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Constraints

Problem passing a list of PDB files to minimize_with_cst

Category: 
Constraints

Hello

I am trying to minimze a structure using the minimize_with_cst script.

However, I keep getting the error message:

ERROR: Cannot open file "ATOM"

Based on this thread , I thoghout that I should use the in:file:s option instead of in:file:l which is recoomende in the ddg_monomer documenation, but I still get this error.

Post Situation: 

known disulfides in Remodel sequence

Category: 
Constraints

I have a protein structure solved by iTasser against a distant relative. But it has a loop that was not solved correctly and it has two cysteines that probably form a disulfide, so I want to remodel the loop with a disulfide (Rosetta Remodel 3.9 on Linux).

I want to keep the sequences as is, so the disulfide scanner is not for me.

I tried with a PDB template with the following lines:

Post Situation: 

Pocket Constraint

Category: 
Constraints

Hi,

I was wondering if anyone has any experience using the pocket constraint in PyRosetta. There doesn't appear to be much documentation and all of my attempts have yielded the error "ERROR ! ! Invalid residue to backrub around" after running the following code:

from pyrosetta import *
init()

from pyrosetta.rosetta.core.scoring import *

pose = pose_from_pdb('core_0001.pdb')

scorefxn = create_score_function('ref2015')
scorefxn.set_weight(pocket_constraint, 1.0)

Post Situation: 

Relax with RDC data gives segmentation fault

Category: 
Constraints

Hi,

When I try to use RDC data together with structure refinement (relax), it faults (see the command I tried below). 

relax.linuxgccrelease -in:file:s test.pdb -in:file:rdc test.rdc -score:weights talaris2013 -score:patch rdc_patch -out:pdb -nstruct 20

The rdc_patch has rdc score term. 

The segmentation fault appears when we use talaris2014 or ref2015 score wts as well. I tried this with a different set of  PDB and RDC files, I see the same issue.

 

Post Situation: 

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

Post Situation: 

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.

Post Situation: 

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).

Post Situation: 

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,

Post Situation: 

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.  

Post Situation: 

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