do not know where to find the launch_on_slave_strict.py script necessary to run it in parallel, to launch the job serially dosen't seem to be feasible. please see

# This is an optional script that you can provide to launch picker and pdb2vall jobs on
# free nodes to run them in parallel. If left as an empty string, jobs will run serially.
# Make sure your script will run the command passed to it on another machine. If it is
# set up to run parallel jobs on the local machine, the local machine may run into CPU

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Rosetta 3 - Applications

mpi mode problem

Submitted by bo on Wed, 2012-08-29 17:41

Hey everyone, I'm trying to compile in mpi mode on a cluster. I used:
./scons.py bin mode=release extra=mpi

After entering the command, it gave me this error:
Running versioning script ... fatal: Not a git repository

But the compiling went on well and gave me "scons: done building targets." at the end.

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Rosetta 3 - Build/Install

Multiple Chain Comparative Modeling - End result is not even close to template structure

Submitted by eskici on Wed, 2012-08-29 08:09

"yes it runs!" was a really early response for the comparative modeling run I started for a multi chain protein. I use rosetta 3.4.

My problem is that the end result looks completely off compared to the template file (also to any other folded structure, the end result is basically a stretch of amino acids). Points that I messed up something at the alignment.

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Rosetta 3 - Applications

ddg dG_separate

Submitted by gw on Wed, 2012-08-22 11:25

What exactly does the filter ddg compute? Does it compute the difference in binding energy from the sequence of the given pose to a mutant? What mutant (perhaps poly alanine)?

I ask because it is somehow different from a binding score (complex minus separated chians), but I'm not sure how.

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Rosetta 3 - Applications

fixbb minimize sidechains with symmetric pose - recompile?

Submitted by Anonymous on Wed, 2012-08-22 06:14

Dear all,

I would like to use the flag -minimize_sidechains with a symmetric pose in fixbb. At the moment, fixbb stops after


core.pack.task: Packer task: initialize from command line()
ERROR: !core::pose::symmetry::is_symmetric( pose )
ERROR:: Exit from: src/core/optimization/AtomTreeMinimizer.cc line: 72

fixbb runs fine without the -minimize_sidechains flag. Therefore I think I need to include the src/protocols/moves/SymMinimizeMover.cc, as pointed out here at the bottom of the page:

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Rosetta 3 - General

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