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Structure prediction

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

Questions regarding fragmentation using Robetta

Submitted by ahmadkhalifa on Thu, 2018-06-28 13:24
Category: 
Structure prediction

First I want to make sure that I understand this correctly. Fragmentation creates L-K+1 fragments, blasts them against some database and finds the homologous secondary structures that are shown below (small portion as an example).  Correct?

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Rosetta 3 - General

ERROR: Unused "free" argument specified: GDP.fa.tors

Submitted by ahmadkhalifa on Fri, 2018-06-15 11:27
Category: 
Structure prediction

I have the following flags in my refinement flag file, I'm getting the error ERROR: Unused "free" argument specified: GDP.fa.tors, I'm not sure why!  

-extra_res_cen GTP.cen.params GDP.cen.params -extra_res_fa GTP.fa.params GDP.fa.params-extra_improper_file GTP.fa.tors GDP.fa.tors

 

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Rosetta 3 - General

Error while converting mol2 to params using molfile_to_params.py

Submitted by ahmadkhalifa on Thu, 2018-06-14 10:30
Category: 
Structure prediction
Docking
Design

I'm trying to run python /home/labusr/rosetta/main/source/scripts/python/public/molfile_to_params.py --keep-names --clobber --extra_torsion_output --centroid gtp.mol2 -p GTP -n GTP, on a gtp.pdb that has been reduced using phenix.reduce and converted to mol2 using openbabel. Below is the error I get. 

 

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PyRosetta - General

Relevant number of cycles of loop closure required

Submitted by vasavi on Mon, 2018-06-11 02:55
Category: 
Structure prediction
Design
Loop Modeling

Dear All,

I have been working on the Domain insertion module of Rosetta. I need to know what are the relevant number of cycles of loop closure I require to enter for larger domain sets. The domain Im inserting is around 175 aa long. I am having trouble launching the same using MPI in parallel, hence the single processor is taking days for the output. Wondered if anyone who has worked on it could suggest a feasible number for AnchoredPDBcretator and also for AnchoredDesign.

Vasavi.

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PyRosetta - Applications

Rosetta CM round_thread.pdb doesn't exist and can't find pose (id = round)

Submitted by ahmadkhalifa on Wed, 2018-05-23 09:51
Category: 
Structure prediction

I'm trying to create a threaded model according to this tutorial: https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM

I'm not sure why I'm getting this error, how to debug it? 

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Rosetta 3 - General

Free FSC score for validating refinement

Submitted by ahmadkhalifa on Thu, 2018-05-10 05:53
Category: 
Structure prediction

According to the Rosetta density tutorial: 

"Generally, we select the best 20% of models by geometry, and selecting the best overall by free FSC. The top 5 models should be inspected for model convergence as well as visually inspected for density map agreement"

I would appreciate if someone explains why we choose the lowest FSC score, and what does it mean to have a negatrive FSC score? Also, according to the paper quoted below, shouldn't we sample for the highest free FSC and bnot the lowest? 

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