Dear all,
I am having a trouble with making an alpha helix example ( http://salilab.org/modeller/wiki/Make%20alpha%20helix).
It works fine for shorter helices, but if I increase helix length and do e.g. m.build_sequence('AAAAAAAAAAAAAAAAAA') then the resulting helix is far from perfect, has local distortions and largely is not recognized as helix by DSSP (it shows mixed H and T conformation), and not drawn as helical cartoon in pymol. The situation does not improve if I increase the number of conjugate gradient steps. The extent of distortions does seem to be somewhat sequence dependent.
Is there a better way of making an ideal alpha helix with Modeller ?
I tested on Modeler 9.11 and 9.12.
Thanks in advance for help, Jan
On 7/9/13 11:30 PM, Jan Kosinski wrote: > I am having a trouble with making an alpha helix example ( > http://salilab.org/modeller/wiki/Make%20alpha%20helix). > > It works fine for shorter helices, but if I increase helix length and do > e.g. m.build_sequence('AAAAAAAAAAAAAAAAAA') then the resulting helix is > far from perfect
Modeller's secondary structure restraints are used to help 'persuade' a model to adopt a given secondary structure - they don't force it at the expense of conforming to the template restraints and/or stereochemistry. So they don't constrict the conformational space enough to always result in perfect helices, and so I wouldn't expect to see such helices, particularly for longer sequences.
Ben Webb, Modeller Caretaker
participants (2)
-
Jan Kosinski -
Modeller Caretaker