Hi Jianghai, by default PyMOL does a distance based bonding (basically when the VDW radii of two atoms overlap, they get connected). To prevent that, you need two settings:
# before saving the correctly bonded but distorted structure set pdb_conect_all # before loading set connect_mode, 1 http://pymolwiki.org/index.php/connect_mode Cheers, Thomas Jianghai Zhu wrote, On 04/30/13 02:39: > Hi, > > In my trajectory movie, there are some minor distortions of some of > the residues, but the sticks presentation in pymol seems fine. > However, after I loaded the trajectory pdb file use discrete=1, extra > bonds would be shown in sticks in those slightly distorted residues. > Is there is way to avoid those extra bonds? Thanks a lot. > > --Jianghai -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 _______________________________________________ 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
