presets-interactive 3-hydrophobicity surface- those water molecules stay!
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
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
Hi, You should try to perform a RMSF analysis focused on the water molecules in your trajectory and identify those with low fluctuation values. Best, Aldo 2014-04-06 11:40 GMT-04:00 Elaine Meng <meng@cgl.ucsf.edu>:
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.h...
There is also a tutorial on MD Movie with occupancy calculations: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#p...
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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-- ========================================= Aldo Segura-Cabrera Postdoctoral Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera@cchmc.org <asegurac@ipn.mx>; aldosegura@gmail.com =========================================
participants (3)
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Aldo Segura -
Elaine Meng -
Ying-Chieh Sun