9 Jul
2013
9 Jul
'13
11:30 p.m.
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