Hi Joel, That looks like it needs correcting. Please post this on the open-source tracker (http://sourceforge.net/tracker/?group_id=4546). I'll update the case there when it's fixed.
Cheers, -- Jason On Wed, Aug 10, 2011 at 11:49 PM, Joel Tyndall <joel.tynd...@otago.ac.nz> wrote: > 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 > > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. > http://p.sf.net/sfu/wandisco-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
