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Structure prediction

Not found some Flags

Submitted by jrcf on Sat, 2015-09-19 12:08
Category: 
Structure prediction

Hello guys.
1) I am running the protocol for comparative modeling, and run the program it tells not find some flags. The question is, is this common? It will really interfere too much in my final result?

2) what the function of this sequence, after calling the program? (@flags >& test.log &)


Thank you

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Rosetta 3 - Applications

RNA add/modify residues

Submitted by galvaner on Fri, 2015-09-18 05:49
Category: 
Structure prediction

Hi,

I wnated to solve this in PyRosetta because of the possibility of easy Windows instalation, but I recieved advice to do it in Rosetta ( https://www.rosettacommons.org/node/9517 ).

So what I need (also described in a link above) is that I have RNA pdb file with hundreds of residues in witch I miss usually about ten segments each max 40 but often 3-4 residues ( I have only FASTA sequence of the missing parts). I want to predict the missing parts and insert it into my pdb.

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Rosetta 3 - General

add missing residues into rna

Submitted by galvaner on Tue, 2015-09-15 16:41
Category: 
Structure prediction

Hi,

I have an rRNA pdb file (up to few hundred residues)  with missing segments of residues (from 3 to 10 residues in one missing segment; about 10 segments ) and I need to add(predict) the missing parts of structure and get a complete pdb.

1)Is it possible to do it  by PyRosetta?

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PyRosetta - General

Is it possible to restart the ddg_monomer.linuxgccrelease?

Submitted by lanselibai on Mon, 2015-09-07 03:46
Category: 
Structure prediction

Dear friends,
 
I am trying to use “ddg_monomer.linuxgccrelease” in our university cluster.
However, since my protein is too large (a dimer, each monomer contains 663 residues), the calculation ends because of the wall-time (72 hours) before it finishes.
I am here to ask if it is possible to restart the program. Or is there a method to make the program faster, like using MPI?  

Thanks. 

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Rosetta 3 - Applications

Models which are not recorded (Abinitio protocol)

Submitted by allan.ferrari on Fri, 2015-08-28 13:39
Category: 
Structure prediction

Hello everyone,

I was running Abinitio protocol and I have noticed that a certain sequence yield sequeced models (S_000001, S_000002, S_000003) in the absence of the secondary structure predicition file. Conversely, in the presence of this file in the protocol some models where not generated (or, at least, not recorded). In fact, I have something like the sequence: S_00002, S_00009, S_00013, etc. From 100,000 models required only around 10,000 were possible to be extract. Is there any resonable reason for this fact?

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Rosetta 3 - General

How to model missing residues on a protein from multiple PDB files?

Submitted by cossio on Fri, 2015-08-21 07:18
Category: 
Structure prediction

I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as possible. How can I do this?

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Rosetta 3 - Applications

How to convert fragments to PDB format?

Submitted by JadAbbass on Wed, 2015-08-19 04:05
Category: 
Structure prediction

Dear Sir/Madam,

I was wondering if there is a tool inside Rosetta that lets me convert a fragment (9-mer for instance) taken from the fragment file of 9-mers into a PDB-like format file.
Any suggestions/information?

Thank you,
Jad

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Rosetta 3 - General

Abinitio protocol and X-Ray diffraction data

Submitted by allan.ferrari on Wed, 2015-08-12 12:49
Category: 
Structure prediction

Hello everyone,

I was wondering if it would be possible to implement in the abinitio modeling (since de beginning) the experimental data from X-Ray crystallography like we do with experimental distances constraint. As far as I am aware there is a molecular replacement protocol but it is used only with relax protocol.

Thank you guys,
Állan.

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Rosetta 3 - Applications

Multi-chain Modelling

Submitted by Sandy on Sun, 2015-08-09 14:41
Category: 
Structure prediction

Hi all,
I am trying to develop a model for a protein composed of multiple identical chains (a fibril actually). I know this might be a good job for the symmetry protocol, but I do not currently have enough data to define the protein's symmetry. All I have is a few constrains and some homology modeled regions. Is there a good protocol for this situation? Broker? Abinito? I am really unsure how to handle the multiple chain aspect, or if this can be handled. On a related note, if I have a multi chain system, how should I handle the fragment files?
Thanks,
Sandy

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