VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jul 20 2011 - 08:57:58 CDT

maria,

On Wed, Jul 20, 2011 at 6:28 AM, maria goranovic
<mariagoranovic_at_gmail.com> wrote:
> Hi
> Thank you all for the suggestions. Axel, I am attaching a link below below.
> http://i56.tinypic.com/mwrym8.jpg
> the middle panel is the most desired, where i have changed the carbon color
> to pink, and have only a single representation using Mark's
> suggestion. Mark's solution thus works very well, except that it is possible
> that someone wants to color 5 different residues with carbons in different
> colors, in which case, the solution can become quite complicated. Secondly,

yes. what you want is not something that is ready as a "primitive"
rep and it is actually quite convoluted.

> one can alter the vdw radii as per Axel's suggestion, but this would again
> be a global change? Even if it is possible to change vdw radii for each

radii of vdw reps are determined by two input parameters: the global radius
value that you set in the representation dialog and the per atom radius that
is stored as an atomic property and that you can set via atomselect.

> selection, the solution will not be as good as the middle panel. Axel, the
> bonds representation does not seem as good as the licorice in your
> suggestion? [right panel vs. left panel]

you didn't add a matching VDW rep for the carbons. licorice is nothing
else but "bonds" and "vdw" but both with the same radius (and ignoring
the atomic radius value).

> by god, i hope the above link to the image works,

yes it does.

for as long as you found something that works for you,
i am satisfied, even if it is not my suggestion. ;-)

cheers,
     axel.
> Maria
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.