[Jmol-users] Branch within problem persists
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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Re: [Jmol-users] Branch within problem persists
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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
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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
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[Jmol-users] Branch within problem persists
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
This message was sent using Marietta College WebMail.
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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Re: [Jmol-users] Branch within problem persists
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, [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.
Steven R. Spilatro
Marietta College
This message was sent using Marietta College WebMail.
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
