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Constraints

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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Explanation of constraint functions?

Category: 
Constraints

Hello,

Can someone explain or show me where to find information about the variables in the constraint function types? For example, in the harmonic function, what are the variables s and dhttps://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file

Thanks!

Amanda

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Cannot create cst files from upl files

Category: 
Constraints

Hi,

I am trying to do structure calculations with CS-Rosetta/Rasrec. Test data from the Rosetta Toolbox work perfectly fine, but my own data make trouble: I am not able to set up a run with NOE data. The .upl files were already trimmed corresponding to trimming the termini as well as renumbered, but converting the cyana .upl files into rosetta .cst files fails, since "there is not enough information to determine the offset". It looks like the sequence information from the upl files cannot be matched with the fasta sequence.

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heads up for constraints using GAUSSIANFUNC

Category: 
Constraints

The documentation tells that the TAG field is NOT optional for the function type GAUSSIANFUNC.
However, this is not demonstrated in the samples given in the same page: 

https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/de/d50/constraint_file.html

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Freezing arbitrary backbone dihedral angles...

Category: 
Constraints

Dear PyRosetta staff,

I'm using your set_bb_true_range() method of the MoveMap class to define the mobile degrees of freedom for some loop. Then, I use a MinMover (min_type="dfpmin") to minimize the loop according to some score function. I want that both backbone dihedral angles (PHI and PSI) were frozen at the Nt end. Unfortunately, it seems that PyRosetta only freezes the PHI angle while keeping mobile the N-terminal (Nt) PSI. In the C-terminal end, the PHI angle is mobile and the PSI is frozen.

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Can't read constraint type

Category: 
Constraints

Hello everyone,

I am running Abinitio protocol with some experimental constraints and I have encountered the following message in the log file:

core.scoring.constraints.util: (2) Constraint choice: {file name}
core.scoring.constraints.ConstraintsIO: (2) read constraints from {file name}
core.scoring.constraints.ConstraintsIO: (2) can't read constraint type
core.scoring.constraints.ConstraintsIO: (2) Read in {n} constraints

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