Oh, I see what you mean. I had never seen the "::" notation for chime, I
guess. From the Jmol documentation:
WITHIN(distance, withinAllModels, atomExpression)
any atom within the specified distance of any atom in the atomExpression.
The optional TRUE/FALSE flag withinAllModels (by default FALSE) may be set
TRUE to allow finding atoms in one model that may be within some distance of
another model. (Jmol 11.4) Starting with Jmol 11.8, if the distance is
negative, then the operation applies to all atoms having normalize unit cell
coordinates within -distance of the designated atoms.
so you want
select 1.10 and within(12.0, true, 1.11)
Bob
On Thu, Oct 7, 2010 at 8:33 AM, Eduardo Harguindey Lopez <
harguindey_lopez_edua...@lilly.com> wrote:
>
> Thanks, Bob!
>
> Should this translation work?
>
> [Chime] select ::10 and within(12.0, ::11)
> [Jmol] select 1.10 and within(12.0, 1.11)
>
> There is no error in the script, however it doesn't really select
> those atoms from model 10 at 12.0 Amstrongs of model 11... as it does in
> Chime... Am I missing anything?
>
> Many thanks!!
> Regards,
> Edu.
>
>
>
>
> *Robert Hanson <hans...@stolaf.edu>*
>
> 06/10/2010 14:50
> Please respond to
> jmol-developers@lists.sourceforge.net
>
> To
> jmol-developers@lists.sourceforge.net
> cc
> Subject
> Re: [Jmol-developers] Within operator and models
>
>
>
>
> select ::10
>
> isn't a recognized selection. Tenth model in the first file is
>
> select 1.10
>
> You can also use
>
> select model=10
>
> if you want to use the MODEL reference number in the PDB file.
>
> restrict
>
> is pretty much deprecated. I would recommend using
>
> display
>
> because it is reversible and just basically makes a whole lot more sense.
>
> Bob
>
>
>
> On Wed, Oct 6, 2010 at 2:00 AM, Eduardo Harguindey Lopez <*
> harguindey_lopez_edua...@lilly.com* <harguindey_lopez_edua...@lilly.com>>
> wrote:
>
> Hello Everyone.
>
> I'm newbie in Jmol, and I'm having some dificulties translating some
> Chime/Rasmol scripts to run with Jmol.
>
> The problem I'm facing is when selecting models, as in the input .pdb
> several models are present.
>
> This is the Chime script to convert:
>
> script="select all; wireframe off;
> select ::10; cartoon 30; color greenblue;
> select ::10 and within(12.0, ::11); wireframe 10;
> color cpk; restrict not hydrogen;
> select ::10 and within(12.0, ::11) and carbon;
> color greenblue; restrict not hydrogen;"
>
> What seems to break the script in Jmol is having a model in "within".
>
> I've seen in the email archive a post from 2005 stating that "Models are
> completely independent. We do not bond across models and the within operator
> does not span models".
>
> Has this been addressed since then?
>
> I'm using jmol-12.0.15 in my tests.
>
> Many thanks.
> Regards,
> Edu.
>
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> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057*
> **http://www.stolaf.edu/people/hansonr*<http://www.stolaf.edu/people/hansonr>
>
> 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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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
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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