Well, I don't know... Please send the file for which this is a problem and
also the state script from
show state
just prior to giving that command. Here's what I see using the application:
load =1crn
select within(branch,{4.N},{4.ca})
326 atoms selected
Are you using the application or the applet? The fact that you are seeing
"pending" suggests to me that this is not 11.6.RC10. As I recall, I removed
that message some revisions back. Or, at least, I'm not seeing that message
anymore.
Bob
On Fri, Aug 29, 2008 at 8:27 AM, Steven R. Spilatro
<[EMAIL PROTECTED]>wrote:
> Bob,
> Thanks again. Sorry to give the impression that I had failed to
> remove the quotation marks. I had tried that without success and so
> then attempted to use verbatim the script from #52 on the Jmol
> examples web page which gives:
> select @{within("branch",{[ala]4.N}, {[ala]4.CA})};selectionHalos on;
> I tried with and without quotations. Although I understand now that
> quotation marks and @{} are not needed, I guess am confused about why
> this works in the Jmol examples page. I'm clearly missing something
> important!
>
> At any rate, the suggested script that you have given is giving the
> following response with jmol-11-6-RC10.
>
> select within(branch,{4.N},{4.ca}); color atoms blue
> pending
> 0 atoms selected
> Script completed
> Jmol script terminated
>
> And as a variation:
>
> select within(branch,{atomno=16},{atomno=17}); color atoms blue
> pending
> 0 atoms selected
> Script completed
> Jmol script terminated
>
> If I cut and paste these scripts into the console for Jmol examples
> #52 they work fine.
>
> Steve
>
>
> You have the quotes there still. The word "branch" cannot be in quotes.
> Check the documentation. There are several entities atoms might be
> "within",
> including
>
> element
> chain
> group
> structure
> branch
> molecule
> model
> boundbox
>
> Quotes are used to indicate a sequence, such as "RGGGAA", not one of these
> keywords.
>
> You want:
>
>
> select within (branch, { [ALA] and 4 and *.N } , { [ALA] and 4 and *.ca }
> )
>
> the @{} is unnecessary as well. The SELECT command requires an atom
> expression, so adding the "evaluate expression" motif, @{...}, is not
> needed.
>
> I'm sure that will work. I'm 99% sure there is no bug here.
>
> You can simplify this further by dropping the [ALA], unless there are
> several chains and it just so happens that the 4th residue of some other
> chain is not ALA. Simpler would be:
>
> select within (branch, { 4.N } , { 4.ca } )
>
>
> On Thu, Aug 28, 2008 at 8:19 PM, [EMAIL PROTECTED] <
> [EMAIL PROTECTED]> wrote:
>
> > Bob,
> >
> > Thanks for your reply concerning my problem getting getting the Branch
> > option of Within to work with jmol-11-6-RC10. I've tried further to
> resolve
> > this but without success. Removing the quotes around branch didn't work,
> so
> > I've gone to a more direct approach of trying to replicate the
> functionality
> > on the Examples-11 page using your ala_5_180_0.pdb file. With this file
> > loaded, if I use the console to send the command:
> >
> > select @{within("branch",{[ala]4.N}, {[ala]4.CA})} (with or without
> > quatation marks)
> >
> > I'm still getting the error message:
> >
> > script ERROR: invalid argument
> > ----line 1 command 1 of file null:
> > select @ { within ( branch , { [ALA] and 4 and *.N } , { [ALA]
> > and 4 and *.ca } >> ) << }
> >
> >
> > Still nervous that I'm missing something obvious, but further help would
> be
> > appreciated.
>
>
>
> Dr. Steven R. Spilatro
> Department of Biology and Environmental Science
> Marietta College
>
>
>
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--
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Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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