VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 13 2010 - 12:38:18 CDT

On Wed, Oct 13, 2010 at 12:31 PM, Brooke Dallas <bdallas_at_ucdavis.edu> wrote:
> Thanks Axel,
>
> The molecule has 38 atoms and it only needs to be a static image.

ok. then the kind of approaches i have in mind, should work for you.
it will need a little tcl scripting, but not too much.

option 1:

re-draw all bonds manually using the cylinder primitive.
you need to get a list of all bonds, match them with the
value that you want to attach to them, identify the coordinates
of the atoms and then draw the bond after setting the color
to a proper value.

option 2:

create 4 representations that use coloring by user, user2, user3, user4
then identify the bonds and set the user field for both atoms to the
rmsf value. if user is != 0 for any of the two atoms use user2 instead,
if that is set then use user3 and so on. if you use a "Bonds" representation
you can overlay it with a CPK or scaled down VDW representation to
show the atoms in their "normal" colors.

perhaps you can try with a couple of bonds manually, which of
the two options would be more convenient and let us know if
you run into problems with the implementation.

cheers,
    axel.

>
> Brooke
>
> On Wed, Oct 13, 2010 at 3:41 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Wed, 2010-10-13 at 14:46 +0100, Brooke Dallas wrote:
>> > Dear Vmd List,
>>
>> dear brooke,
>>
>> > I need to draw a molecule with bond colors indicating the RMS bond
>> > length fluctuation for each bond, e.g. blue for small RMS fluctuations
>> > continuous to red for large RMS fluctuations. Does anybody have any
>> > suggestions for how to do that?
>>
>> how large a molecule?
>> does it have to be dynamics or only a static image?
>>
>> VMD doesn't have any internal provisions for things like this,
>> so you would either have to do some kind of hack with multiple
>> representations, or draw the bonds manually from a script.
>>
>> if you can give some more details about what you want to
>> achieve and for what purpose you need this, somebody may
>> be able to come up with some suggestions for doing this.
>>
>> cheers,
>>    axel.
>>
>> > Thanks in advance,
>> >
>> > Brooke Dallas
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
>> http://sites.google.com/site/akohlmey/
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.