VMD-L Mailing List

From: Patrick Burney (pburney_at_u.washington.edu)
Date: Wed Oct 13 2010 - 14:41:43 CDT

I have done some things similar to option 1 in creating porcupine plots for principle component analysis

Let me tell you the things I found very helpful:
Create a proc that draws the cylinder between the two atoms (in your .vmdrc file). Then make a data file containing 3 columns: atom_i atom_j RMS. Then you can run a script that reads in each line, sets the object color based on the RMS, then draws the cylinder.
Should work like a charm.

Good luck,
Patrick

On Oct 13, 2010, at 10:38 AM, Axel Kohlmeyer wrote:

> 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.
>