[Chimera-users] how to hide just H-bonds between water molecules with themselves?

[masoud aliyar]

Hello

I want to find H-bonds between 3 residues and the ligand and the water
molecules around the ligand in 3 angstrom, but I don’t want H-bonds between
water molecules. I Just want h-bonds between residues together and residues
with ligand and residues and ligand with water. I have used Per-Frame
script system. But I have two problems. First, if I set selection mode on
replace mode and write this script:

*********************

~display :SOL

zonesel :279 3 :SOL

select up

display sel

select :38:53:147:279

findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279

*********************

The result is fine and H-bonds that I want were display. But if I apply
this script, the system searches every water residues for find H-bond and
take a lot of time per frame.

second, if I set selection mode on append and write this script:

*********************

~display :SOL

zonesel :279 3 :SOL

select up

display sel

select :38:53:147:279

findhbond linewidth 3 color blue selRestrict both

*********************

The calculations are going faster, but also, show H-bonds between water
molecules with themselves that I don’t want it.

How can I hide H-bonds between water molecule with themselves but H-bonds
between selected residues and ligand and water retain?



Thank you, everyone,
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