Re: [Jmol-users] Branch within problem persists

[Robert H. <ha...@st...>]

Steven,

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, spi...@ma... <
spi...@ma...> 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.
>
> Steven R. Spilatro
>
> Marietta College
>
>
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-- 
Robert M. Hanson
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