Re: [PyMOL] Builder Question

-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jim Nettles Sent: Monday, August 15, 2005 8:56 AM To: James R. Graham Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Builder Question Hello James, There is really a lot of room for d

RE: [PyMOL] Builder Question

0)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Jim Nettles > Sent: Monday, August 15, 2005 8:56 AM > To: James R. Graham > Cc: pymol-users@lists.s

Re: [PyMOL] Builder Question

Hello James, There is really a lot of room for discussion regarding your questions. Considering peptide conformations is complicated business and there is generally not "a" structure. There is great conformational flexibility even for small, constrained, cyclic peptides. As for the MD - yes,

[PyMOL] Builder Question

Hello All, How "physiological" are the structures that are produced from builder? Meaning, how are the angles, etc. determined? Might such a resulting structure mimic a chemically-synthesized peptide? I have taken peptides I created using builder and done some MD simulations and the struc