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

[Elaine Meng]

HI Francesco,
Just put the model number wherever you need it, with no space before residue name or number, maybe something like:

sel #0:residuename & #0:residuenumber z<5

Elaine

On Aug 18, 2011, at 9:46 AM, Francesco Pietra wrote:

> Hi Elaine:
> Thanks a lot. Could you also help me as how to find the environment of
> the moved ligand, when there are three of them with the same residue
> number?
> 
> While define centroid works nicely with:
> 
> define centroid radius# color # :residuename & :residuenumber
> 
> sel #modelnumber :residuename & :residuenumber z<#
> 
> does not. Could the command be modified to refer to only one of the residues?
> 
> Thanks
> francesco
> 
> On Wed, Aug 17, 2011 at 7:34 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 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
>>>>>> 
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Chimera-users mailing list
>>>>> Chimera-users at cgl.ucsf.edu
>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>> 
>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
>> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>