[Dock-fans] dms density

Sudipto Mukherjee sudmukh at yahoo.com
Wed Sep 2 06:32:04 PDT 2015


Hi Amali,
The DMS program creates a point surface for a molecule. The density controls the density of the points on the molecular surface. Lower values of density produce more points per sq. angstrom (1.0 corresponds to 5 points per sq. angstrom). If you are concerned about this, you can reduce the density to 0.5 at the expense of increased computation time and dms file sizes. The dms manual has more details: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html 

Further, chimera can now write molecular surfaces as dms files compatible with DOCK sphgen. Options for dms parameters in chimera are in Favorites > Preferences > New Surfaces. The default is 2 points per sq. angstrom, so you may want to increase this to 5 or 10. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/surface.html

Regards
Sudipto Mukherjee, PhDDept. of Chemistry, Temple University1901 N 13th St, Philadelphia, PA 19122 


     On Wednesday, September 2, 2015 6:52 AM, Amali Guruge <amaligg2010 at gmail.com> wrote:
   

 Dear All,

When we use dms to generate the surface, we have to use the command
./dms input_file [-a] [-d density] [-g file] [-i file] [-n] [-w radius] [-v] -o file

I have a problem regarding to the density [-d density].

Usually I use "1.0" for that. But I want to know, If I change that value, how it affect to the surface generation?

Thank you.

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