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Problem with Scoring function and PlaceStub mover

Category: 
Design
Scoring

Hi everyone,

I am using PlaceStub application (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/PlaceStubMover) for placing two sets of different stubs on the scaffold.

Post Situation: 

Secondary Structure Relax

Category: 
Design

Hello everyone,

I have generated a protein, and as you can see it seems to have almost a good backbone structure (the helices and the sheets are clearly visible but not quite there). Attached are two photos, Figure 1 is what I have generated, Figure 2 is the original crystal structure.

Is there a way to relax the structure as to emphasise for the secondary structures. In other words, push the structure to form secondary structures? or complete the hydrogen bonds for secondary structures?

Post Situation: 

ddg_monomer consumes massive RAM

Category: 
Design

I am trying to run the ddg_monomer high-res protocol on a protein. I am running this on a Linux system with 4 GB of RAM. Immediately after the protocol begins to run, RAM usage gets very high and my computer freezes. It remains frozen indefinetely. Is this normal? Usually when I run other ROSETTA protocols, the computer is perfectly usable with the job running in the background.

I am using all the default settings from the high-res protocol (row 16 of Kellogg et al) from the documentation:

Post Situation: 

An issue with GenericMonteCarloMover()

Category: 
Design

Dear All,

I  have the following code that i wrote back in summer 2017 and it worked perfectly until February. But then I started to get strange errors (and I have not modified my code at all). After investigating it seems that the GenericMonteCarloMover() is deleting the content of the pose after the .apply(pose). In other words, after the mover is done i get an empty pose (no length and no sequence).

Post Situation: 

demos/public/ideal_proteins Segmentation fault

Category: 
Design

Dear All,

I am using rosetta_bin_linux_2017.52.59948_bundle to run demos/public/ideal_proteins. The running command is 

"rosetta_scripts.static.linuxgccrelease -s input.pdb -parser:protocol input.xml -nstruct 10 -restore_talaris_behavior".

Since I got 

"

score_typeextract failed: fa_plane

 

ERROR: bad line in file myweight.wts:fa_plane 0

ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 453

Post Situation: 

remodel gives no output

Category: 
Design

Dear all,

I am following the tutorial http://2016.rosetta.ninja/day-3/rosettaremodel-basic-tutorial.

I am using version 2017.52, and run command "nohup remodel.static.macosclangrelease -s 1pgaA_0001.pdb -blueprint template.blueprint -jd2:no_output -num_trajectory 1 -save_top 1 -out:prefix long_loop -remodel:quick_and_dirty > output.txt"

The output.txt was attached. No long_loop_1.pdb can be found.

Many thanks.

Post Situation: 

The algorithm of adding missing Hydrogen to a backbone

Category: 
Design

Hello people,

You know how when you import PDB structures into Rosetta and relax them Rosetta adds the missing hydrogens? What is the algorithm that does that?

I want to know the mathematical aproach, not the code; does it use rotation vectors and a rotation matrix to find the orientation and position the hydrogens? Does it use another approach?

I beleive this same algorithm is used to add/replace sidechain? it finds the orientation and angles of the side chains and replaces them?

Post Situation: 

Fix corrupted Backbone

Category: 
Design

Hello people,

I have a protein topology with a strange backbone (attached).

You can see that there is structure (several helices), but the backbone itself is not good enough to be able to do anything computationally with it, if ported into PyRosetta, PyRosetta it gets confused. So my question is how can I fix this backbone, nothing fancy just replace each position with Glycine or Valine or Alenine, but the proper ideal structure of the amino acid that will not result in clashed nor atoms occupying the same space?

Post Situation: 

RestrictToRepackingRLT and PreventRepackingRLT

Category: 
Design
Post Situation: 

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