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ΔG Calculation with PyRosetta

Submitted by Sandra on Tue, 2019-05-21 00:26
Category: 
Scoring

I have been reading some post looking for an anwer to my question but I still not complitely sure about it. I understand that for a complex, what rosetta gives you is a score that it is no exacly the DG. I would like to know if with the next code, using the standard score funcion, I can calculate for a comple of 2 chain the DG with the formula:

DG= Score_complexe - (Score_chain_A + score_chain_B)

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PyRosetta - General

How to define a theozyme from the .pdb crystal structure without ligand?

Submitted by weifulei on Mon, 2019-05-20 21:18
Category: 
Design

I  want to graft a coenzyme binding sites to a scaffold,  so the first thing is to define a theozyme. However, the exsiting .PDB structures  binding the coenzyme are not accessible, what I can download is only protein crystal structure without ligand. I that way, what should i do？ Should i DOCK the ligand to the protein at first? could anyone explain me the procedure? Thanks a lot!

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Rosetta 3 - General

Question about the error when using pyrosetta.distributed.io

Submitted by cuiyoutian on Sun, 2019-05-19 00:54
Category: 
PyRosetta

I have tried the latest version of Pyrosetta Anaconda python3.6 (PyRosetta4.Release.python36.mac 2019.19+release 5adc612fd9dee20f808a07e761610d95698b0f35) and previous version, PyRosetta4.Release.python36.mac 2019.18+release on MacOS, but run into the same errors when I do, for example,

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PyRosetta - General

RosettaScripts LinkResidues

Submitted by Yero on Fri, 2019-05-17 05:26
Category: 
Design
Symmetry

Hey,

I want to redesign the interface of two three-fold symmetrical proteins and I thought of using RosettaScripts.
I first wanted to make it work on one three-fold symmetrical protein and then continue with the interaction, but I am stumbling on some errors.

I'm using LinkResidues, because the protein is three-fold symmetrical, so a mutation on residue a should also occur on residue b and c, thus without breaking the symmetry of those residues.

I'm using:

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Rosetta 3 - Applications

Behavior of nstruct

Submitted by johnnytam100 on Wed, 2019-05-15 22:22
Category: 
Design

Hi, I need your help on your experience of the number of structures generated from Rosetta by specifying nstruct:

Have you ever met a situation, for example, you specify nstruct = 100, and Rosetta generates less than 100 structures at the end of the run?

More information:

1)  I am using RosettaScripts to design a protein interface. I have specified a cutoff of SASA but I don't think it would affect the final number of structures.

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Rosetta 3 - Applications

protein protein interaction design

Submitted by Negarsardar on Wed, 2019-05-15 06:13
Category: 
Design

 

Hello

I have docked two proteins  and Now I am going to design the binding interface of one of them while fix everything in the other. I mean I want to do protein protein interaction design. which part of rosetta would be for this job?? is it fixbb?

 

 

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Rosetta 3 - Applications

How to use the <CavityVolume> filter in the released version of Rosetta

Submitted by BioPython on Sun, 2019-05-12 20:07
Category: 
Design

I am trying to replicate the work of the paper entitled "De novo design of potent and selective mimics of IL-2 and IL-15”​.

However, I get the following error when I run Rosetta Script (Rosetta 2019.14) with deNovoPreprofiledMimeticsDesign_gen2.xml:

Error messages were:
From line 38:
Error: Element 'CavityVolume': This element is not expected.

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Rosetta 3 - General

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