First of all, I would like to express my gratitude to both Tsjerk and Thomas. If only the rest of the world were like you!!
The script works very well indeed. Thanks! I would like to make my own humble contribution, though, so that other people can benefit from the impressive work by Thomas and Tsjerk. As a result of my docking studies I get a lot of candidate poses for my ligands. But, if you want to use the ring_angle.py program to measure the angle between an aromatic ring in your pose and a protein residue, you have to manually edit the pose pdb. Why? Because all of the carbons in the pose will probably be labeled just "C", as it was my case, but all atoms labeled as "C"'s are removed from the arguments in the ring_angle.py program, and you get either an error or an incorrect result. Here is step by step what you should do: 1) Load the pose.pdb in a text editor, the simpler the better. I use KDE, so I loaded it in KWrite. 2) Find the C atoms belonging to the aromatic ring. This can be puzzling, though 3) Label them as CG, CD1, CE1, CZ, CE2 and CD2 in the pdb file (clockwise, starting from CG which should rest pointing down on the paper). 4) Save the modified pose.pdb 5) Load the protein and the pose in pymol. 6) Select, atom by atom, the aromatic ring from the pose in pymol and name the selection (for instance pose-ring). 7) Load the ring_angle.py program 8) Finally, run the command "ring_angle chain X and resi Y, pose-ring). Be careful that, depending on the relative position of both rings, the correct answer may be the return value or its difference with 180º. If you don't select the aromatic ring in the pose, but instead you issue the command on the whole pose, the result is not correct. I can provide a demo file if anyone is interested. Hope this helps. Ramiro Tellez Sanz Dept. Physical Chemistry University of Almeria Spain ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ 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
