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Structure prediction

De novo backbone trace from fragments

Category: 
Structure prediction
Design
Loop Modeling

Dear Rosetta experts,

I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.

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helical bundle predict

Category: 
Compilation
Structure prediction

Hi everyone,

I'm interested in using the helical_bundle_predict method. In this link (https://www.rosettacommons.org/docs/latest/structure_prediction/helical-bundle-predict) it is described as an application but I cannot understand how to make the system install it. It may have something to do with the fact that it is a pilot application, but still it is not clear to me which files I need to modify in order to install it with scons. 

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Using Rmsd RosettaScripts filter with alignment files

Category: 
Structure prediction

I have a homology model that contains a residue insertion and thus a 1:1 residue RMSD calculation cannot be performed. I would like to try the Rmsd RosettaScripts Filter with an alignment file to get the correct C-alpha RMSD calculation. However, I'm not sure how to create this alignment file. I've tried the alignment Grishin file I used for Homology modelling but receive this error:

File: src/protocols/protein_interface_design/filters/RmsdFilter.cc:217

[ ERROR ] UtilityExitException

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Comparatively modelled chains are far apart in final structure while the template pdb has all chains in a close-knit complex

Category: 
Structure prediction

I tried to model a protein sequence (4 chains) using RosettaCM. The structure of the protein is already available in PDB (2ERJ). The issue I am facing - the final modelled structure has all the 4 chains very far apart, unlike the pdb. What exactly is going wrong? 

I am obtaining the alignment file from Clustal omega. The target fasta sequence is given as chain1/chain2/chain3/chain4 and the 2ERJ fasta is also given in the same format in clustal omega so that the final alignment has only 2 unique identifiers in the ali file, like this:

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Membrane Abinitio modeling error

Category: 
Structure prediction

Hi,

I am modeling a 178 residue membrane protein sequence using the abinitio protocol

To briefly describe what I have done:
1. generate structure fragments using Robetta server
2. generate a span file using OCTOPUS server and the script, octopus2span.pl
3. generate lipophilicity prediction file (.lips4 file) using run_lips.pl

4. generate PDB using membrane_abinitio2.linuxgccrelease

I can run the BRD4.fasta in the tests successfully following above protocols.

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Extracting PDBs from a Silent file: "Can't find residue type for ARG"

Category: 
Structure prediction

Hello everyone,

I am refining protein structures into Cryo-EM maps, and my output is a silent file. Currently, I am attempting to extract the pdbs from the silent file so that I can analyze and score the structures. The protein has a missing loop, and it is failing on the C-terminus right before the missing loop. Specifically, my error for each structure is "ERROR:  can't find residue type for ARG:CtermTruncation at pos 114 in sequence G". 

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not knowing which one of three ways to run rosettascript

Category: 
Structure prediction

Hello,

I meet a question when I am to run rosettascript. I found three executables but I do not know which one to choose. I am wondering whether some one can help me out. I would be much appreciated. 

I found three ways, as below, to run rosetta scripts I am wondering what are differnece in these three executables. Will they give same results for the same inputs. whether settings are same in these three ways. 

rosetta_scripts.default.linuxgccrelease 

rosetta_scripts.linuxgccrelease

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