Reply To: How to reconstruct full atom structure from silent file

[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?
> >
> >