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Structure prediction

Centroid mode minimization

Category: 
Structure prediction

Hi everyone,

I was wondering if there is something like the Relax Application but to use it directly in centroid mode. I know AbInitio uses fragment insertion to start building structures in centroid mode that are later fed to the All-Atom relax application, but is there something that can do a montecarlo local exploration without leaving centroid representation?

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Error of compiling AbrelaxApplication.cc

Category: 
Structure prediction

Hi,I want to use ResolutionSwitcher in Montecarlo.cc to relax pdb after stage1-4,when i add "#include<protocols/abinitio/ResolutionSwitcher.hh> in MonteCarlo.cc",it turn to be a error"Resolution switcher was not declared in this scope".

I included all the header files but still not working.

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What is the best protocol to predict the missing residues in X-ray crystallisation?

Category: 
Structure prediction

I know the full amino acid sequence for my protein. I have obtained its X-ray crystal PDB structure, as well as the mtz file from the crystallisation. There are several loops and termini not resolved. Can I ask what is the best protocol to predict the missing part? I understand it would still not be fully "true" after Rosetta's modelling. I just want to have a "mostly likely" one that can be used as the starting point for my molecular dynamic simulation.

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Can remodel really handle multiple insertions in one simulation?

Category: 
Structure prediction

The tutorial at https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling  says "You can build multiple loops in the same simulation by altering the blueprint file to indicate where these loops are". 

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Remodel: the pose does not have residue with chain=H, PDBnum=114

Category: 
Structure prediction

I am exactly using the same files in the tutorial of https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling

In the "Extending the Termini" section, I use "3gbn_missing_cterm.pdb", "3gbn_missing_cterm.remodel" and "flag_missing_cterm" files as input, with a command 

$ROSETTA3/bin/remodel.linuxgccrelease @flag_missing_cterm

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Rosetta scripts crash in CM workflow

Category: 
Structure prediction

I'm trying to get started with comparative modeling for soluble proteins. I tried working through the demo/tutorial for membrane protein and adjusting for soluble, then also tried working with the RosettaCM workflow (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM). I'm having no trouble creating the input files, but seem to keep getting crashes at the step of calling rosetta_scripts.

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Does Rosetta have a class diagram for each class in the source code?

Category: 
Structure prediction

When reading the source code, follow the function to find the class definition, but there is no way to know which class it inherits from or whether there is a defined subclass of the class. At the same time, I don't know which file the virtual function of the virtual base class is implemented in.So I would like to ask if there is a class diagram of the code

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Error in Hybridize of Rosetta Comparative Modeling.

Category: 
Structure prediction

After threading my target fasta on template pdb, I ran Hybridyze rosetta_scripts. The terminal stopped in the error "Segmentation fault: 11". I checked my command line and input files, and tried to find out what was going wrong, but I had no idea to find out what the problem was. All the tracebacks are listed below.

 

#

zpro:3-hybridize zzl$ /Users/zzl/rosetta_bin_mac_2019.22.60749_bundle/main/source/bin/rosetta_scripts.mpi.macosclangrelease @rosetta_cm.options

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AbInitioRelax.mpi Hangs - Waiting for Job Request

Category: 
Structure prediction

Hi guys,

 

I recently downloaded and compiled Rosetta with MPI capabilities to take advantage of the 32 core processor we have on our workstation. Compilation went well, and I can call protocols - but they all seem to hang.

 

To help narrow things down, I am working out of the DeNovo Structure Prediction tutorial demo directory - I can call the protocol and it seems to start running as normal:

 

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