How to reconstruct full atom structure from silent file

This topic has 7 replies, 2 voices, and was last updated 16 years, 6 months ago by Anonymous.

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- June 23, 2008 at 2:25 pm #297
  Sally Ride
  Participant
  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?
- June 24, 2008 at 3:52 pm #3980
  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?
  >
  >
- June 24, 2008 at 7:47 pm #3981
  Sally Ride
  Participant
  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.
- June 25, 2008 at 5:01 pm #3983
  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?
  >
  >
- June 26, 2008 at 6:50 pm #3986
  Sally Ride
  Participant
  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
  >
- June 27, 2008 at 1:15 pm #3990
  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?
  >
  >
- June 27, 2008 at 1:53 pm #3991
  Sally Ride
  Participant
  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?
  > >
  > >
- June 27, 2008 at 8:55 pm #3992
  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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