Cutout part of a protein – Rosetta Commons

This topic has 6 replies, 3 voices, and was last updated 7 years, 7 months ago by Anonymous.

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- May 31, 2017 at 6:55 pm #2663
  Anonymous
  Hello People,
  
  I am trying to find a way to cut out part of a protein and save to a new .pdb file.
  
  So i have a protein and i want to cut out a section (from amino acid 315 to 330 for example), and save that cut out (and maintain the original 3D structure) into a new .pdb file.
  
  I tried searching if there is a built-in PyRosetta function/method that does this, or if there is a script that does this, but i could not find.
  
  Anyone can help me or guide me?
  
  Thank you
  
  AC Research
- May 31, 2017 at 7:09 pm #12353
  Anonymous
  A) text editor
  
  the Pose object supplies a dump_pdb interface that takes a vector1(Size) – so you can tell it which residues to print to some output stream
  
  C) pose/util.hh has a ton of functions for this, including create_subpose and pdbslice. pdbslice(new_pose, old_pose, vector1(Size) residues) is probably the one you want.
- May 31, 2017 at 7:09 pm #12874
  Anonymous
  A) text editor
  
  the Pose object supplies a dump_pdb interface that takes a vector1(Size) – so you can tell it which residues to print to some output stream
  
  C) pose/util.hh has a ton of functions for this, including create_subpose and pdbslice. pdbslice(new_pose, old_pose, vector1(Size) residues) is probably the one you want.
- May 31, 2017 at 7:09 pm #13395
  Anonymous
  A) text editor
  
  the Pose object supplies a dump_pdb interface that takes a vector1(Size) – so you can tell it which residues to print to some output stream
  
  C) pose/util.hh has a ton of functions for this, including create_subpose and pdbslice. pdbslice(new_pose, old_pose, vector1(Size) residues) is probably the one you want.
- May 31, 2017 at 7:50 pm #12354
  Anonymous
  This should get you started. Additionally, there are movers that do each of these things – accessible in the rosetta.protocols.grafting namespace.
  
  http://www.pyrosetta.org/faq#TOC-5.-Can-I-split-a-Pose-delete-residues-or-insert-residues-
  
  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/grafting/DeleteRegionMover
  
  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/grafting/KeepRegionMover
  
  Hope this helps,
  
  -Jared
- May 31, 2017 at 7:50 pm #12875
  Anonymous
  This should get you started. Additionally, there are movers that do each of these things – accessible in the rosetta.protocols.grafting namespace.
  
  http://www.pyrosetta.org/faq#TOC-5.-Can-I-split-a-Pose-delete-residues-or-insert-residues-
  
  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/grafting/DeleteRegionMover
  
  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/grafting/KeepRegionMover
  
  Hope this helps,
  
  -Jared
- May 31, 2017 at 7:50 pm #13396
  Anonymous
  This should get you started. Additionally, there are movers that do each of these things – accessible in the rosetta.protocols.grafting namespace.
  
  http://www.pyrosetta.org/faq#TOC-5.-Can-I-split-a-Pose-delete-residues-or-insert-residues-
  
  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/grafting/DeleteRegionMover
  
  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/grafting/KeepRegionMover
  
  Hope this helps,
  
  -Jared
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