Hi Mina, Badoo Mina wrote, On 04/05/13 16:49: > This is my first post to the group. I hope it would be a great experience :)
I hope so too :) > I am trying to compare the H-bonds in two NMR strcutures. So, I need to > calculate H-bonds with a cutoff 2.5 and angle 35 angestrom that are > availbale in 10 structures out of 20. I run list_hbonds.py as below: > list_hb, selection1, cutoff=2.5, angle=35 > but it doesn not meet what I want. Can you be more precise why it does not meet what you want? What result do you get, and what result do you expect? I would use the hb_list script like this: PyMOL> fetch 2m1c, async=0 PyMOL> split_states 2m1c, prefix=s PyMOL> list_hb s_0001, cutoff=2.5, angle=35, hb_list_name=hb1 PyMOL> list_hb s_0002, cutoff=2.5, angle=35, hb_list_name=hb2 PyMOL> list_hb s_0003, cutoff=2.5, angle=35, hb_list_name=hb3 ... > I want to look at inter and intra > H-bonds (between two complexes of the protein and in each chain, too). > How can I do that when I have splitted the ensemble to the 20 structures > in pymol? Actually I would be prefer PyMOL's distance command for such a job, it works on all states at once, so you don't need to split states. PyMOL> fetch 2m1c, async=0 PyMOL> set h_bond_max_angle, 35 PyMOL> distance hbAB, chain A, chain B, 2.5, mode=2 PyMOL> distance hbAA, chain A, chain A, 2.5, mode=2 PyMOL> distance hbBB, chain B, chain B, 2.5, mode=2 This doesn't print the H-bond pairs to the console output. If you need that, use this script: http://pymolwiki.org/index.php/Get_raw_distances See also: http://pymolwiki.org/index.php/Distance Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html _______________________________________________ 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
