how to hide just H-bonds between water molecules with themselves?
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,
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@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,
participants (2)
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Elaine Meng -
masoud aliyar