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Constraints

radius of gyration as constrain

Category: 
Constraints

Hi 

I am trying to model missing C terminus of my protein using FloppyTail. I have experimental data regarding the radius of gyration that I want to use as constrain to narrow down the search space. How can I put that constrain?

 

Thank you

Dhiraj

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Structure refinement with RDC constraint

Category: 
Structure prediction
Constraints

Hi~

I've done a structure refinement of a protein by Rosetta3.8.

However, I'm not sure that what I've done is correct or not.

The protocol that I followed are list below:

First, I put my protein sequence(.fasta file), torsion angle(predicted by talos+), RDC value(experimental data) into the website( http://robetta.bakerlab.org/fragmentsubmit.jsp) to do fragment generation.

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cyclization_type flag in simple_cycpep_predict

Category: 
Structure prediction
Design
Constraints

Dear Rosetta users or developers,

 

I'm trying to model small, cyclic peptides with the simple_cycpep_predict routine. While I explicitely asked for a terminal disulfide cyclization (using the flag -cyclic_peptide:cyclization_type terminal_disulfide), the output models are cyclized with a mainchain bond (the default n_to_c_amide_bond).

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comparative modelling of a complex

Category: 
Structure prediction
Docking
Constraints

Hello All,

I have a protein sequence that consists of two domains: A and B. The two domains presumably interact and there are some residue pairs that can be used as constraints. However, I don't know whether these domains interact within a single protein (A-B) or a dimer (A-B', B-A'). Given the fact that both A and B have many good templates in PDB, I thought that Rosetta comparative modeling protocol could be used to investigate these two scenarios. I would appreciate suggestions on how to set up such an analysis.

Best wishes,

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What is the expected behaviour when minimizing a jump edge?

Category: 
Docking
Constraints
PyRosetta

I have seen references to minimization of a jump edge (e.g using a MinMover object) leading to both rotations and translations downstream of the jump. 

I am modelling an interaction between two proteins, connected in the fold tree by a single jump edge, with atom pair constraints defined to bring them into close proximity.

I allow movement of this jump in the movemap (set_jump), atom_pair_constraints is activated in the scorefunction, and the fold tree is valid.  

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Using logic in resfile, Rosetta Scripts

Category: 
Constraints

Hi,

I am designing a protein-protien interface using Rosetta Scripts, and would like to use logic in the resfile. 

For example, if one amino acid at a given position is re-designed to be [list of aa], then the redesign at this other defined position should be limited to [list of aa]

Is this possible?

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Remodel with residue constraints

Category: 
Constraints

Hi,

I am trying to remodel a given structure where I want to replace a chain say B with same residues say alanines. How can I use remodel with constraints? To be more specific, how to write constraint files. I did look up the remodel documentation for the cst file. But, they describe atom level information. Is there a way to just do it at the residue level? (I mean, just give the residues I want to replace in the new structure?)

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Perform MPI relax with movemap files

Category: 
Constraints

Hi,

I want to relax around 3K structures. Also, I have a movemap file for each of these structures. How do I trigger mpi runs for relax with movemap files?

Earlier, when I did not need the movemaps, I used the following command:

mpiexec -np 32 $ROSETTA/bin/relax.mpi.macosclangrelease -in:file:l <pdb list file> -nstruct 20

But, now I want to perform relax with move map associated with each of the pdb file in the pdb list file. How do I do it?

Post Situation: 

Design with limited number of aminoacids at given position

Category: 
Design
Constraints

Hi!

What is the easiest way to allow only a single residue type (e.g. Trp) at a given position during the design?

I use FastDesign Mover with symmetry. I thought about ReadResfile and PIKAA command, but perhaps it could be done directly from the Rosetta Script? Via task_operations=... ?

Best wishes,

Staszek

Post Situation: 

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