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

[Ying-Chieh Sun]

Hi,

 

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

 

 

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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