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Constraints

Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo

Category: 
Constraints

I'm running into some issues applying the DRRAFTER instructions to model RNA loops between several distinct rigid-body helices, and am asking for advice here on how to proceed.

My goal is to rebuild the loop structures between two base-paired regions opf a stem loop. A fake secondary structure is like so:

>...5'-strand-of-pieceA...stemloop...3'-strand-of-pieceA

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Relax with constraints

Category: 
Constraints

Hi everyone,

I am a newbee in Pyrosetta, and I am trying to learn how to relax with constraints. I wanted to do distance constraints, but I am not sure if I am doing it right or wrong at all.  The score came out to be almost the same for with and without the constraint. Can anyone give me any advise? 

#------------------------Set up Score Function-----------------------

scorefxn = get_fa_scorefxn() 
score_before = scorefxn(pose)

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problems with implementing NOE constraints

Category: 
Constraints

Hi I'm running csRosettaCM with POMONA alignments and I would like to include NOE constraints in my models. Some of my constraints are on the side chains, therefore I cannot implement them in centroid mode, and would like to implement them in the full atom mode. However, it seemed like csRosetta has ignored my cst_fa_file and did not take in the constraints on the side chain. Any suggestion on how to fix this? And if it is possible to run csRosetta in full atom mode directly?

I have the following in my flags file:

-cst_fa_file noe_fa.cst

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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.

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Incorporating Rosetta Binary and Database to a Web Server Pipeline

Category: 
Design
Scoring
Enzyme Design
Constraints
Small Molecules
ROSIE

Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline. 

We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.

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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:

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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)

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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.

 

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