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Structure prediction

Question about wrong homology design

Category: 
Structure prediction

Hi everyone, I have been using rosetta 3.4 and 3.5 to build an homology model of a protein and the result is the same, the structure is broken just in one of the amino acids. I made a control test and made the homologue model of the same template and also the structure is broken. In figure A is the template an in figure B is the homologue model where appears the some fragments of one residue outside of the structure, How can I solve that?
there is my script:

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Ambiguous constraints are ignored in ab initio

Category: 
Structure prediction

Dear Rosetta Commons,

I recently wanted to use a set of ambiguous constraints in structure prediction and I prepared a file that looks like this:

AmbiguousConstraint
AtomPair CB 26 CB 38 BOUNDED 1.5 8.0 1.5 NOE
AtomPair CB 28 CB 61 BOUNDED 1.5 8.0 1.5 NOE
AtomPair CB 26 CB 61 BOUNDED 1.5 8.0 1.5 NOE
END_AMBIGUOUS

Unfortunately, it seems that the ab initio application is ignoring the ambiguous constraints. No constraints are used in the prediction and also there is not constraint score term in the final score file.

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no template pdb provided for alignment

Category: 
Structure prediction

Dear rosetta user:
I have try to learn the tutorial in electron_density/cryo_em tutorial /scenario2_close_homology/, but when I run the run2_relax_cm_inputs.sh, there is no output, and only a warning messege, say "protocols.comparative_modeling.ThreadingJobInputter: Warning: no template pdb provided for alignment ". Can any one tell me how to solve this problem, thanks a lot. The content in run2_relax_cm_inputs.sh is show as follow, and I have a file 1OJ8A.pdb in the fold.

!/bin/bash

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ddG_monomer

Category: 
Structure prediction

I am trying to use ddG_monomer in Rosetta 3.5 to examine the structural effects of a single point mutation. Based on experimental data, it appears as if the mutation causes changes to the backbone of the structure. I would like to use the Monte Carlo ensemble method (protocol 20) from Kellogg et al. paper to model these changes but have not been able to locate the ensemble_generator_score12_sidechain_ver2.linuxgccrelease application listed in the supplementary methods section of the paper. Is the backrub application equivalent to ensemble_generator the application?

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Creating model of 89-90 residues by ab initio methodology-help

Category: 
Structure prediction

Dear rosetta users,
This is my first time using ab initio modelling in order to obtain a protein's structure (though i have some experience on comparative/homology modelling).
I'm trying to obtain the structure of 2 proteins of 89 (COR15A) and 90 (COR15B) residues respectively. Sadly i can't use the homology-modelling methodology because i don't have a proper template to use it.
Anyway, i have already built 100 structures of one of my protein (COR15B) by using the following command:

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Access sigma values for rotamers

Category: 
Structure prediction

Is it possible to get access, through the class structure, to *other* fields of the Dunbrack rotamer library? After building the rotamers for a particular pose I would like to be able to get the sigma values of each chi as well as the Dunbrack probability values, for each rotamer.

I've been drilling down through the class structure and think I see how to get the probability values, but I'm not seeing the sigmas anywhere.

Jason

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Connecting linkers

Category: 
Structure prediction
Design

Hello,
I plan to design a small protein fragment using flexible linkers (to connect the breaks) out of a larger protein.
Using which rosetta application i should use to put the residues of the flexible linkers to get the complete 3D structure of the shorter protein.

Please Help me!
Thanks in advance
K.Prasanth

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