VMD-L Mailing List

From: Joshua Anderson (joaander_at_umich.edu)
Date: Mon Oct 01 2012 - 06:31:58 CDT

There is a "feature" in VMD where color by type only uses the first character of the type name to choose colors. Thus if you have one type named Bead and another Bob, they will be colored the same. One way around this is to create a different representation for each type and color by colorid (since the atom selection understands the full type name).
--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

On Sep 30, 2012, at 5:49 PM, John Stone wrote:

> Hi,
> If one of you can send me one of you structure files, I can give
> you a suggestion on how to get this done. I would have expected this
> to work already with the "type" field, but perhaps not. It likely
> depends on how they are named, so if you can send me the structure, I'll
> have a closer look and give you some suggestions, or make a change to
> the code to make this easier.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Sun, Sep 30, 2012 at 04:00:13AM -0400, Andrew Jewett wrote:
>> I'd like to second this request.
>>
>> I've had a similar problem when attempting to view molecules with many
>> atom types. In my case I was using Axel's topotools to load a LAMMPS
>> data file and view it in VMD.
>>
>> I was not sure if this was a topotools issue or a VMD issue. It seems
>> like it's a VMD issue. It would be very nice to be able to specify
>> the color of more than 10 atom types. (We run into this limit fairly
>> frequently.)
>>
>> (For example, I had this problem trying to generate the following image:
>> http://www.moltemplate.org/images/microtubule/LPN_119984atoms.jpg)
>>
>> Cheers!
>> Andrew
>>
>>
>> On Thu, Sep 27, 2012 at 12:59 PM, Ivan Moncayo <idmoncay_at_gmail.com> wrote:
>>> Hello all,
>>>
>>> I simulated a surfactant adsorption over a wall. I need change the color of
>>> the atoms in VMD, but I have more than 9 atoms types and the next atoms
>>> types were coloring with the same color to 1 atom type. Can you help me and
>>> say me how change the color to the atoms type with id more big than 9. Thank
>>> you for your advice.
>>>
>>> --
>>> Saludos
>>>
>>> Iván Moncayo R.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078