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

Aldo Segura aldosegura at gmail.com
Sun Apr 6 15:12:03 PDT 2014


You should try to perform a RMSF analysis focused on the water molecules in
your trajectory and identify those with low fluctuation values.



2014-04-06 11:40 GMT-04:00 Elaine Meng <meng at 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.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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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 at cchmc.org <asegurac at ipn.mx>;
aldosegura at gmail.com
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