Hi all,
I just wanted to raise an issue a colleague pointed out recently. When you
generate an ideal peptide in the form of an alpha helix using the builder
function in Pymol, the intra-molecular H-bonds that characterise an alpha helix
(I to i+4) are too close (2.2 Angstrom O-N). If you generate such a peptride,
save it then reopen in Pymol, extra bonds are drawn between N-H and O=
indicating the close proximity. Whilst I realise Pymol is not currently
designed to "Model" structures, could this be updated.
Cheers
Joel
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
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