[Chimera-users] selecting/displaying zones

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 24 13:24:58 PDT 2008

On Jun 24, 2008, at 11:56 AM, Thomas C. Marlovits wrote:
> Am using Chimera and would like to do the following:
> - would first like to focus on specific side chain residues (for  
> example lysines)
> - at a specific atom of either one or all lysines present in my  
> sample, I would like to draw a region of interest (which should be  
> a sphere with a given distance ... then make it rather transparent  
> like soap bobbles ...) ... the idea of this is to highlight areas  
> within a given distance away from this atom
> - then I would like to read out all other side chains that are  
> within such an area (  in a table or so) ... and eventually  
> highlight them with specific colors ...
> Elaine, is there an easy way to do this ?
> Tx,
> -Thomas
> ---------------------------------------------------------------------- 
> ---------
> Thomas C. Marlovits, PhD, M.A.S.
> IMP-IMBA Research Center
> 	- Research Institute of Molecular Pathology (IMP)
> 	- Institute of Molecular Biotechnology, Austrian Academy of  
> Sciences (IMBA)

Hi Thomas,
You can definitely (1) select the atoms or residues within a  
specified cutoff of some other atoms and write a list of what is  
selected to the Reply Log or to a file.  Slightly trickier is (2)  
displaying a "bubble."

(1) The following command selects all atoms within 4.5 angstroms of  
atom NZ in lysine 92, chain A (example structure 2gbp):

select :92.a at nz za<4.5

to select the whole residues with any atom in the zone, use "z" or  
"zr" instead of "za", and to use all the atoms of that lysine, just  
omit "@nz" from the command.
This selection process can also be done by Ctrl-clicking to select  
the atom and then using Select... Zone.  You can write out a list of  
the selection with Actions... Write List (click Log if you want to  
send it to the Reply Log instead).  The default is a list of all the  
atoms individually, but you can set it to "residues" instead to just  
get one line of output per residue.  The command to do that same  
thing is "writesel"

(2) The "bubble."
I imagine something like Volume Eraser would be nice (check it out:   
Tools... Volume Data... Volume Eraser).  However, that does not let  
you specify particular coordinates for the center.  You have to move  
it around by hand.  Volume Eraser really just makes a big atom and  
gives it a transparent color.  You could add an atom in Build  
Structure (under Tools... Structure Editing), color it a transparent  
color, and change its radius with "vdwdefine"
It doesn't let you enter specific coordinates for the atom.  However,  
if you add the atom as a "new model" you can match it to different  
locations on the first.  For example, if the new atom is model 1 and  
the structure of interest (say 2gbp) is model 0:

rep sphere #1
colordef tpink 1 .6 .6 .6
color tpink #1
vdwdef 3.0 #1
vdwdef +1 #1
vdwdef +1 #1
match #1 #0:147.a at nz
select #1 za<5 & #0
[... etc. ...]
The radius would just be for display purposes.  You'd still have to  
specify the zone distance when selecting.

A couple of failed ideas:
(a) You can make a spherical surface of specified radius with the  
command "shape"
but you cannot directly specify coordinates for the center or easily  
modify radius after it has been created.

(b) Create a spherical object in BILD format.
Disadvantages are inability to make it transparent and having to  
delete/recreate the object just to change its radius.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


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