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restrict PackRotamersMover

Category: 
Design

Hello Everybody,

I'm using Rosetta to find a sequence that fits a given main chain using the fixBB or the PackRotamersMover. What I haven't been able to find out: How do I tell Rosetta to use the amino acid, which was selected by the alorithm for position X, also at position X+Y? In other words, the sequence should be identical at positions X and X+Y, but I would like to leave it to Rosetta to select a suitable residue and find suitable rotamers.

Thanks for your help.

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Issue with Loop Analyzer Mover ouput

Category: 
Design

Dear Rosetta Users,

I am trying to design a loop present in a protein-protein interface. At the end of my design protocol, I inserted a LoopAnalyzerMover to assess the output decoys. To my dismay, I find very high LAM score, for all loop designs. An example LAM output is below:

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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DDG_monomer ΔΔG question

Category: 
Design

I read the  paper Role of conformational sampling in computing mutation-induced changes in protein structure and stability (Kellogg etal.2011),

and  set the flags as row 3 , 13 and 16, and some questions comfuses me.

The paper shows  the predicted ΔΔG of row 3 is the mean of the mutant energies subtracted by the mean of the wildtype energies.

while that of row 13 and row 16 are defined as the difference between the mutant and wildtype mean of the lowest 3 energy models out of 50.

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Error running GenericMonteCarlo mover within MultipleOutputWrapper mover

Category: 
Design

Hello Rosetta Users,

I have been trying to write and test some design protocols using rosetta_scripts. While testing a script, I have come across the following error:

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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.

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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?

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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:

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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).

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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

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