VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 19 2011 - 10:02:52 CDT

On Tue, Jul 19, 2011 at 9:52 AM, maria goranovic
<mariagoranovic_at_gmail.com> wrote:
> I tried what axel suggests, using a licorice representation by color and a

i suggested to use Bonds not Licorice.

> vdw representation of non-carbon atoms by name (native colors, oxygen is red
> for example). This works somewhat all right, but the non-carbon spheres
> which are represented in their native color (color by name), appear as
> little balls, and not as an extension of a bond as in a licorice
> representation. Increasing the bond radius in licorice, or decreasing the
> sphere size in the vdw representation completely hides the vdw
> representation.  The effect is not  the same at all. Is there another way?

you can finetune the radii by resetting the atomic radii using atom selections.

can you produce a reference image that does not
require a password get access to?

axel.
>
> On Tue, Jul 19, 2011 at 3:44 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> maria,
>>
>> you can achieve what you describe by overlaying a "Bonds" representation
>> with a "VDW" representation and using different coloring schemes and
>> adjusting the radii of the respective representations accordingly.
>>
>> cheers,
>>    axel.
>>
>> On Tue, Jul 19, 2011 at 8:53 AM, maria goranovic
>> <mariagoranovic_at_gmail.com> wrote:
>> > Hi
>> > I am wondering if this feature is already present in VMD?
>> > In Pymol, it is possible to color an amino acid residue represented as
>> > licorice in say, orange, and yet one can distinguish between different
>> > atoms
>> > of the residue. For example, all bonds will become pink, but a nitrogen
>> > will
>> > still appear blue and an oxygen red. If I try to color all carbons in
>> > VMD
>> > pink,  a C-N bond still appears in the cyan color, and the effect is not
>> > the
>> > same.
>> > Such a representation can be very useful in visualization. for example:
>> > http://hwmaint.jbc.org/cgi/content/full/285/34/26245/F4
>> >
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> 

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