How to reconstruct full atom structure from silent file

[Sally Ride]

Hi,

I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.

Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).

I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.

Is there any dedicated protocol?

[Anonymous]

You can use the extract.pl scripts in rosetta_scripts package to extract PDB from a silent mode file.

> Hi,
>
> I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
>
> Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
>
> I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
>
> Is there any dedicated protocol?
>
>

[Sally Ride]

Well, yes I could but extract.pl returns only backbone. I think rosetta -extract only reformats torsion angles to Cartesian.

What I am looking for is a crude reconstruction of side chains using rosetta and starting with backbone only structures in silent format.

> You can use the extract.pl scripts in rosetta_scripts package to extract PDB from a silent mode file.

[Anonymous]

I believe that if you use the command-line flag -fa_input flag, rosetta++ will extract
full-atom coordinates. If that doesn’t work, please let me know

> Hi,
>
> I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
>
> Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
>
> I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
>
> Is there any dedicated protocol?
>
>

[Sally Ride]

I guess you meant -fa_output.

I tried this and it does not work with -extract but it does work with the -refold -score which extract.pl uses. So the final rosetta command which works looks like that:

rosetta.gcc -refold -score -fa_output -scorefile test -silent_input -nstruct 1 -s test.out -l tagfile

Thanks a lot for a hint!

> I believe that if you use the command-line flag -fa_input flag, rosetta++ will extract
> full-atom coordinates. If that doesn’t work, please let me know
>

[Anonymous]

I’m forwarding an expert suggestions;
—
Here’s the command line to extract fullatom PDBs:

rosetta.gcc -extract -s test.out -all -paths ~/paths.txt -fa_input

You can replace -all with -l , or with -t .

Cheers,

—

> Hi,
>
> I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
>
> Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
>
> I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
>
> Is there any dedicated protocol?
>
>

[Sally Ride]

Hmm, this does not work for me at all. I get a parse error:

parse error2: S_0001_8516 1 1 1 1 158

…

parse error2: S_0206_1379 1 1 1 1 158

parse error2: S_0207_4013 1 1 1 1 158

parse error2: S_0208_8411 1 1 1 1 158

EOF error?

STOP:: couldnt open silent-file!!

ERROR:: Exit from: pose_main.cc line: 256

But anyway, the other solution (-refold) seems to work.

> I’m forwarding an expert suggestions;
> —
> Here’s the command line to extract fullatom PDBs:
>
> rosetta.gcc -extract -s test.out -all -paths ~/paths.txt -fa_input
>
> You can replace -all with -l , or with -t .
>
> Cheers,
>
> —
>
> > Hi,
> >
> > I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
> >
> > Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
> >
> > I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
> >
> > Is there any dedicated protocol?
> >
> >

[Anonymous]

Hi, Kosa,

Can you forward the silent file to the user support email? Or you can attach it here. We could look at it in more detail.

Yi

> Hi,
>
> I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
>
> Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
>
> I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
>
> Is there any dedicated protocol?
>
>

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