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algebric library for rosetta

Category: 
Design

Hi,

I'm currently integrating an application ( i developed ) with rosetta, and this app needs to perform matrix diagonalization.
The current (stand alone) application uses an open source algebric library named Eigen.
I guess that due to leagal reasons this library cannot be integrated with rosetta,
and i would like to know if there is a specific algebric library i should use?

Yigal.

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ddg_monomer mutations list: How to specify chain ID?

Category: 
Design

I want to use ddg_monomer with multiple simultaneous mutations. According to the documentation (https://www.rosettacommons.org/docs/latest/ddg-monomer.html) this requires a mutation file, instead of the resfile used by other applications.

However, in the example provided by the documentation, there is no use of a chain ID. My structure has multiple chains.

How can I specify a chain ID in the mutation file?

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Does a negative Rosetta dG imply a favorable process?

Category: 
Design

I know that Rosetta's energies are given in Rosetta Energy Units (REU), which are not real free energy units, but which sometimes correlate linearly with real free energies.

This means that if I have a bunch of dGs given by Rosetta, I compare them and interpret these values as Rosetta's telling me that this process is more favorable than this other process, and so on.

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Instructing design scripts to use noncanonical AA instead of canonical

Category: 
Design

Hi, novice Rosetta user here (so apologies in advance for simple / silly questions).

I have small peptide ligands that I am using in standard grafting / design. This has been relatively straightforward. However, one monkey wrench I'd like to throw into the works would be for the design scripts to use a noncanonical amino acid instead of the corresponding canonical one. For example, instead of tyrosine, design interfaces assuming all tyrosines are phosphorylated, or alternatively, impose acetylation or methylation on certain residues.

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How to create a rotamer set that includes all possible rotamers of all possible amino acids

Category: 
Design

I would like to learn how to create a rotamer set that includes all possible rotamers of all possible amino acids. I want to design residues at certain positions in a protein chain manually by creating rotamer sets that include all rotamers of all amino acids.

I define a resfile for designing residues at positions 3, 5, 7, 20, 26, 30, 34, 39, 43, 52, 54 and packing all the remaining residues in 1PGA.pdb as follows:

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Abinitio Relax Error from -kill_hairpins

Category: 
Design

I am using Rosetta 3.5 to predict protein structures using AbinitioRelax protocol.
When I specify -kill_hairpins I always got the following errors:

ERROR: [ERROR] invalid header input for kill_hairpins file.
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
Exception :

[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
ERROR: [ERROR] invalid header input for kill_hairpins file.

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