Rotate chain – Rosetta Commons

This topic has 3 replies, 2 voices, and was last updated 3 years, 5 months ago by Anonymous.

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- May 9, 2021 at 11:36 pm #3766
  Anonymous
  I have a pdb with a homodimeric conformation for two alpha helix transmembrane domains.
  
  This structure features a cross-like conformation, interacting at known residues.
  
  I want to rotate each of the domains 15º along the z-axis
  
  So for exmaple, something like this would be fine:
  
  select :.A (select chainA)
  
  turn < 15 @ca,cb (rotate chain A 15º, from the residues given as an anchoir point)
  
  is there anything like this? Thx
- May 10, 2021 at 12:14 am #15891
  Anonymous
  Hello,
  
  What you want to do appears to be relatively easy using the RollMover, have you tried that?
  
  https://new.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/RollMover
  
  (i have never used the RollMover before but I assume it will work)
  
  If the RollMover does not suit your needs, I would suggest trying to solve your problem in pyrosetta rather than via rosetta_scripts XML!
- May 10, 2021 at 11:14 am #15892
  Anonymous
  Thanks a lot @danpf
  
  I ‘m executing this script
  
        $rosetta3/bin/rosetta_scripts.default.linuxgccrelease -s tm_dimer.pdb -parser:protocol roll_mover_integration.xml
  
  With this xml:
  
     <RollMover name=”randomroll” start_res=”1″ stop_res=”30″ min_angle=”0″ max_angle=”-90″>
  
               <axis x=”34.910″ y=”33.490″ z=”50.200″ />
  
               <translate x=”0″ y=”0″ z=”0″ />
  
  It seems to work properly. If I understand it correctly, the axis determines the point at which I want to make the rotation, in this case, x, y and z correspond to an atom of the residue where the rotation occurs, and translate remains at zero since i don’t want to carry out any translation.
  
  However, for 70 degrees of rotation, the change in tilt of the chain is very small, why is this?
  
  I’m also getting several warnings:
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it’s missing too many mainchain atoms:    1 A ARG ARG:NtermProteinFull:triazolamerC
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CT1
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it’s missing too many mainchain atoms:   31 B ARG ARG:NtermProteinFull:triazolamerC
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CT1
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected lower terminus type to residue 2,    2 A
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected lower terminus type to residue 32,   32 B
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 2 in file trkb_tm_dimer.pdb. Best match rsd_type: GLU:NtermProteinFull
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 3 in file trkb_tm_dimer.pdb. Best match rsd_type: HIS_D
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 4 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 5 in file trkb_tm_dimer.pdb. Best match rsd_type: SER
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 6 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 7 in file trkb_tm_dimer.pdb. Best match rsd_type: TYR
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 8 in file trkb_tm_dimer.pdb. Best match rsd_type: ALA
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 9 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 10 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 11 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 12 in file trkb_tm_dimer.pdb. Best match rsd_type: ILE
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 13 in file trkb_tm_dimer.pdb. Best match rsd_type: ALA
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 14 in file trkb_tm_dimer.pdb. Best match rsd_type: SER
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 15 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 16 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 17 in file trkb_tm_dimer.pdb. Best match rsd_type: GLY
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 18 in file trkb_tm_dimer.pdb. Best match rsd_type: PHE
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 19 in file trkb_tm_dimer.pdb. Best match rsd_type: CYS
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 20 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 21 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 22 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 23 in file trkb_tm_dimer.pdb. Best match rsd_type: MET
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 24 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 25 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 26 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 27 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 28 in file trkb_tm_dimer.pdb. Best match rsd_type: LYS
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 29 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 30 in file trkb_tm_dimer.pdb. Best match rsd_type: ALA:CtermProteinFull
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 32 in file trkb_tm_dimer.pdb. Best match rsd_type: GLU:NtermProteinFull
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 33 in file trkb_tm_dimer.pdb. Best match rsd_type: HIS_D
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 34 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 35 in file trkb_tm_dimer.pdb. Best match rsd_type: SER
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 36 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 37 in file trkb_tm_dimer.pdb. Best match rsd_type: TYR
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 38 in file trkb_tm_dimer.pdb. Best match rsd_type: ALA
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 39 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 40 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 41 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 42 in file trkb_tm_dimer.pdb. Best match rsd_type: ILE
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 43 in file trkb_tm_dimer.pdb. Best match rsd_type: ALA
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 44 in file trkb_tm_dimer.pdb. Best match rsd_type: SER
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 45 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 46 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 47 in file trkb_tm_dimer.pdb. Best match rsd_type: GLY
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 48 in file trkb_tm_dimer.pdb. Best match rsd_type: PHE
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 49 in file trkb_tm_dimer.pdb. Best match rsd_type: CYS
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 50 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 51 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 52 in file trkb_tm_dimer.pdb. Best match rsd_type: VAL
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 53 in file trkb_tm_dimer.pdb. Best match rsd_type: MET
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 54 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 55 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 56 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 57 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 58 in file trkb_tm_dimer.pdb. Best match rsd_type: LYS
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 59 in file trkb_tm_dimer.pdb. Best match rsd_type: LEU
  
  core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 60 in file trkb_tm_dimer.pdb. Best match rsd_type: ALA:CtermProteinFull
  
  I guess the atoms that are discarded correspond to hydrogens, in which case they can be added later, it’s also removing two residues, what can I do about it?
  
  Thx again
- May 10, 2021 at 5:04 pm #15893
  Anonymous
  Hello,
  
  I’m not sure why youre 70 degree angle change is only appearing as a small angle change.
  
  Since it does not seem to work easily out of the box, I will again suggest switching to pyrosetta.
  
  XML based rosetta_scripts are amazing for a lot of things, but very specifically manipulating poses is usually best done in pyrosetta.
  
  As for the removed two residues : Rosetta is unable to build residues that are missing an N, CA, or C atom. It would appear that your input pdb file is missing one of those atoms for two residues.
  
  EDIT: I would try removing the hydrograns for the residues that are on the residues that are getting deleted. I think it might be messing with how rosetta is reading the residues
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