- This topic has 3 replies, 3 voices, and was last updated 10 years ago by Anonymous.
November 15, 2013 at 8:30 am #1754Anonymous
I am interested in changing the psi-psi angles of two residues in a turn. When I use set_phi/set_psi command to change the angles, it completely disrupts the structure. Is there any way to only change the dihedral of those two residues alone without changing/disrupting the structure. I tried the same thing in Pymol, but there also I get the same disrupted structure. Can anybody suggest some other tool ??
Is it wrong to change dihedral angles of certain region and freeze the other regions of protein ??
November 15, 2013 at 3:23 pm #9499Anonymous
I think that what you’re looking for is loop modeling. You may want to check Workshop #8 for an introdcuction into fold trees: https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxweXJvc2V0dGF8Z3g6NDBhNmY5ZThmZjE5Y2U0OA
November 15, 2013 at 11:03 pm #9500Anonymous
The issue you’re running into is that if you change the backbone dihedral, you either have to move one side of the protein, or you have to disconnect the bond connecting the residue to the rest of the protein.
So what you would need to do is to introduce a cutpoint between the C-terminus of the residue you’re changing the backbone angles for and the N-terminus of the next residue. Take a look at the protocols.protein_interface_design.movers.AddChainBreak mover for a mover which will add a chainbreak at a given position. If you add the cutpoint and then move the backbone, you’ll keep the rest of the protein constant, although the bond length connecting the angle will no longer be reasonable.
The other alternative is to use the loop modeling framework, as mentioned by ñ. The benefit of using this approach is that this gives you the opportunity to reclose the chainbreak that you insert, by moving other residue backbone dihedrals.
November 16, 2013 at 11:17 am #9501Anonymous
Thank you both for your responses. I solved the problem by following loop modeling protocol..
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