# See http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties
reinitialize
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
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2012/9/29 Mona Kab Omir <[email protected]>
> Hei
> 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!
>
> regards
>
> Mona
>
>
>
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