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
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 :
> Hi, Pymol Users,
>
> I used this script to find hydrogen-bond in protein,
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/774A/MET`261/O/8342.87
Also, the angle is not right for certain pair
A/HIS`400/NE2/29
