[PyMOL] shade on transparent spherical surface

2015-02-12 Thread SongJianHui
Hello, everyone, I've been trying use pymol to generate an image based on C-alpha coordinates only. I tried to set the sphere to be transparency by the command "set sphere_transparency, 0.5". However, the surface of the sphere shows some shading which looks quite odd. If I ray trace the image,

[PyMOL] Align C-alpha based backbone

2014-10-01 Thread SongJianHui
Hi, all, I'm wondering if it is possible to align a number of unfolded conformations (C-alpha based backbone only) according to their principal axis. Thanks. Dr. Jianhui Song Postdoctoral Fellow Department of Biochemistry University of Toronto ---

[PyMOL] incorporating a spherical surface in pymol

2010-09-09 Thread SongJianHui
Hi all, I am using pymol to monitor the structure evolution of one protein which could be bound to some fixed points on a spherical surface. However, I have no idea about how to incorporate these active points in pymol. Any suggestion is welcome. Thanks in advance. Cheers, Jay