Hi Evgeny and Chen, Unfortunately, if Chen wants the list of atoms that form H-bonds, "distance" only provides a displayed object and only returns the average distance between all atoms. Also unfortunately, that script list_hb.py (which I wrote) uses the find_pairs function which warns that it "only checks atom orientation, not atom type" (https://pymolwiki.org/index.php/Find_pairs). It is difficult therefore to provide list_hb.py with two selections that can only result in real H-bonds without actually figuring out for yourself which pairs of atoms should H-bond!
Cheers, Rob On Thu, 2021-04-08 16:50 +0200, Evgeny Osipov <joe.fen...@gmail.com> wrote: > 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 > > -- Robert L. Campbell, Ph.D. Academic Advisor, BHSc Program Assistant Professor, Dept. of Biomedical & Molecular Sciences, Queen's University, Kingston, ON K7L 3N6 Canada Botterell Hall Rm 644 Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc _______________________________________________ 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
