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A problem with "make_fragments.pl" script dependencies

Category: 
Structure prediction

Dear fellows,

I would like to generate fragments for protein sequence structure prediction ab initio locally, on my laptop, without involving any server, such as Robetta. I carry out it with a help of make_fragments.pl script. And I met with several problems with make_fragment.pl dependencies. I want to solve these problems. Could you advise me, if you can, how to solve them, please?

My first problem consists in follows:

Post Situation: 

How does the label in pdb files looks like when using ResiduePDBInfoHasLabel?

Category: 
Design

I want to use ResiduePDBInfoHasLabel to select a subset of residues.

However, I could not find an example pdb that shows me how the residues are labeled (i.e. the format of labelling in pdb).

May I have an example from anyone who has used ResiduePDBInfoHasLabel before?

Thank you very much!

Post Situation: 

Does it make sense if I do backrub after sequence design?

Category: 
Design

Hi all, just a very simple question that I want to have your opinion:

Usually, we do sequence design after backrub (i.e. flexible backbone sampling).

Does it make sense if I do backrub after sequence design?

Just curious how will it be different, with an opposite order.

Thank you!

Post Situation: 

PDB file name too long to be handled by file system

Category: 
Structure prediction

Hello,

in ddg_monomer module, we have encountered a problem with the length of the PDB file name when predicting mutant with 50+ mutations. Since Rosetta constructs the PDB file name based on the mutations included in the predicted mutant as prefix + list of mutations, with a large number of mutations this file name can be longer than 255 characters which causes the file system to be unable to store the PDB file. Is there any way how to prevent this behavior, for example set rosetta to store PDB file under user given name? Thank you for you answer.

Post Situation: 

Where to find old version of Rosetta with git version number

Category: 
Compilation

Hi, there:
    I am reading some papers using Rosetta for modeling work. In the papers, they mentioned rosetta git version number. I am just wondering  if anyone can tell me where I can find some old version of rosetta according to git version number. Thank you very much for your help.

 

Best,

Mao

Post Situation: 

bin folder does not appear after compiling

Category: 
Compilation

Hello, 

I've previously never had trouble downloading Rosetta (I've done it twice successfully before) until now.

I'm trying to install Rosetta on Linux 3.1. When I go to Rosetta/main/source and type in ./scons.py -j3 mode=release bin it doesn't ever throw an error, but the bin file does not appear. 

Does anyone know how I can fix this?

Thank you

Post Situation: 

InterfaceAnalyzer:“too many tries in fill_missing_atoms!”

Category: 
Scoring

Hey Guys,

We are trying to use  "InterfaceAnalyzer"  to  analyze a  PDB,  then we get this:

......

.....

core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue pdb_HSD 152
core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue pdb_HSD 152
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'complex_0_0001'
Error: [ ERROR ] 

Post Situation: 

Design with non-canonical amino acids (NCAA)

Category: 
Non-Canonical Peptides

Hello everyone, I would like to ask, how to add the following lines when creating a parameter in the rosetta for a non-standard amino acid containing a methyl group on the backbone? M ROOT 13 M POLY_N_BB 13 M POLY_CA_BB 14 M POLY_C_BB 15 M POLY_O_BB 16 M POLY_IGNORE 2 3 4 5 6 8 9 10 11 12 M POLY_UPPER 7 M POLY_LOWER 1 M POLY_CHG 1 M POLY_PROPERTIES PROTEIN POLAR CHARGED M END

Post Situation: 

Ab initio structure prediction for long amino acid sequence

Category: 
Structure prediction

Hi

I'm a postgraduate student, interested in protein structure prediction.

I noticed that the document said:

  • Abinitio: max 150 amino acids are cosidered possible

So, I want to know, how to use rosetta to predict number of protein of  amino acids more than 150 (e.g. 500)?

Post Situation: 

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