[Chimera-users] How to select whole molecule ?

[Elaine Meng]

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
>> 
>> 
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> 
> 
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