Dear all,
I would like to build a perfect helix as an initial structure for some further manipulations. (Without a good initial structure the homology modelling part I apply later does not converge).
Right now I'm using
mdl.build_sequence(d.entire_sequence)
to build the sequence, then I save it to a PDB, load it in VMD, set the backbone angles there (to get an alpha helix) save it to another PDB and load at back into modeller.
So I guess my basic question is: *Is it possible to set backbone dihedral angles to a specific value? Or is there any other way to use mdl.build_sequence to get an alpha helix?*
Thank you & best regards, Ajasja Ljubetič National Institute of Chemistry Slovenia
On 10/9/15 9:10 AM, Ajasja Ljubetič wrote: > So I guess my basic question is: *Is it possible to set backbone > dihedral angles to a specific value? Or is there any other way to > use mdl.build_sequence to get an alpha helix?*
build_sequence builds the 3D coordinates from the internal coordinates given in the CHARMM topology file. These are per-residue-type and for an extended chain, so you'll always get an extended chain using that function. There are no functions in Modeller to exactly set backbone dihedral angles, sorry. You could query the current values (see e.g. http://salilab.org/modeller/9.15/manual/node353.html) and then rotate the model about the central bond to get the desired value, or you could add dihedral restraints and then optimize the model - but both approaches are probably no better than your current solution.
Ben Webb, Modeller Caretaker
Hi Ajasja,
Have you tried the modeller function "restraints.add(secondary_structure...)"? If you don't really need to set exact values, but rather just need to generate a nice helical conformation, that may be good enough for you.
The example on this page http://www.salilab.org/modeller/wiki/Make%20alpha%20helix will not give you a "perfect" or ideal helix, but the minimization step should give you something reasonably stable to start from.
Good luck! -J'n
On Fri, Oct 9, 2015 at 11:10 AM, Ajasja Ljubetič ajasja.ljubetic@gmail.com wrote: > Dear all, > > I would like to build a perfect helix as an initial structure for some > further manipulations. > (Without a good initial structure the homology modelling part I apply later > does not converge). > > Right now I'm using > > mdl.build_sequence(d.entire_sequence) > > to build the sequence, then I save it to a PDB, load it in VMD, set the > backbone angles there (to get an alpha helix) save it to another PDB and > load at back into modeller. > > So I guess my basic question is: Is it possible to set backbone dihedral > angles to a specific value? Or is there any other way to use > mdl.build_sequence to get an alpha helix? > > Thank you & best regards, > Ajasja Ljubetič > National Institute of Chemistry > Slovenia
-
Ajasja Ljubetič -
Jonathan Sheehan -
Modeller Caretaker