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Symmetry

"No Python class registered..." when trying to access SymDofs

Category: 
Symmetry

I can create symmetric systems without any issue in PyRosetta, but I can't access the symmetric dofs at any stage. It produces a message like this:

In [84]: dofs = symm_info.get_dofs()
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-84-f37670432e61> in <module>()
----> 1 dofs = symm_info.get_dofs()

Post Situation: 

Pmut_scan with symmetry

Category: 
Design
Symmetry

Dear developers

I am trying to use pmut_scan for a symmetric dimer. I don't know if this is possible but when I run it with a symmetry definition file the program crashes with the following message:

protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average_ddG average_total_energy
terminate called after throwing an instance of 'std::bad_cast'
what(): std::bad_cast
Pmut_sym.sh: line 29: 678 Aborted (core dumped) pmut_scan_parallel.default.linuxgccrelease

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.

Post Situation: 

Symmetric assembly and output reconstruction

Category: 
Symmetry

Hi

I am modeling an helix assembly and I was wondering how to reconstruct the assembly from SymDock output pdb. The output only includes the chains that are in direct contact with the master subunit, and hence I don't have the next chain along the fiber/helix to include in the command line (make_symmdef_file.pl)

Thanks in advance!

felipet

Post Situation: 

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