Hi Chen, you can use distance command or cmd.distance for scripting purposes. Just specify mode 2 in order to search for polar contacts: https://pymolwiki.org/index.php/Distance
пн, 22 мар. 2021 г. в 18:53, Chen, Qiang <q...@pitt.edu>: > Hi, Pymol Users, > > I used this script to find hydrogen-bond in protein, list_hb.py. > > list_hb all, all, write_distances_file=hb > > I find there are some pairs are clearly not hydrogen bonds, e.g. > A/VAL`257/O/774 A/MET`261/O/834 2.87 > > Also, the angle is not right for certain pair > > A/HIS`400/NE2/2977 B/GLN`403/OE1/7093 2.66 > > In the protein, the angle between NE2-H-OE1 is 100.8 deg > > Any suggestion to find out the correct hydrogen-bonding pairs? > > Thanks! > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
