Hi Mike, These bonds have bond order zero. Incentive PyMOL 1.8 renders those as dashed lines and sticks. Previous versions of PyMOL had no proper support for zero-order bonds, they did render as solid lines, but had no stick representation.
You can set all bond orders to 1 with: PyMOL>valence 1, *, * Or PyMOL can guess the bond orders for you, if double bonds matter: PyMOL>valence guess, *, * I will look into the amber topology loading code to see if we are importing those bonds wrong. Cheers, Thomas On 01 Feb 2016, at 07:08, Michael F. Summers <summ...@umbc.edu> wrote: > Colleagues, > > When I load an amber topology file and associated trajectory file, the lines > for all heteroatoms are drawn as dashed lines (but bonds to hydrogens drawn > as solid lines). > I can’t seem to find a flag that would turn this feature off… I’d rather see > all bonded atoms connected as solid lines. I couldn’t find an explanation on > the WIKI (earlier versions of pymol didn’t behave this way). Everything else > works fine (movie plays as it normally would). Any advice would be > appreciated. > > Thanks, > > Mike -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ 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
