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RosettaDesign improvements

Category: 
Design

Hello everyone,

 

I wrote a forum entry here (https://www.rosettacommons.org/node/10258) asking about details on RosettaDesign, and I am continuing the conversation here since I ran my script on several structures and got different results and I want a better understanding.

 

Please find attached a summery of the results. If you look closely you can see the green relaxed structure on the bottom left (sorry if it is not clear).

 

Post Situation: 

cartesian_ddg error: "Assertion `files.size() == 1` failed."

Category: 
Design

I am trying to run the cartesian_ddg protocol (https://www.rosettacommons.org/docs/latest/cartesian-ddG).

I am using the following command:

cartesian_ddg.static.linuxgccrelease \
 -database $ROSETTADB \
 -s min_2b5i-A_0001_clean_0011.pdb \
 –ddg:mut_file themutfile.txt  \
 -ddg:iterations 3 \
 -ddg::cartesian \
 -ddg::dump_pdbs false \
 -bbnbr 1 \
 -fa_max_dis 9.0 \
 -beta_cart

 

Post Situation: 

ab initio

Category: 
Design

Hello!

 

I am using the standalone version of Rosetta, and so do for the Fragment picker application. in the tutorial, 3 SS prediction programs are used with weightage  of 0.6 for psipred and 0.2 each for other two programs; however, the Robetta server, produce results based on only 02 programs, i.e. psipred an Jufo so in this case, what is the weightage for both programs?

Thanks!
Malkeet

Post Situation: 

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.

Post Situation: 

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:

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

Post Situation: 

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.

Post Situation: 

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:

Post Situation: 

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: 

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