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Phenix / MR Rosetta
I met such kind of error informaiton when I tried to excute the Rosetta in my mac pro by running the command "rosetta.build_phenix_interface nproc=2" .
Can anyone tell me how to solve this issue?
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).
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:
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
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:
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.
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: