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Segmentation Fault in Fragment picking

Submitted by ashu4487 on Fri, 2018-07-06 20:47
Category: 
Fragment Generation

Hello Everyone

I am trying to generate fragments for a short peptide  (12 residues) to use them further in Flexpepdock. Following are the flag and weight files

Flag file

-in::file::vall /disk/software_sources/rosetta_bin_linux_2018.09.60072_bundle/tools/fragment_tools/vall.apr24.2008.extended.blast.gz

-in::file::fasta seq.fasta
-frags::ss_pred seq.psipred.ss2 predA
-frags::scoring:config weights.wghts
-frags::frag_sizes 3 5 9

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Rosetta 3 - Applications

error with extend_terminus.py

Submitted by bigjim1309 on Wed, 2018-07-04 00:47
Category: 
Compilation
Structure prediction

Hi all

I try to run the script extend_terminus.py with the following command :

python extend_terminus.2.py -c A -o 1.c.pdb -a 1.clean.pdb AAGAAGAGAG

and i end up with the following error

pack_rotamers = rosetta.protocols.simple_moves.PackRotamersMover(sfxn, task)
AttributeError: 'module' object has no attribute 'PackRotamersMover'

Does anyone know how to fix that ?

Cheers

JM

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PyRosetta - Scripts

Calbur vs Energy Based Clustering

Submitted by Swillard on Sun, 2018-07-01 13:24
Category: 
Structure prediction

Heyo,

I've got 10,000 output structures from the rosetta CM protocol and am looking to cluster the results to analyze these structures. I've been having issues running calibur (seperate post) and noticed that there was an energy_based_clustering program published recently.

In my quick browse of each I see that the way in which clusters are found is different for each. I am wondering if there is a significant difference in applicability of each, and if so, which one would be more applicable for homology modelling.

Thanks

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Rosetta 3 - Applications

Calibur not listing cluster members

Submitted by Swillard on Sun, 2018-07-01 13:07
Category: 
Structure prediction

Hi,

I generated 10,000 structures using the rosetta CM method. I then tried to cluster them using calibur in Rosetta 3.9, build# 60072 using the command "calibur.mpi.linuxgccrelease -pdb_list pdblist.txt" but it won't display the members of each cluster. It only shows the following at the end:


Largest 2 cluster centers: S_0445_4.pdb(35), S_0001_2.pdb(28). Margin = 20.00000%

cluster = 0; center = S_0445_4.pdb; n_decoy_members = 35; members =

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Rosetta 3 - General

problem in downloading result from backrub server

Submitted by ladimafakher on Sun, 2018-07-01 00:50
Category: 
Design

Hello 

I used backrub server for flexible modeling and the results of my run sent to my email address. but unfortunately I can not download my results and I got an error. I tried to download my results in several days but I got an error again. what is the problem and how can I solve it? thanks

 

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ROSIE - General

Pyrosetta protocol to move protein-peptide docked complex closer to active site.

Submitted by eduardoftoliveira on Fri, 2018-06-29 02:50
Category: 
Design
Enzyme Design

Hi,

I have a protein-peptide(15 a.a) system with alreaddy a good guess for the binding mode of the peptide. Now I want to move slightly the peptide to a more reactive conformation and design mutants in this reactive conformation.

The “enzdes” application with a constraint file would do exactly what I need but I think it was created for “protein-small ligand” systems and I cannot use it with a multiple residues ligand like my peptide.

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PyRosetta - General

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