[Chimera-users] How to select whole molecule ?

Marek Maly marek.maly at ujep.cz
Mon May 23 09:43:06 PDT 2011

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  
individual molecules using chain ID (e.g. visualization of frames from MD  

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,


Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng <meng at cgl.ucsf.edu>  

> 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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