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Structure prediction

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:

Post Situation: 

Unexpected Error with RosettaCM -

Category: 
Structure prediction

Hi all,

I am hoping to get some insight, my RosettaCM is crashing for an issue I haven't seen before. See below:

Terry

Error:

 

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: stage3.wts

score_typeextract failed: fa_plane

ERROR: bad line in file stage3.wts:fa_plane 0

ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 458

BACKTRACE:

[0x5e10498]

[0x459a6ec]

[0x459aa36]

[0x459ab31]

[0x45b4083]

Post Situation: 

How to correctly incorporate constraint information into ab initio structure prediction?

Category: 
Structure prediction

Hi, I am now trying to do an ab initio structure prediction with the constraint information generated from Gremlin.

My script of ab initio structure prediction with Rosetta is as follows, with the part related to constraint data bolded:

Post Situation: 

Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB

Category: 
Structure prediction

Hi all,

 

       I'm sorry if this is an old thread, I did find other forums dealing with unrecognized atoms but in those threads my problem was not resolved.  I am trying to follow the rosetta_CM tutorial and I got through the setup_rosetta_CM.py script and it generated the .xml file which I checked and it looked good. However, when I run the hybridized steps using rosetta scripts I get this error:

 

ERROR: unrecognized atom_type_name 'CS'

Post Situation: 

Rosetta3.10 on macOS segmentation fault 11

Category: 
Structure prediction

 

I have tried several times to install Rosetta3.10 for macOS version 10.14.2. My system info is:

Model Name: MacBook Pro

  Model Identifier: MacBookPro15,2

  Processor Name: Intel Core i7

  Processor Speed: 2,7 GHz

  Number of Processors: 1

  Total Number of Cores: 4

  L2 Cache (per Core): 256 KB

  L3 Cache: 8 MB

  Memory: 8 GB

Post Situation: 

RosettaMP: issue with generating .lips4 file

Category: 
Structure prediction

Hi Rosetta users,

I am experiencing trouble using RosettaMP to predict membrane protein structures. I am currently following the RosettaMP tutorial, which can be found here (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/membrane-abinitio).

Post Situation: 

Add hemes to cytochrome structures

Category: 
Structure prediction

Dear all,

I am using abintio protocol to predict a cytochrome structure. After I generated the model, it did not give HEME locations. The pdb output only contains the regular protein residues, but missing the location of hemes. I am wondering is there anyway to tell Rosetta also predict the hemes? 

Thank you

Post Situation: 

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