I dont know about JMol, but this can be easily done with UCSF Chimera.
I loaded the 1a1x structure.
Then selected: Tools > Structure Analysis > FindHBond
I kept the default values and selected Write information to reply log
Then clicked OK
On the structure the H Bonds will be identified with a coloured line.
To view which is the donor and acceptor go to: Favorites > Reply log
An output of the reply log is below:
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ASP 12.A N GLU 25.A OE2 no hydrogen 3.012 N/A
HIS 13.A N GLU 25.A OE1 no hydrogen 3.338 N/A
HIS 13.A ND1 ASP 12.A OD2 no hydrogen 2.835 N/A
LEU 14.A N TRP 70.A O no hydrogen 2.934 N/A
TRP 15.A N ARG 23.A O no hydrogen 2.866 N/A
...
120 hydrogen bonds found
As you can see the donor and acceptor has been identified as defined in the header line.
If you wish, the information can also be written to a file by selecteing Write to text file
in the FindHBond
window.
No comments:
Post a Comment