Hi Appu, if I understand you correct then you have a structure with at least two domains. If you align two conformations of that structure, one domain does not get superposed nicely. Right?
The "psico" module provides the command "angle_between_domains", which is what you are looking for I guess. Example: (tilted domain spans residues 100 to 150) PyMOL> align s1, s2 PyMOL> select d1, s1 and resi 100-150 PyMOL> select d2, s2 and resi 100-150 PyMOL> angle_between_domains d1, d2 This requires "numpy" and "psico" installed. Download psico: https://github.com/speleo3/pymol-psico Hope that helps. Cheers, Thomas Appu kumar wrote, On 11/01/12 04:50: > Dear user > Can you please help me in finding the angle > between two structure upon alingment. I have aligned two structure and > one structure is not perfectly aligned on other. There is domain of two > structure tilting outward upon alignment. IS there any way to find the > angle between two structure. Thanks in advances. ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct _______________________________________________ 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
