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

[Elaine Meng]

Hi Francesco,
If your movies are different model numbers, you can put model number before residue name, for example:

#0:hem

You can see what models you have in the Model Panel (under Favorites in menu).
Elaine

On Aug 17, 2011, at 7:11 AM, Francesco Pietra wrote:

> Hi Elaine;
> I selected with line command the molecule that was giving the centroid
> sequence. I was interested in the surroundings of that biatomic
> molecule at various frame numbers. What I said, is that this is
> possible only for the first movie. On subsequent movies, superimposed
> to the first one, the line command always refers to that molecule of
> the first movie.
> 
> francesco
> 
> On Tue, Aug 16, 2011 at 7:38 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 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.
>> Elaine
>> 
>> 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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>> 
>> 
> 
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