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Motif Graft Mover error

Submitted by ac.research on Tue, 2019-03-26 13:25
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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PyRosetta - General

Denovo prediction from multiple fragment lengths

Submitted by ahmadkhalifa on Sun, 2019-03-24 03:55
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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Rosetta 3 - General

hybrid approach - comparative and ab initio modelling

Submitted by eprates on Wed, 2019-03-20 11:58
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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Rosetta 3 - Applications

Specifying resfile in rosetta scripts

Submitted by johnnytam100 on Mon, 2019-03-18 02:19
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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Rosetta 3 - Applications

Two questions on the RosettaScripts flexbb-interfacedesign.xml

Submitted by johnnytam100 on Fri, 2019-03-15 04:54
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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Rosetta 3 - Applications

PyRosetta on a HPC

Submitted by ac.research on Thu, 2019-03-14 02:00
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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PyRosetta - General

Adding Custom AtomTypes to Pyrosetta

Submitted by garrettameek on Wed, 2019-03-13 15:06
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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PyRosetta - General

Docking to TM protein plus lipid bilayer

Submitted by renedominik on Tue, 2019-03-12 06:58
Category: 
Docking

Hi, I want to dock a protein to a TM protein embedded in a lipid bilayer.

Is there a way to do that with an implicit membrane model?

My current approach is to place explicit POPC lipids around the TM protein. 

What would be the simplest way to make Rosetta being able to read the pdb file containing POPC?

Thanks!

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Rosetta 3 - Applications

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