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

[Francesco Pietra]

On Thu, Aug 18, 2011 at 7:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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

For me  that works between the three ligands only. I.e, with a large
z<20, all the three residues are highlighted, while with z<3 only the
residue with the specified residue number is highlighted. The number
of atoms at the bottom line correspond. For example, with z<20,  6
atoms, 3 bonds (three diatomic molecules)

francesco

>
> 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
>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>
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