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domain:domain fusion

Submitted by felipet on Thu, 2017-06-15 13:13
Category: 
Design
Loop Modeling

Dear all

I would like to insert a domain at the N-terminus of protein and at the same time build different linker sizes. Which application is the best suited? My impression is that domain insertion protocols, like remodel, broker or AnchoredPDBcreator, assumes that we are not at the end or a protein. Is there a way to do this?

thanks in advance

best

felipet

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Rosetta 3 - Applications

How to minimize the decoys obtained from backrub?

Submitted by Vedasheersh on Wed, 2017-06-14 10:26
Category: 
Design

Hello there!

I am trying to design a protein using backrub application. I have two questions.

1. Is nstruct 100 enough to sample such a problem? (I am only trying to design 15-20 out of 560 amino acids)

2. From the output of backrub, what is the best way to minimize the decoys to score them so that I can compare with the wild type?

Thank you

Veda

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Rosetta 3 - Applications

error extracting PDB from silent from AbinitioRelax with constraints

Submitted by attesor on Wed, 2017-06-14 04:15
Category: 
Structure prediction

I am using Rosetta 3.8 under Ubuntu 16.04 64 bit. I performed AbinitioRelax to predict structure for my protein with certain AtomPair constraints. I also applied filters by using -abinitio::use_filters true. 

First, I notice there are different numbers of items in the scores generated for "failed" and "successful" decoys.

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Rosetta 3 - Applications

Rosetta build error on MacOS Sierra

Submitted by Vedasheersh on Tue, 2017-06-13 22:27
Category: 
Compilation

Hello everyone!

I am trying to build rosetta with mpi in macOS sierra. But, it gives the following errors. 

I tried rebuilding without mpi (after deleting build/ contents), but it gives the same error.

Could any one please help?

$ sudo ./scons.py -j 3 mode=release bin extras=mpi

1 error generated.

scons: *** [build/src/release/macos/16.0/64/x86/clang/8.1/mpi/protocols/init/init.os] Error 1

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Rosetta 3 - Build/Install

Error with -patch_selectors

Submitted by subha on Tue, 2017-06-06 14:40
Category: 
Structure prediction

 HI there,

I am trying to predict the structure of a protein which has some diordered regions in it. I found a paper that performed the modeling of a protein with disordered regions by considering the disordered region as -replonly. So, I am trying to use the same approach, but ended up with the below error. 

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 349

ERROR: Failed to apply a PatchOperation to CYZ

Can anybody help me understand what it is and how to fix it?

 

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Rosetta 3 - Applications

Fold Tutorial

Submitted by ac.research on Sat, 2017-06-03 19:39
Category: 
Structure prediction

Dear Everyone,

 

I am going through the PyRosetta Tutorial kindly written by the Gray Lab. I am going through it one chapter at a time sequencially and i have reached the folding tutorial: http://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshop4_Folding.pdf

 

My question:

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PyRosetta - General

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