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Structure prediction

ddg_monomer: what is the theoretical solution condition for the scoring?

Category: 
Structure prediction

As I understand, the Gibbs free energy not only depends on the structure but also depends on the surrounding solution conditions. That is why under certain conditions (e.g. pH, temperature, ionic strength), the protein tends to unfold or remain native structure. So I wonder if there is a theoretical assumption to set the scoring background? For example, is it under pH 7, 25 degree C, or vacuum state? Thank you.

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CDR Cluster Constrained Relax Equivalent

Category: 
Structure prediction
Loop Modeling

Hi,

Looking through the doucmentation, I found references to an application called "relax_cdrs", which enables relaxation of CDRs with constraints derived from their corresponding CDR cluster.  (link to documentaiton below).

https://www.rosettacommons.org/docs/latest/application_documentation/antibody/CDR-Cluster-Constrained-Relax

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Comparative modeling Error: potential mismatch between sequence from alignment  and sequence from PDB!

Category: 
Structure prediction

Hi!

I´m very new at Rosetta Commons and not an expert.

We wanted to predict comparative models using a standard protocol.

Then, we always got the Error:

unknown atom_name: CA  CB

 

Is this because of the Error before? :

Error: potential mismatch between sequence from alignment  and sequence from PDB! ??

 

This error is because no secondary structure is defined at 20 residues and therefore the coordinates for the atoms of these missing amino acids are missing.

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Multiprocessor Execution

Category: 
Structure prediction

Hello,

My apologies in advance if this has already been addressed, but I haven't found the answer elsewhere.

I have a powerful workstation with dual Xeons with 16 cores each. dual booting Windows 7 and Ubuntu Linux.  Running on the Windows partition I have used two commercial solutions as well as allowing Rosetta@Home to utilize the system a few hours each night.  Modeling done on all three solutions pegs all 32 processing cores at 100% and the completion times on high quality homology modeling is very low (around 10 hours).

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Files for Spatial Constraints

Category: 
Structure prediction
Enzyme Design
Constraints

Hi guys,

I am trying to locate the files to generate spatial constraints from homologous template structures for comparative modelling as given in the Thompson and Baker paper from 2011. I can't find them anywhere in the ROSETTA directories. Are they available anywhere?

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Finding lowest energy structure among generated structures

Category: 
Structure prediction

Hi Rosetta community,

After finally getting the CS-HM-Rosetta run to successfully generate structures, now I'm at the point where I want to select the lowest energy structure among generated structures which suppose to be the closest to the native structure. But in this website:

https://www.rosettacommons.org/demos/latest/public/clustering/README

there're no instructions on plotting.

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backbone-independent density

Category: 
Structure prediction

Hello everyone!

Is it possible to get backbone-independent density for amino acid as a continuous function of rotameric chi[1-4] using some classes from dunbrack namespace? As shown in the picture A http://dunbrack.fccc.edu/bbdep2010/Tutorial.php#TraditionalLibrary

If it's possible, please give me any hint or example what should I use.

Thanks in advance

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Error: Some problem with atom_id_mask in defining atom_id_map

Category: 
Structure prediction

Hello everyone,
I am using rna_denovo prediction (FARFAR) and today I got this error message:
ERROR: Some problem with atom_id_mask in defining atom_id_map
ERROR:: Exit from: src/protocols/farna/RNA_ChunkLibrary.cc line: 154

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