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Structure prediction

How to analyse multiple silent files from "Abinitiorelax" output to find best models?

Category: 
Structure prediction

Dear freinds,

 

I read more about rosetta and came up with this command line for denovo structure prediction of 382 residue long protein:

I ran it in silent mode.
 

Post Situation: 

Options "-out:prefix" didn't work

Category: 
Structure prediction

Hello everyone.

I used AbinitioRelax application to predict structure and added "-out:prefix ab"  into options.

The log shows " protocols.abinitio.AbrelaxApplication: Finished ab_0001 in 169 seconds." but I still got "S_00000001.pdb" file. So I can't simulation on multiple CPUs.

Any help would be appreciate.

Post Situation: 

How to make new VALL database?

Category: 
Structure prediction

Dear Friends,

When going through the rosetta tutorials, I see that the vall database is old, and I want to build new vall database. 

could you please let me know how to efficiently build new vall database from PDB structures. When I run pdb2vall, it gives me this:

 

./pdb2vall.py 
Usage: pdb2vall.py [options]

Post Situation: 

Unable to understand fragment picking tutorial points.

Category: 
Structure prediction

Dear Friends,

 

I am performing abinitio structure prediciton of a 382 long protein sequence by following the tutorial:

https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction

Post Situation: 

"Make_fragments.pl" can't connect to dependencies links

Category: 
Structure prediction

Dear fellows,

I am studying to generate fragments for structure prediction ab initio locally, on my laptop (OS - Linux OpenSUSE), with a help of appropriate script "make_fragments.pl". I met with several problems during its running.

Firstly, "make_fragments.pl" can not connect to dependencies links. When I run such command, as "~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/make_fragments.pl name.fasta >& make_fragments.local", it gives me such error:

Post Situation: 

"sparks failed" error when running "make_fragments.pl"?

Category: 
Structure prediction
-Precision-7920-Tower:make_fragments.pl -verbose myfasta.fasta 
no id specified. parsing filename instead.
cannot parse id from filename so using 't001_'
ID: t001 CHAIN: _
File for psipred not found! Generating from scratch instead.
picking fragments with options:
                       DEBUG: 1
            add_pdbs_to_vall: 
                       chain: _
                     cleanup: 1
             csbuild_profile: 0
exclude_homologs_by_pdb_date: 0
                           f: myfasta.fasta
                   fastafile: t001_.fasta
Post Situation: 

/database folder after running "install_dependencies.pl" size 657 GB?

Category: 
Structure prediction

Dear Friends,

 

I nearly ran out of space after running "install_dependencies.pl". Among the programs it installs, /database folder whcih includes "nr" sizes up to 657 GB. Can you please let me know if this is possible? 

 

Post Situation: 

AbinitioRelax of RCSB PDB structures

Category: 
Structure prediction

When I try to model a protein from the PDB (4WYH) I follow the abintio protocol correctly and generate fragments from Robetta. Yet I do not get a funnel shaped plot after 25,000 decoys.

Though it’s sequence clearly folds into this particular structure (as proved by the crystal structure) why can’t abinitio performs a successful simulation and result in a funnel shaped plot?

Post Situation: 

"make" error in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7"

Category: 
Structure prediction

Dear friends,

 

I am trying to run "make" in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7", follwing the installation instructions in "pdb2vall.README"; however, when running "make", I get this error (error is very long, so I have pasted the first and last lines of STDOUT) :

Post Situation: 

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