[Chimera-users] atoms/residues within a certain distance of another structure

Kenward Vaughan kvaughan at bc.cc.ca.us
Tue Jun 12 00:25:59 PDT 2007

On Mon, 2007-06-11 at 19:15 -0700, Terry Nelson wrote:
> Hi,
>      1. I was wondering if Chimera has the option of finding for
>         instance : "residues within 5 Angstrom of a bound protein
>         inhibitor" or "residues within 3Ang. of solvent molecules",
>         etc. I use a similar command in VMD that specifies the
>         residues. 
>      2. Does Chimera archive mails have a search engine that I
>         missed? 
> Cheers,
> Terry

Hi Terry,

This can be done from the select menu or from the command line.

For the menu approach, first select the species/residue(s) you are
focused upon (say, the inhibitor mentioned above).  Then, under Select,
choose Zone... and finish off the details found in the window that
appears (the choices are straighforward).

>From the command line, use the "select" command, which has the format 

	select <description of atoms/residues>

and add to the end of this one of the following:

	select <description of atoms/residues> z<5.0     # or zr<5.0
	select <description of atoms/residues> za<5.0

The first (using z or zr) will pick up all residues less than 5.0
angstroms from the described atoms/residues, while the second gets only
the atoms.  You can use either greater than or less than.

A more complete description of this can be found in the help files.
Search for both "select" and "atom specification" for further
information and specific examples.

You may find it useful to start naming these selections if you plan to
do more within each group.  Check out "Name selection..." and (then)
"Named selection" under the Select menu once you get the above working.


Dr. Kenward Vaughan                    `:,'~~~~~
Professor of Chemistry                 \;:/
Bakersfield College                    |,;|
1801 Panorama Drive                   / ', \
Bakersfield, CA  93305               / o  O \
http://www2.bc.cc.ca.us/kvaughan    (oOoOOoOo)

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