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RemodelMover() and the blueprint file

Category: 
Design

Hello people,

 

I my attempt to get a working RosettaDesign protocol, I have come across the RemodelMover() class.

 

From the Rosetta C++ documentation, the RemodelMover should take a blueprint file in order to specify which residues to remodel. but the RemodelMover() class in PyRosetta has no method to input a blueprint file nor a resfile.

 

on its own the RemodelMover works without any errors, but would remodel the entire structure.

 

Post Situation: 

Multistate design output

Category: 
Design

Hi all,

Sorry to trouble again.

I understand that the multistate design protocol outputs structures where the chains A and B will become AA, AB and BB.

However, I get the output of chains A and B even in the output files AA and BB.

May I find out how I could produce the output files AA and BB homodimers?

Is this something to do with my corr file?

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Error while converting mol2 to params using molfile_to_params.py

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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Multistate design on Rosetta - no generations produced

Category: 
Design

Hi,

I am currently running a multistate design protocol (mpi_msd.linuxgccrelease) for bispecific antibody design. After I have run the protocol with my options, the program runs and is "stuck" at this point for a long time:

core.pack.pack_rotamers: built 39485 rotamers at 58 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DoubleLazyInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 22325380 bytes

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Relevant number of cycles of loop closure required

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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GenericMonteCarloMover accept/reject moves

Category: 
Design

Hello People,

I have setup a generic montecarlo mover with backrub, but I do not get any accepted nor rejected moves, the following is my code:

backrub = pyrosetta.rosetta.protocols.backrub.BackrubMover()
backrub.pivot_residues(pose)

GMC = pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover()
GMC.set_mover(backrub)
GMC.set_scorefxn(scorefxn)
GMC.set_maxtrials(500)
GMC.set_temperature(1.0)
GMC.set_preapply(False)
GMC.set_recover_low(True)
GMC.apply(pose)

 

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RosettaDesign Result Evaluation

Category: 
Design

Hello everyone,

I wrote a script to perform RosettaDesign (both fixbb and flxbb) and I benchmarked it. Attached is the Abinitio folding simulation of three proteins, and my full script can be found here: https://github.com/sarisabban/RosettaDesign/blob/master/RosettaDesign.py

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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).

 

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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: 

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