# See http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties

cd /sbinlab2/tlinnet/Desktop
fetch 2xml, async=0
show_as cartoon, 2xml

select OGA, ////OGA
select EDO, ////EDO
select ZN, ////ZN
select NI, ////NI
select CL, ////CL

show sticks, OGA or EDO
show spheres, ZN or NI or CL
dist hydbonds_OGA, OGA, 2xml, mode=2
dist hydbonds_EDO, EDO, 2xml, mode=2

print cmd.get_setting_text('h_bond_cutoff_center')
print cmd.get_setting_text('h_bond_cutoff_edge')

select OGA_A_near_resi, byres 2xml within 3.6 of OGA and chain A
select OGA_B_near_resi, byres 2xml within 3.6 of OGA and chain B

show sticks, OGA_*

Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
+45 60210234

2012/9/29 Mona Kab Omir <kzq652@alumni.ku.dk>
I have  a question about how to introduce hydrogen bonds between ligands and target molecule in pymol that runs on linux ubuntu 12.04 operative system.
I have searched and tried to type following command:
set h_bond_cutoff_center, 3.6
set h_bond_cutoff_edge, 3.2
 and I tried to choose [A]-> [find]-> polar contacts-> different options, but it also don't helped at all.
Do any of you have a suggestion to what might have been gone wrong?

Many big thanks!



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