RMSD values for symmetric_docking clockwise vs counterclockwise cyclical outputs
Submitted by AdoCbl on Sun, 2015-10-18 12:49
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Symmetry
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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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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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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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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"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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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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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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Symmetry-aware Backrub?
Submitted by gamacy on Fri, 2014-11-14 02:18
Category:
Symmetry
Greetings,
I needed to know if it is possible (and how) to implement symmetry definitions in a backrub simulation. Can this be done either with the backrub application or alternatively through rosettascripts (Backrub or BackrubDD movers)?
Thanks in advance!
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Symmetric assembly and output reconstruction
Submitted by felipet on Wed, 2014-07-02 10:23
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
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