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Symmetry

multiple symmetry definition files

Category: 
Symmetry

Hello,

Multiple input structures are provided as a list (in:file:l) or in a single silent file (in:file:silent).

Is there an easy way to provide also symmetry definition files for the individual structures? (symmetry:symmetry_definition)

Thanks you for suggestions!

Best wishes,

Staszek

 

Post Situation: 

RosettaScripts - SetupNCS mover

Category: 
Design
Constraints
Symmetry

Dear all

I was trying to mix ligand docking with protein design of a symmetric dimer by using the SetupNCS mover. I still don't know why the mover is not being used...the resultant pdbs were modified at the sequence level but both chains are different.

thanks in advance

felipet

 

The script used is:

 

        <MOVERS>

                <SetupNCS name=ncs bb=1 chi=1 symmetric_sequence=1>

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wallpaper symmetry definition file

Category: 
Symmetry

Hello All

The supporting information of the Science paper by Gonen et al. refers to a perl script for generating wallpaper symmetry definition files. But I cannot find it even in the recent version of Rosetta.

The manuscript points to a file make_Pn_tiling.pl

"It can be found in the Rosetta directory path ‘apps/public/symmetry/make_Pn_tiling.pl’.

I was wondering if may be any of the current users had access to it.

Thanks

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Symmetry definition for apolar helix

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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Ways to improve ROSIE symmetric_docking jobs

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?

Post Situation: 

Score and I_sc in ROSIE symmetric_docking output

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?

Post Situation: 

How to generate symmdef file for translational symmetry only?

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.

Post Situation: 

SymDock with constraints

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

Post Situation: 

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