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Does Snugdock remodeling of H3 loops include the kink constraint as in RosettaAntibody?

Category: 
Structure prediction
Docking

I am docking an antibody that has 20 residues in the H3 loop.  I realize that this is a very challenging case.  From the 2017 paper by Weitzner and Gray, I understand the importance of a kink constraint in H3 loop modeling.  I want to know if the H3 loop remodeling that occurs during snugdock includes the kink constraint.  If not, I am concerned that the kink will be lost during remodeling, especially for this long loop.

 

 

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help surface_docking peptide on ice

Category: 
Docking

Hello everyone,

I am trying to use Rosetta surface_docking protocol to dock a 12 residues peptide on an ice slab.

I tried different formatting options of the input ice - peptide PDB file, but the software crashes.

After looking at the existing (Unsolved) posts on the forum, I created a PDB file formatted in this way:

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Motif Graft Mover error

Category: 
PyRosetta

hello everyone,

I was using a script i wrote last year regarding motif grafting, but it no longer works, i suspect a pyrosetta update issue.

anyway, i am looking through the errors and it seemed the pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover's init_parameters() have some additional arguments that is must have.

my code is as follows:

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Denovo prediction from multiple fragment lengths

Category: 
Structure prediction

I read that a combination offragment lengths is best for prediction. I tried to cat different fragment legnth and gave it to Rosetta, but it complained: 

 

caught exception 

[ERROR] EXCN_utility_exit has been thrown from: src/core/fragment/ConstantLengthFragSet.cc line: 139
ERROR: aframe->length() == max_frag_length()


caught exception 

[ERROR] EXCN_utility_exit has been thrown from: src/core/fragment/ConstantLengthFragSet.cc line: 139
ERROR: aframe->length() == max_frag_length()

 

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hybrid approach - comparative and ab initio modelling

Category: 
Structure prediction

Hi, 

Kind of a newbie to Rosetta. My protein has two structured domains connected by a short non-floppy loop (6 residues).  One of the domains can have the structure accurately solved by comparative modelling. The other doesn't have related templates available, but I do have co-evolutionary information to probably obtain a nice structure via ab initio modelling. I am looking for the best way to do a hybrid approach to solve the whole structure of this protein. I am considering these options:

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Specifying resfile in rosetta scripts

Category: 
Design

Hi, I want to design a protein interface by rosetta scripts with the positions I want to mutate stated in a resfile.
However, the output generated included mutations in other positions which were not stated in the resfile. 
I wonder if there is something wrong with my scripts.
Would you mind glancing through the following (.xml, flags, resfile and the command of running)?
Thank you very much for your help!!!

 1) design_script.xml

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Two questions on the RosettaScripts flexbb-interfacedesign.xml

Category: 
Design

I am trying to use flexbb-interfacedesign.xml from rosetta 3.9 to do the design of a protein interface.

I have two questions:

1) The top of flexbb-interfacedesign.xml reads as the following, is there a missing open bracket before "ProteinInterfaceDesign...", as highlighted in red?
2) How does rosetta define "chain1" and "chain2", as highlighted in yellow? I have tried many times by changing either "1" or "0" and even changing the chain name in the pdb (e.g. A->B, B->A) but still I cannot control which chain to design.

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PyRosetta on a HPC

Category: 
Compilation

Hello people,  i have been trying to compile PyRosetta on a HPC (Red Hat 6.4) for several weeks now without success.

I tried many different approaches so i will write the gist of it.  I tried compiling PyRosetta which did not work, then I read i have to compile it from source, so this is what I am trying to do. I uploaded Rosetta to the HPC.

most of the programs are old, so I had to install python3.6.1, Cmake 3.5.9, GCC 5.3.0, and Ninja 1.9.0

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Adding Custom AtomTypes to Pyrosetta

Category: 
PyRosetta

 

Hello everyone,

 

Does anyone have experience adding custom atom types to Pyrosetta? I have tried creating my own `atom_properties.txt` file, shown below.

```

NAME  ATOM LJ_RADIUS LJ_WDEPTH LK_DGFREE LK_LAMBDA LK_VOLUME
A1     X 2.0000         0.0486       1.0000           3.5000 23.7000
A2     X 2.0000        0.2000  1.0000 5.0000           23.7000
VIRT    VIRT 0.0000         0.0000 0.0000            3.5000 0.0000 VIRTUAL

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