[Chimera-users] Showing more than a single centroid trace
Eric Pettersen
pett at cgl.ucsf.edu
Thu Aug 18 10:48:19 PDT 2011
Try selecting just the one ligand first with this:
sel #0:residuename & #0:residuenumber
then it and the environment around it with:
sel sel z<5
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
On Aug 18, 2011, at 10:36 AM, Francesco Pietra wrote:
> 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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>>>>>>> Chimera-users at cgl.ucsf.edu
>>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>>>>
>>>>>>
>>>>>>
>>>>>
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>>>>
>>>
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>>
>
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