VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jun 29 2006 - 17:50:24 CDT

On Thu, 29 Jun 2006, Berit Hinnemann wrote:

BH> Dear John, Axel and all other VMD developers/users,

dear berit,

BH> About a month ago I asked a question on how to plot a Gaussian cube file. I
BH> have now written a converter for VASP charge density files to Gaussian cube
BH> and everything works very well. There is one thing, however, which I do not
BH> understand, when I make a volume slice plot, I cannot figure out to adjust
BH> the color scale and I do not understand how it is chosen. I saw that there

if you want to adjust the color scale, you have to choose the 'Volume'
colorization method. then you can select the coloring sequence in the
Color Controls menu under the Color Style and the parameters as well
as the range of values to apply the color scale to.

BH> is something about the color scale under "Trajectory" but I am not sure how
BH> to use it. Also, is it possible to display a color bar, which shows which
BH> color corresponds to which value? Also, can these things be done in the
BH> graphic interface, or does one need to use tcl?

tcl right now. please check out:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/colorscalebar/

BH> Typically, the volumetric data is from 0 to some value and all positive (if
BH> it is the charge density), or centered around 0 (charge density difference).

you can set this in the trajectory tab. especially for the density
differences you want to make sure that you set the min/max values
symmetrically, so the plot makes sense (same is true if you map the
electrostatic potential on surfaces, btw).

good luck, and let us know if you need more help.

cheers,
   axel.

BH> Thanks! Best, Berit
BH>
BH>
BH>
BH> Berit Hinnemann, Ph.D.
BH> Princeton University
BH> Department of Mechanical and Aerospace Engineering
BH> D310 Engineering Quadrangle
BH> Princeton, NJ 08544
BH> email: bhinnema_at_princeton.edu
BH> tel: (609)-258-2651
BH> fax: (609)-258-5877
BH>
BH>
BH>
BH> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.