Hi Ying-chieh,
The "hydrophobicity surface" refers to the surface coloring only: blue for the most hydrophilic amino amino acids, orange-red for the most hydrophobic.
I would not give special meaning to which water molecules are displayed. The preset may display atomic detail including water molecules near a ligand, but only based on a simple distance cutoff from ligand atoms, like the "ribbons" interactive preset. The presets are described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>
One idea for trying to find more tightly bound water molecules is to use the "MD Movie" tool (in menu under Tools... MD/Ensemble Analysis) to view your Amber trajectory and to calculate an occupancy map for water atoms relative to parts of the protein. This might or might not be useful depending on the protein flexibility and on which parts of the protein are held steady for the calculations.
MD Movie, see the "occupancy analysis" section:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
There is also a tutorial on MD Movie with occupancy calculations:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
_______________________________________________
On Apr 6, 2014, at 7:16 AM, Ying-Chieh Sun wrote:
> 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
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