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Symmetry definition for apolar helix

Submitted by vanrooyenjason on Tue, 2016-01-05 05:20
Category: 
Symmetry

Hi,

I am struggling to generate a symmdef file for a helical model and I am hoping someone can help.

The helical parameters are as follows: rise = 17 Angstrom with 4.674 subunits per turn. The helix is apolar i.e. the ends of the helix are the same as related by 180 degree rotation. The repeating unit is a dimer with C2 symmetry. In the attached pdb (ca only to avoid upload limit) the A and B chains form the dimer which is related to the next C/D pair by the helical symmetry I mentioned.

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Rosetta 3 - Applications

Ways to improve ROSIE symmetric_docking jobs

Submitted by AdoCbl on Wed, 2015-09-23 13:39
Category: 
Symmetry

Below are some ideas for improving symmetric_docking jobs:

(1) If you choose dihedral instead of cyclical symmetry, it seems like you also need an even number of subunits. Could you have the input page block dihedral jobs with odd numbers of subunits?

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ROSIE - General

Score and I_sc in ROSIE symmetric_docking output

Submitted by AdoCbl on Sun, 2015-08-09 00:26
Category: 
Symmetry

If one is doing a symmetric_docking run with 6 sub_units in cyclical symmetry,
is the I_sc value the total for all 6 interfaces or just 1 of the 6 interfaces?
Is the score the total for all 6 sub_units or just 1 of the 6 sub_units?
Does the score already include the appropriate contribution from I_sc?

Also, in each docking2 run, 2 plots are made: "Interface score I_sc / RMSD" and "Score/RMSD".
Why not make both of these plots for each symmetric_docking run as well?

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ROSIE - General

How to generate symmdef file for translational symmetry only?

Submitted by pitmand on Thu, 2015-05-14 11:34
Category: 
Symmetry

I'm attempting to generate a symmetry file for a system comprised of two parallel beta sheets symmetrically related only by translation: the beta strands within the sheets are symmetric translations, and the sheets themselves are symmetric translations. I additionally want to keep the z-axis offset between the beta sheets constant, if possible, so I can change the x- and y- spacing between the beta sheets.

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Rosetta 3 - General

SymDock with constraints

Submitted by felipet on Thu, 2015-05-14 09:01
Category: 
Docking
Constraints
Symmetry

Dear all

I been trying to perform a symmetric docking with constraints and it is not working. Reading old post residue number must be carefully set. For some reason the low-res filter is dumping all the solutions ("STRUCTURE FAILED LOW-RES FILTER"). I imagine that has to be with how I define the constraints but I even tried using AtomPair CA 52 CA 182 GAUSSIANFUNC 50.0 50.0. Please can someone have a hint of what is going on?

thanks in advance

felipet

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Rosetta 3 - Applications

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

Submitted by pitmand on Tue, 2015-03-17 14:29
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()

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PyRosetta - General

Pmut_scan with symmetry

Submitted by felipet on Thu, 2015-02-05 08:53
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

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Rosetta 3 - Applications

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
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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