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Does Rosetta have a class diagram for each class in the source code?

Submitted by ylwang on Thu, 2019-11-21 04:24
Category: 
Structure prediction

When reading the source code, follow the function to find the class definition, but there is no way to know which class it inherits from or whether there is a defined subclass of the class. At the same time, I don't know which file the virtual function of the virtual base class is implemented in.So I would like to ask if there is a class diagram of the code

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Rosetta 3 - General

Issue with Rosetta LinkResidues Script

Submitted by adityapadhi on Wed, 2019-11-20 22:00
Category: 
Design

Hi All,

I am trying to design a 2 fold-symmetrical protein where I want to design a selected number of residues in each half and not mutate the remaining residues in both the halves. For e.g., what I want Rosetta to do is in "Half-A, the residues at position 32, 49, 56, 65, 66 should be mutated to certain residues, and the exact same mutated residues should appear after designing position 32, 49, 56, 65, 66 in Half-B.

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Rosetta 3 - Applications

Ddg calculation for a metalloprotein using APBS

Submitted by dfcoelho on Tue, 2019-11-19 10:06
Category: 
Scoring

Hi all,

I am trying to calculate Ddg for a protein complex, which is made of 3 chains: A, B and C.

The chains B and C have a zinc-finger each, which are a zinc ion complexed by four CYS side-chains.

To calculate the Ddg I am using the SetupPoissonBoltzmannPotential mover followed by the Ddg filter, in order to separate chain B from chain A+C and calculate the binding energy.

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Rosetta 3 - General

Linear peptide versus cyclic peptide binding prediction

Submitted by gabr on Mon, 2019-11-18 12:25
Category: 
Design

I have used ROSIE server to analyze protein-antibody interaction and predict peptide sequences of antibody that would interact with the protein.

The analysis revealed 3 hotspots of the antibody sequence as in the picture attached. It did make sense to me that the predicted linaer peptides from antibody sequence were chosen from 1st and 3rd hotspots from the figure with highest contact points with the protein.

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ROSIE - General

./scons.py error in building

Submitted by the gaming engineer on Sat, 2019-11-09 08:48
Category: 
Compilation

I am in the stage of trying to install and build rosetta and I have reached the point where I am using scons.py.

I have been following the guide (https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build) so far, but I reach a road block when I build with scons.py. my commands and the results are as follows:

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Rosetta 3 - Build/Install

Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.

Submitted by daniloboskovic on Fri, 2019-11-08 08:24
Category: 
Design

Dear caretakers/kind strangers,

I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error. 

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Rosetta 3 - Applications

Linux Ubuntu build is missing Dynamically Linked Libraries (fail during unit test)

Submitted by denatured on Tue, 2019-11-05 21:04
Category: 
Compilation

 Hello,

I've installed Rosetta 3.11 for Linux ubuntu 16.04 without any failure.

However, I encountered some missing binaries after running unit tests. This is the general command I use for the unit test. 

python scons.py -j #numproc mode=debug cat=test

 

The snippet below is the output returned from the unit test.

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Rosetta 3 - Build/Install

Symmetry mode in Remodel for N-terminal extension

Submitted by yvonne.chan2 on Mon, 2019-11-04 13:41
Category: 
Design
Loop Modeling
Symmetry

Hello, 

I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error: 

File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

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Rosetta 3 - Applications

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