[Chimera-users] presets-interactive 3-hydrophobicity surface- those water molecules stay!

Ying-Chieh Sun sun at ntnu.edu.tw
Sun Apr 6 07:16:36 PDT 2014



I did a simulation using Amber package and saved a snapshot into its pdb
file, and use Chimera to open it. The pdb file contains a protein-ligand
complex plus a box of about 20000 TIP3P water molecules.


When I pressed presets-interactive 3-hydrophobicity surface, there are 8
water molecules stayed close to the ligand binding site. 


I am wondering how these 8 water molecules were determined? The reason I ask
is because we are trying to find a way to determine 'crystal (or say,
ordered) water molecules'.


This presets-interactive 3-hydrophobicity surface seems to perform this
function in some way.


Thank you for your help.





Ying-Chieh Sun, Professor of Computational Chemistry

Chemistry Department

National Taiwan Normal University

Taipei, Taiwan 11617


Tel: +886-2-7734-6215

Fax: +886-2-2932-4249


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