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Constraints

lysine-aspartate isopeptide bond

Category: 
Constraints

Hello,
I am working with protein which have isopeptide bonds in them and I am not sure how to handle them.

An isopeptide bond is when a lysine residue forms an amide bond with an aspartate or asparagine (same result). Isopeptide bonds —in bacteria at least— have an O or N atom missing from the Asp, Asn or Lys and a CONECT at the end of the file and to the best of my knowledge there is no special HETATOM O-lysylaspartyl double residue.

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How to transform a pose from symmetric into non-symmetric?

Category: 
Design
Scoring
Constraints
Symmetry

Hello,

Is there a way to break the symmtery of a pose in the middle of a Rosetta script? I want to avoid writing the PDBs and feeding them again to a new script.

Any suggestion is highly appreciated!

Thanks!

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DomainAssembly Mover with constraints (using RosettaScripts)

Category: 
Docking
Scoring
Constraints

Hello,

I am trying to run the domain assembly protocol while atom_pair constraints . I am using RosettaScripts for my application.

I have tried including the constraint file in the xml script using the ConstraintSetMover and Reweighting the score function. I have also tried included the constraint file in the flag file using -constraint:cst_fname. Yet the output silent do not seem to include the atom_constraints score term.

I would appreciate any help on how to include the constraints in the scoring function for domain assembly.

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dock & design

Category: 
Docking
Design
Constraints
Symmetry

Dear All,

I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.

Input:

- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.

Simulation:

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Enzyme Design with additional covalent backbone bonds

Category: 
Design
Enzyme Design
Constraints
Non-Canonical Peptides

Hey everyone,

I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.

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Files for Spatial Constraints

Category: 
Structure prediction
Enzyme Design
Constraints

Hi guys,

I am trying to locate the files to generate spatial constraints from homologous template structures for comparative modelling as given in the Thompson and Baker paper from 2011. I can't find them anywhere in the ROSETTA directories. Are they available anywhere?

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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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Rosetta relax problem

Category: 
Constraints

Hi, I recently got an electron map at 3.8 angstrom resolution. And I have built a protein structure by hand in COOT. Then I refined this structure in PHENIX.real_space_refine package. After refinement, I found that the ramachadran favored percentage was not good. So I followed the simple relax tutorial and did the simple relax refinement to improve the ramachadran. However, during refinement procedure, it appeared that

" core.optimization.Minimizer: (1) WARNING: LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! "

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