[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
-
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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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Re: [Jmol-users] problem in firefox
mosty I think you will find that the jmolGetStatus() business won't be
helpful. I'm probably the only who ever used that. It was an early attempt
to get around callbacks, and I can't think of any good reason to use it now.
Try something else, like the following:
alert(jmolGetPropertyAsString(auxiliaryinfo, , divInc))
For getting that property, these days I just use:
var x = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)')
rather than doing all the translation of the auxiliaryInfo array into
JavaScript just to get that one element.
But you are using Jmol 11.6.RC6 -- be sure to upgrade that to 11.6.RC11.
Bob
On Thu, Aug 28, 2008 at 11:00 PM, Jeff Hansen [EMAIL PROTECTED] wrote:
Thanks Bob. If gas prices weren't so high and my family wouldn't miss me
too much I would take you up on the offer.
Of course jmolScriptWait didn't break anything, just my failed attempts to
use it broke something.
I tried your second alternative (callbacks are still a mystery to me
although that code doesn't look too bad). So after loading the file I
called a function.
this.loadString = load ../Jmol/jmol/Models/ + molecule + ;javascript
myFunc();;
divWrite(divID,jmolApplet(400, this.loadString,divInc));
In the function I tried to use jmolGetStatus.
function myFunc(){
var result = jmolGetStatus(scriptStatus,divInc);
alert(result);
}
As with all of my attempts thus far this displayed undefined. I guess I
still don't get how this works.
I think ultimately I will put the load command along with some other
commands in a script file rather than continuing to make these long (and
going to get longer) strings.
I'm making progress and having fun. Does that make me a geek?
Thanks for the help and encouragement.
You can see how far I've come at
http://web.mac.com/jhansen4/Jmol/NewJmolDivSTD.html.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how this works!
:)
Seriously, hang in there. You are trying to do a lot all at once, and you
will catch on. This is precisely what this list is for. Just keep at it.
jmolScriptWait would not break anything.
jmolScriptWait should only be used if you absolutely have to pause the
JavaScript until that operation is complete. There are times this is
necessary, but it's not a great idea.
Most Jmol commands are given asynchronously using jmolScript() rather
than jmolScriptWait(). Jmol has a built-in queuing system, so you can fire
as many commands at it as you wish, and they will be processed in order as
processing becomes available. You can also clear the queue using
!exit
and you can abort a specifically running script (but continue processing
later scripts) using
!quit
An alternative to waiting is to have the issued script notify the web page
when it is complete. Eric Martz and Tim Driscoll masterminded this idea
using scriptcallback methods that see a comment go by and then know it is
time to do something. Something like this:
set scriptcallback myfunc;set debugscript true;load whatever;#--file is
loaded
then myfunc() gets a message every time a script command is executed, and
the #--file is loaded message comes through as well:
function myfunc(app, msg) {
var s = + msg // converts Java string msg into a JavaScript string
if (s.indexOf(#--file is loaded) == 0) {
[do something]
}
}
Alternatively, I've used the following quite effectively:
jmolScript(load whatever;javascript modelLoaded())
That would run the JavaScript function
function modelLoaded() {
}
as soon as the model is loaded.
Basically, good event driven code is asynchronous. Nothing waits for
anything. Things happen because they get a message that they need to happen.
The more you can do that, the better.
Still, I do use jmolScriptWait() myself at times. Also jmolEvaluate() is
synchronous, and I use that a lot as well.
Bob
On Thu, Aug 28, 2008 at 6:30 PM, Jeff Hansen [EMAIL PROTECTED] wrote:
I tried jmolScriptWait but couldn't get it to not break the load
command.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 6:03 PM, Jeff Hansen wrote:
Sorry I wasn't clear about this, but the applet corresponding to
result1 is loaded when the page loads. I'll try jmolScriptWait to see
if that does anything for the result2.
f
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle,
Re: [Jmol-users] problem in firefox
I guess I really didn't need the jmolGetStatus() I just wanted some
way to check that the applet was being loaded and I could communicate
with it. I'll just forget using that.
Getting the zeroPoint wasn't too bad. This is what I did.
var _dataInfo = jmolGetPropertyAsArray(auxiliaryInfo);
var _jmolText = document.getElementById('jmolText');
var Energy = _dataInfo['ZEROPOINT'];
Of course your way is more succinct so I'll probably do that from now
on. I'm sure it will also be faster. Grabbing all the auxiliaryInfo
can take some time.
I'll update to RC11 today. Changes come too fast for me to keep up
with, which is a good thing.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 29, 2008, at 10:40 AM, Robert Hanson wrote:
mosty I think you will find that the jmolGetStatus() business won't
be helpful. I'm probably the only who ever used that. It was an
early attempt to get around callbacks, and I can't think of any good
reason to use it now.
Try something else, like the following:
alert(jmolGetPropertyAsString(auxiliaryinfo, , divInc))
For getting that property, these days I just use:
var x = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)')
rather than doing all the translation of the auxiliaryInfo array
into JavaScript just to get that one element.
But you are using Jmol 11.6.RC6 -- be sure to upgrade that to
11.6.RC11.
Bob
On Thu, Aug 28, 2008 at 11:00 PM, Jeff Hansen [EMAIL PROTECTED]
wrote:
Thanks Bob. If gas prices weren't so high and my family wouldn't
miss me too much I would take you up on the offer.
Of course jmolScriptWait didn't break anything, just my failed
attempts to use it broke something.
I tried your second alternative (callbacks are still a mystery to me
although that code doesn't look too bad). So after loading the file
I called a function.
this.loadString = load ../Jmol/jmol/Models/ + molecule +
;javascript myFunc();;
divWrite(divID,jmolApplet(400, this.loadString,divInc));
In the function I tried to use jmolGetStatus.
function myFunc(){
var result = jmolGetStatus(scriptStatus,divInc);
alert(result);
}
As with all of my attempts thus far this displayed undefined. I
guess I still don't get how this works.
I think ultimately I will put the load command along with some other
commands in a script file rather than continuing to make these long
(and going to get longer) strings.
I'm making progress and having fun. Does that make me a geek?
Thanks for the help and encouragement.
You can see how far I've come at http://web.mac.com/jhansen4/Jmol/NewJmolDivSTD.html
.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how
this works! :)
Seriously, hang in there. You are trying to do a lot all at once,
and you will catch on. This is precisely what this list is for.
Just keep at it.
jmolScriptWait would not break anything.
jmolScriptWait should only be used if you absolutely have to pause
the JavaScript until that operation is complete. There are times
this is necessary, but it's not a great idea.
Most Jmol commands are given asynchronously using jmolScript()
rather than jmolScriptWait(). Jmol has a built-in queuing system,
so you can fire as many commands at it as you wish, and they will
be processed in order as processing becomes available. You can also
clear the queue using
!exit
and you can abort a specifically running script (but continue
processing later scripts) using
!quit
An alternative to waiting is to have the issued script notify the
web page when it is complete. Eric Martz and Tim Driscoll
masterminded this idea using scriptcallback methods that see a
comment go by and then know it is time to do something. Something
like this:
set scriptcallback myfunc;set debugscript true;load whatever;#--
file is loaded
then myfunc() gets a message every time a script command is
executed, and the #--file is loaded message comes through as well:
function myfunc(app, msg) {
var s = + msg // converts Java string msg into a JavaScript
string
if (s.indexOf(#--file is loaded) == 0) {
[do something]
}
}
Alternatively, I've used the following quite effectively:
jmolScript(load whatever;javascript modelLoaded())
That would run the JavaScript function
function modelLoaded() {
}
as soon as the model is loaded.
Basically, good event driven code is asynchronous. Nothing waits
for anything. Things happen because they get
[Jmol-users] branch within problem resolved
Bob, Bingo! I do feel dumb now. Your comment was the clue I needed: 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. I had revised this line: script language=JavaScript src=../jmol-11-6-RC10/Jmol.js/script but failed to change the jmolInitialize statement (which loads from a different file) to: jmolInitialize(../jmol-11-6-RC10). Having done so has resolved the problem. Sorry for distracting you from other more important issues. I really appreciate all of your work and readiness to help us users. Steve 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=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
Thanks Angel -- Yes, it definitely turned out to be a memory issue. My inexperience is another! I was stumped since the Jmol graphic stopped responding, but Jmol itself was still running and doing stuff -- I could still enter commands into the console and get appropriate responses. Now I know that that is a hallmark of Java exceptions, including out-of-memory errors. With regard to large windows and the memory issue, I've settled here on creating a pop-up window that is large enough for end-users to have a big view but which is fixed in size so that I know that it won't immediately eat up all of the memory. I've given up the ability for them to re-size, but it seems a reasonable trade-off. Thanks very much, Tom On Thu, Aug 28, 2008 at 11:13 AM, Angel Herráez [EMAIL PROTECTED]wrote: Hi Tom I'm probably late in joining this thread, but since there has been no final comment, here's my 2 cents 1) Your problem looks to me as more related to a specific browser and JVM that to Jmol version (but I may be wrong). Of course, memory is an issue. 2) i) be able to stipulate the size of the popup Applet and have it be a fixed size, or You can always specify a fixed size applet; if the user maximizes the window, he will see blank space around the applet. (But it's great to be able to increase the applet size at will; maybe you could include a warning in yor pop-up window; after all, the memory allocated to Java is an user option. To the point: jmolApplet(600,script javascript:getState()) will give you a fixed size, 600 pixels, square applet. 3) is there a means of specifying the size of the popup window and not allowing it to be resized once created?? Certainly! Say you are using woptions=menubar=yes,resizable=1,scrollbars,alwaysRaised,width=600,height=600,left=50 newwin=open(JmolPopup.htm,jmol_+sm,woptions) Then, change to woptions=menubar=yes,resizable=0,scrollbars,alwaysRaised,width=600,height=600,left=50 4) ii) your idea, to have an upper limit on how big it can get. I find this very tricky to implement, if even possible. 5) Curiously, the popup window is more resistant to this blanking effect using MS IExplorer than with Firefox (3.0.1). In my experience, Firefox (2.0) implementation of JVM (1.5 - 1.6) is much more unstable than IE's - 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 - 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
Re: [Jmol-users] a related popup window question....
I've gone ahead and added for Jmol 11.6.RC12 the applet param tag
maximumSize. This can be set to a maximum size for which the height and
width are not allowed to exceed when resizing. I think this will be a more
user-friendly option. The way to invoke it would be
jmolInitialize(...)
jmolSetCallback(maximumSize, 400)
jmolApplet()
It may seem odd to set this using jmolSetCallback(), but jmolSetCallback is
really just a general jmolSetParameter function. I suppose we should add
to Jmol.js
function jmolSetParameter(param, value) {
jmolSetCallback(param, value)
}
So that's clearer.
I didn't make it settable via a script command because it seems to me more
an aspect of building the applet that the developer might set rather than
something that the user should be able to set on the fly.
Bob
On Fri, Aug 29, 2008 at 12:30 PM, Thomas Stout [EMAIL PROTECTED]wrote:
Thanks Angel --
Yes, it definitely turned out to be a memory issue. My inexperience is
another! I was stumped since the Jmol graphic stopped responding, but Jmol
itself was still running and doing stuff -- I could still enter commands
into the console and get appropriate responses. Now I know that that is a
hallmark of Java exceptions, including out-of-memory errors.
With regard to large windows and the memory issue, I've settled here on
creating a pop-up window that is large enough for end-users to have a big
view but which is fixed in size so that I know that it won't immediately
eat up all of the memory. I've given up the ability for them to re-size,
but it seems a reasonable trade-off.
Thanks very much,
Tom
On Thu, Aug 28, 2008 at 11:13 AM, Angel Herráez [EMAIL PROTECTED]wrote:
Hi Tom
I'm probably late in joining this thread, but since there has been no
final comment, here's
my 2 cents
1)
Your problem looks to me as more related to a specific browser and JVM
that to Jmol
version (but I may be wrong). Of course, memory is an issue.
2)
i) be able to stipulate the size of the popup Applet and have it be a
fixed size, or
You can always specify a fixed size applet; if the user maximizes the
window, he will see
blank space around the applet. (But it's great to be able to increase the
applet size at will;
maybe you could include a warning in yor pop-up window; after all, the
memory allocated to
Java is an user option.
To the point:
jmolApplet(600,script javascript:getState())
will give you a fixed size, 600 pixels, square applet.
3)
is there a means of specifying the size of the popup window and not
allowing it to be
resized once created??
Certainly!
Say you are using
woptions=menubar=yes,resizable=1,scrollbars,alwaysRaised,width=600,height=600,left=50
newwin=open(JmolPopup.htm,jmol_+sm,woptions)
Then, change to
woptions=menubar=yes,resizable=0,scrollbars,alwaysRaised,width=600,height=600,left=50
4)
ii) your idea, to have an upper limit on how big it can get.
I find this very tricky to implement, if even possible.
5)
Curiously, the popup window is more resistant to this blanking effect
using MS IExplorer
than with Firefox (3.0.1).
In my experience, Firefox (2.0) implementation of JVM (1.5 - 1.6) is much
more unstable
than IE's
-
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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
-
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
Re: [Jmol-users] a related popup window question....
Rolf Huehne wrote: Thomas Stout wrote: Thanks Angel -- Yes, it definitely turned out to be a memory issue. My inexperience is another! I was stumped since the Jmol graphic stopped responding, but Jmol itself was still running and doing stuff -- I could still enter commands into the console and get appropriate responses. Now I know that that is a hallmark of Java exceptions, including out-of-memory errors. With regard to large windows and the memory issue, I've settled here on creating a pop-up window that is large enough for end-users to have a big view but which is fixed in size so that I know that it won't immediately eat up all of the memory. I've given up the ability for them to re-size, but it seems a reasonable trade-off. Instead of providing an automatic resize function you could provide a manual resize option using input fields. This way you could easily set a maximum size limit by your Javascript code that does the actual resizing. You wouldn't even need input fields. You could tie for example the 'body' tag with the 'onResize' event to a Javascript function that resizes the applet with an upper limit. I just did a similar thing (with a lower limit) a few days ago for our PDB file viewer: http://www.fli-leibniz.de/cgi-bin/idb_send-rh.pl?CODE=1dehMIME=html Regards, Rolf - 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
Re: [Jmol-users] a related popup window question....
Thomas Stout wrote: Thanks Angel -- Yes, it definitely turned out to be a memory issue. My inexperience is another! I was stumped since the Jmol graphic stopped responding, but Jmol itself was still running and doing stuff -- I could still enter commands into the console and get appropriate responses. Now I know that that is a hallmark of Java exceptions, including out-of-memory errors. With regard to large windows and the memory issue, I've settled here on creating a pop-up window that is large enough for end-users to have a big view but which is fixed in size so that I know that it won't immediately eat up all of the memory. I've given up the ability for them to re-size, but it seems a reasonable trade-off. Instead of providing an automatic resize function you could provide a manual resize option using input fields. This way you could easily set a maximum size limit by your Javascript code that does the actual resizing. Regards, Rolf - 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
Re: [Jmol-users] problem in firefox
Must use 11.6.rc11
Sent from my iPhone
On Aug 29, 2008, at 10:14 AM, Jeff Hansen [EMAIL PROTECTED] wrote:
I spoke too soon.
var x = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)')
isn't working for me. It returns an error message about the
getProperty command.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 29, 2008, at 10:40 AM, Robert Hanson wrote:
mosty I think you will find that the jmolGetStatus() business won't
be helpful. I'm probably the only who ever used that. It was an
early attempt to get around callbacks, and I can't think of any
good reason to use it now.
Try something else, like the following:
alert(jmolGetPropertyAsString(auxiliaryinfo, , divInc))
For getting that property, these days I just use:
var x = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)')
rather than doing all the translation of the auxiliaryInfo array
into JavaScript just to get that one element.
But you are using Jmol 11.6.RC6 -- be sure to upgrade that to
11.6.RC11.
Bob
On Thu, Aug 28, 2008 at 11:00 PM, Jeff Hansen [EMAIL PROTECTED]
wrote:
Thanks Bob. If gas prices weren't so high and my family wouldn't
miss me too much I would take you up on the offer.
Of course jmolScriptWait didn't break anything, just my failed
attempts to use it broke something.
I tried your second alternative (callbacks are still a mystery to
me although that code doesn't look too bad). So after loading the
file I called a function.
this.loadString = load ../Jmol/jmol/Models/ + molecule +
;javascript myFunc();;
divWrite(divID,jmolApplet(400, this.loadString,divInc));
In the function I tried to use jmolGetStatus.
function myFunc(){
var result = jmolGetStatus(scriptStatus,divInc);
alert(result);
}
As with all of my attempts thus far this displayed undefined. I
guess I still don't get how this works.
I think ultimately I will put the load command along with some
other commands in a script file rather than continuing to make
these long (and going to get longer) strings.
I'm making progress and having fun. Does that make me a geek?
Thanks for the help and encouragement.
You can see how far I've come at http://web.mac.com/jhansen4/Jmol/NewJmolDivSTD.html
.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how
this works! :)
Seriously, hang in there. You are trying to do a lot all at once,
and you will catch on. This is precisely what this list is for.
Just keep at it.
jmolScriptWait would not break anything.
jmolScriptWait should only be used if you absolutely have to pause
the JavaScript until that operation is complete. There are times
this is necessary, but it's not a great idea.
Most Jmol commands are given asynchronously using jmolScript()
rather than jmolScriptWait(). Jmol has a built-in queuing system,
so you can fire as many commands at it as you wish, and they will
be processed in order as processing becomes available. You can
also clear the queue using
!exit
and you can abort a specifically running script (but continue
processing later scripts) using
!quit
An alternative to waiting is to have the issued script notify the
web page when it is complete. Eric Martz and Tim Driscoll
masterminded this idea using scriptcallback methods that see a
comment go by and then know it is time to do something. Something
like this:
set scriptcallback myfunc;set debugscript true;load
whatever;#--file is loaded
then myfunc() gets a message every time a script command is
executed, and the #--file is loaded message comes through as well:
function myfunc(app, msg) {
var s = + msg // converts Java string msg into a JavaScript
string
if (s.indexOf(#--file is loaded) == 0) {
[do something]
}
}
Alternatively, I've used the following quite effectively:
jmolScript(load whatever;javascript modelLoaded())
That would run the JavaScript function
function modelLoaded() {
}
as soon as the model is loaded.
Basically, good event driven code is asynchronous. Nothing waits
for anything. Things happen because they get a message that they
need to happen. The more you can do that, the better.
Still, I do use jmolScriptWait() myself at times. Also
jmolEvaluate() is synchronous, and I use that a lot as well.
Bob
On Thu, Aug 28, 2008 at 6:30 PM, Jeff Hansen [EMAIL PROTECTED]
wrote:
I tried jmolScriptWait but couldn't get it to not break the load
command.
[Jmol-users] autobond and bond tolerance
Has something changed recently with defaults related to autobond. Ball and stick structures that were fine in the past seem to end up with nearly every adjacent atom being bonded to each other (i.e. hydrogens bond to their carbon as well as to each other) . Questions: 1. What are the default values and typical values for: bondTolerance minBondDistance and most importantly, what are the units for these (I was surprised the docs described these as decimal as opposed to decimal in angstroms or something else)? 2. Have later versions of Java possibly caused a change in how these parameters are initially set? We've been running with a frozen version of Jmol on our website and just noticed problems with methyl groups. Since our code and data have not changed, Java update seem like the only source of changes. --Andrew - 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
Re: [Jmol-users] autobond and bond tolerance
1. What are the default values and typical values for: bondTolerance public final static float DEFAULT_BOND_TOLERANCE = 0.45f; minBondDistance //minimum acceptable bonding distance ... from OpenBabel ... mth 2003 05 26 public final static float DEFAULT_MIN_BOND_DISTANCE = 0.4f; All specified distance units in Jmol are Angstroms. 2. Have later versions of Java possibly caused a change in how these parameters are initially set? We've been running with a frozen version of Jmol on our website and just noticed problems with methyl groups. Since our code and data have not changed, Java update seem like the only source of changes. I don't recall anything changing in that regard any time recently. But perhaps years ago. How old is that version? Send me a file or two so I can take a look at what you have. Certainly this is very unusual. Bob Hanson On Fri, Aug 29, 2008 at 8:59 PM, Andrew M. Simms [EMAIL PROTECTED]wrote: Has something changed recently with defaults related to autobond. Ball and stick structures that were fine in the past seem to end up with nearly every adjacent atom being bonded to each other (i.e. hydrogens bond to their carbon as well as to each other) . Questions: 1. What are the default values and typical values for: bondTolerance minBondDistance and most importantly, what are the units for these (I was surprised the docs described these as decimal as opposed to decimal in angstroms or something else)? 2. Have later versions of Java possibly caused a change in how these parameters are initially set? We've been running with a frozen version of Jmol on our website and just noticed problems with methyl groups. Since our code and data have not changed, Java update seem like the only source of changes. --Andrew - 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
[Jmol-users] proposed change to Jmol.js
I'd like to propose a change to Jmol.js. The change would be an addition. If the page URL contains JMOLJAR= then Jmol.js would be instructed to ignore the jmolInitialize() command and instead use the codebase directory and jar file as defined after that tag. For example: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar This would allow quick checking of sites with different JAR files. Bob -- 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
[Jmol-users] which jmol applet?
If I use a function like this:
function getEnergy() {
var _jmolText = document.getElementById('jmolText');
var Energy =
jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)');
var text = Energy = + Energy + kJ/mol\n;
var node = document.createTextNode(text);
_jmolText.appendChild(node);
}
and I have more than one Jmol applet on the page, how do I select
which applet I'm getting the info from?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
-
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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