[Chimera-users] Showing more than a single centroid trace

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 16 10:38:40 PDT 2011

Hi Francesco,
You cannot select centroid objects with a command -- they do not have residue or atom names.  You can only select them by clicking their lines in the Axes/Planes/Centroids dialog, or by Ctrl-clicking on them in the Chimera graphics window.

On Aug 16, 2011, at 9:36 AM, Francesco Pietra wrote:

> Hi Elaine:
> I'll try your advice as soon as possible. However, turning mode1 out
> of view in model window while playing movie for model 1, the centroid
> for mode1 is still seen above model 0 and the trace for centroid for
> model 0 . What I could not do was to select the centroid for model 1,
> in order to highlight it. Command "sel :residuename" always selected
> the centroid for model 0.
> francesco
> On Tue, Aug 16, 2011 at 5:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Francesco,
>> I'm not sure I understand what you are asking.  Maybe you are saying that when you hide a model, the centroid is also hidden?
>> Instead of hiding the model with the Model Panel "Shown" checkbox or command "~modeldisplay", which hides everything in the model, you can undisplay the protein parts and leave the centroid displayed.  For example, if I had protein models #0 and #1 and also centroids for each of those, I could undisplay the protein part only of #0:
>> ~display #0
>> ~ribbon #0
>> ~surf #0
>> (commands to undisplay atoms/bonds, ribbon, and molecular surface of model #0).  Then, you would have the protein #1 plus the centroids of both #0 and #1 displayed.  I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On Aug 15, 2011, at 11:36 PM, Francesco Pietra wrote:
>>> Hello:
>>> I would like to show several centroid traces for model 0, 1, 2, ..
>>> Actually, it is the same model, differing, in the movies, for the
>>> protein fluctuations.
>>> What I did, was to superimpose movie for model 1 to the already done
>>> movie for model 0, hiding the protein for model 1 and choosing a
>>> different color for the centroid. Doing that, the instant position of
>>> the centroid can only be color-highlighted for model 0.
>>> I wonder whether there is a better procedure to show the various
>>> centroid traces above a single protein model.
>>> thanks
>>> francesco pietra
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