[Chimera-users] How to select whole molecule ?

[Marek Maly]

Dear Elanie,

thanks again very much !

Your suggestion ( the "select chain(s)" function in the Model Panel has a  
"by connectivity" ) was exactly
what I was looking for !

   Best wishes,

      Marek




Dne Mon, 23 May 2011 19:04:56 +0200 Elaine Meng <meng at cgl.ucsf.edu>  
napsal/-a:

> Hi Marek,
> There is nothing exactly like that in Chimera, but here are a couple  
> more ideas:
>
> - the "select chain(s)" function in the Model Panel has a "by  
> connectivity" option that could allow you to get the whole bonded  
> molecule even if the chain ID or the whole model would include more  
> atoms than that.
>
> - you could use the "select" command with specific chain ID, residue  
> numbers, and atom names.  However, figuring out what they are is more  
> work for you.
>
> I remember someone else on the chimera-users list asking about selection  
> through a specified number of covalent connections, but I don't remember  
> the details -- that person may have written some python code to do it.
> 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 May 23, 2011, at 9:43 AM, Marek Maly wrote:
>
>> Dear Elaine,
>>
>> first of all thank you very much for your prompt response !
>>
>> Unfortunately your suggestions do not cover cases when one has molecular
>> system composed of two or more
>> molecules loaded as one "Chimera molecular model" without possibility to
>> recognize
>> individual molecules using chain ID (e.g. visualization of frames from  
>> MD
>> trajectory).
>>
>> For such cases only solution (in my opinion) is, some general routine
>> which can quickly
>> find all the atoms which could be accessed from the previously selected
>> one through several
>> (1,2 ....N) covalent bonds. Is something like this implemented in actual
>> version of Chimera ?
>>
>> Do you see any solution for above described case ?
>>
>>    Thank you very much in advance for this additional info,
>>        Best wishes,
>>               Marek
>>
>> Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng <meng at cgl.ucsf.edu>
>> napsal/-a:
>>
>>> Hello Marek Maly,
>>> If you already have the one atom selected, you can press the up arrow
>>> key (on the keyboard) to expand the selection to whole residue, then
>>> again for the whole chain, then whole molecule model.  Depending on the
>>> structure, there may be fewer layers; for example, the whole chain may
>>> be the same as the whole molecule model.  To go back down, you could  
>>> use
>>> the down arrow key.  Also, the commands "select up" and "select down"  
>>> do
>>> the same thing.
>>>
>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#expandselect>
>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>
>>>
>>> If you didn't have any atom selected but you know you want to select  
>>> all
>>> the atoms in a particular model, you can use the select command with  
>>> the
>>> model number (example: select #0), or you could open the Model Panel
>>> from the Favorites menu, and in that panel choose the model  on the  
>>> left
>>> side and click the "select" button on the right side.
>>>
>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
>>>
>>> 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 May 23, 2011, at 7:39 AM, Marek Maly wrote:
>>>
>>>> Hello all,
>>>> is there any possibility how to select all atoms which belongs to the
>>>> given
>>>> molecule ?
>>>>
>>>> I mean something which allow me to select whole molecule to which
>>>> belongs  previously
>>>> selected atom. Unfortunately ZONE selection is not useful here as it
>>>> allow  to select
>>>> only atoms or residues, not whole molecular structures.
>>>>
>>>> Selection by hand/mouse is not possible to use in cases when
>>>> two or more molecules are very close together.
>>>>
>>>> Thanks a lot in advance for advices !
>>>>  Best wishes,
>>>>     Marek Maly
>>>
>>>
>>> __________ Informace od ESET NOD32 Antivirus, verze databaze 6145
>>> (20110523) __________
>>>
>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>
>>> http://www.eset.cz
>>>
>>>
>>>
>>
>>
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>
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 6145  
> (20110523) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
>
>


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