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

[Elaine Meng]

Hello Masoud,
If I understand correctly, you want all H-bonds among 3 residues, ligand, water except not the water-water ones. I guess SOL is your waters?

You could try 

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

Then SOL (water) is only in the second set of atoms and you will only get H-bonds between the two sets.

The zonesel part may take some time too.  If you only want to show the waters that are h-bonding to those residues and ligand at each step, you could instead use findhbond option “reveal true” to display them.  Also if the selected residues stay the same, you wouldn’t put that in your script unless you are also unselecting them at each frame.  In other words, just do this one time: 

sel :38:53:147:279

…then in per-frame script:

~disp :SOL
findhbond linew 3 color blue selRestrict :SOL:38:53:147:279 reveal true

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 22, 2019, at 12:39 PM, masoud aliyar <masoud.aliyar at gmail.com> wrote:
> 
> 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,