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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