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Phenix / MR Rosetta

Change in Gibbs free energy (delta delta G) of RNA

Category: 
Phenix / MR Rosetta

Hello,

I'm trying to load a .pdb file for an RNA molecule, change a single base in the molecule, and calculate the change in free energy. I was looking at this tutorial (http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf) and it doesn't work with newer versions of PyRosetta. Has anyone else done something like this? The documentation hasn't been very helpful so far for RNA (though it's relatively extensive for protein).

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rosetta_scripts_BOGUS coords warning message

Category: 
Phenix / MR Rosetta

 

 Hi,

I am using rosetta scripts to build a protein into electron density.

However, I am getting some warning messages, which relate to my CYX residues. I understand the message itself, but I don't know why it appears, what it means to my structure and whether I should be worried about it. As I said, I have several CYS residues, which I mutated to CYX (CYX name in PDB file) and when I start my calculations I am getting the following warning message for all CYX residues:

Post Situation: 

Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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Phenix-Rosetta integration tests

Category: 
Phenix / MR Rosetta

Hi there,

I'm a HPC systems administrator trying to setup Phenix and Rosetta for use with MR Rosetta. I find that the MR Rosetta test suite (phenix_regression.wizards.test_command_line_rosetta_quick) fails at test_fixed_model with the following error in Rosetta:

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why can't I find the folder of "main"? Did anybody succeed in using phenix.rm_rosetta?

Category: 
Phenix / MR Rosetta

I found someone had solve a difficlut proble by combine the rosetta with phenix, which can help calculate the x-ray structure with low resolution.
http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2648.html
http://link.springer.com/article/10.1007%2Fs10969-012-9129-3
So I want to copy this as well to solve my problem, and I found a way to combine rosetta with phenix. Here is the website about phenix.rm_rosetta:

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