Looks to me like you are using the wrong notation there. You want:
select within(5.0, 113 and protein)
select within(5.0, atomno=1795)
-- no braces
-- specify protein
-- "5.0, not 5,0" -- US notation there on numbers, not EU -- not "select
within(5, 0, 113)"
I think what that does is to say within 5.0 angstroms of either group 0 or
group 113. In your case, group 0 is a water molecule. 113 is also both a
water molecule and a GLU. So the result is two regions, roughly.
Bob
On Mon, Dec 6, 2010 at 10:12 AM, Alexander Rose <alexander.r...@weirdbyte.de
> wrote:
> Hi,
>
> I think there is some bug in the WITHIN(distance, withinAllModels,
> atomExpression) function. It selects more then it is supposed to:
>
> http://proteinformatics.charite.de/jmol-test/html/select_within.html
>
> the page shows two examples where you can select for each first the
> atomExpression around which the within-function is secondly targeted.
>
>
> The pdb file is quite big and the 'Residue sequence number' overflows (>
> 9999) once. this might be the reason?!
>
>
> Best
> Alexander
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
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phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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