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Error src/core/scoring/MembraneTopology.cc line: 139

Submitted by Daniel Hall on Thu, 2017-07-13 04:58
Category: 
Structure prediction

Hello, following the tutorial for Comparative Modelling on under the Support section I ran the command /home/dhall/Rosetta/main/source/bin/rosetta_scripts.default.linuxgccdebug @rosetta_cm.options I know this is not the command shown in the tutorial. After editting the following files; Rosetta_cm.xml and rosetta_cm.options to suit my files i get the following error src/core/MembraneTopology.cc line: 139 , this is what is shown on line 139 in the MembraneTopology file if ( total_tmhelix_==0 ) {

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Rosetta 3 - Applications

Minimizing across jumps

Submitted by SenyorDrew on Thu, 2017-07-06 06:26
Category: 
Structure prediction

Hi,

What are the degrees of freedom that are minimized when minimizng across a jump?  Is it just a rotation (spin) about the jump vector and movement along the vector? I'm working on an interface design probelm and I've set up my movemap where sidechains are allowed to minimize, backbones are held fixed, and jumps are allowed to minimize. I'd like to perform a rigid-body minimization between my two chains and I'm trying to understand which degrees of freedom are minimized.

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Rosetta 3 - General

Converting -patch replonly residues to original sequence

Submitted by subha on Mon, 2017-06-26 13:39
Category: 
Structure prediction

Hi There,

I am trying to model a protein with disordered regions and found a paper that mentioned using -replonly_residues will be helpful in such case. I have run the simulation and when I checked the output structures , all of the replonly residues are mapped as 'GLY'. Is there a way to re-map them to the original sequence in the PDB coordinate file?

Thanks,

Subha

 

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Rosetta 3 - Applications

Repeat study

Submitted by thomashrabe on Tue, 2017-06-20 11:21
Category: 
Structure prediction

Hi everyone,

I would like to repeat and extend this study with PyRosetta, yet I am new to it. I have the PyRosetta tutorial book here in front of me and working through it.

How should I go about creating the fragment database? Manually select the fragments and go from there?

How can I re-create similar structures and expand from there? 

Some general pointers would be great. 

Thanks,

Thomas

 

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PyRosetta - General

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

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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