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Sent: 25 April 2007 16:04
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Subject: Jmol-users Digest, Vol 11, Issue 16
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Today's Topics:
1. Re: jmolAppletInline and defaultloadscript (Angel Herraez)
2. Re: Mol2 files (again!) (Aidan Heerdegen)
3. Re: page design: flexible size, scrollable, no frames
(Angel Herraez)
4. Class Not Found Exception while using the applet tag
(Harini Gopalakrishnan)
5. Re: Class Not Found Exception while using the applet tag
(Bob Hanson)
6. Re: isosurface options POCKET, INTERIOR, MINSET n (Alan Hewat)
7. Re: isosurface options POCKET, INTERIOR, MINSET n (Bob Hanson)
----------------------------------------------------------------------
Message: 1
Date: Mon, 23 Apr 2007 20:04:06 +0200
From: "Angel Herraez" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] jmolAppletInline and defaultloadscript
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII
Hi Mauricio
I think that "set defaultLoadScript" will oly work after the applet
has been inserted with "JmolApplet", and before the molecule is
loaded.
Since you are doing everything inline, it probably won't work.
You may get what you want using "jmolLoadInlineScript" instead of
"jmolLoadInline", so:
onClick="jmolLoadInlineScript(theMolecule, theDefaultScript)"
Maybe you could also do it:
jmolAppletInline(whatever)
jmolScript("set defaultLoadScript whatever")
and then
onClick="jmolLoadInline(theMolecule)"
------------------------------
Message: 2
Date: Tue, 24 Apr 2007 09:34:20 +1000
From: Aidan Heerdegen <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Mol2 files (again!)
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
> # applySymmetryToBonds
> #
> # When set TRUE, this flag instructs Jmol when applying symmetry
> # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry
> # to the bonds indicated in the file. The flag is useful when
> # normal Jmol autobonding would not properly connect atoms, but
> # the model is "molecular" -- the base atom coordinates are correct
> # for whole molecules. The flag should NOT be used in cases where
> # the application of symmetry operations creates new bonds that
> # were not present in the original set, as for quartz.cif, where
> # there is only one bond initially, and after applying symmetry
> # new bonds are created that are between atoms that were created
> # using two different symmetry operations.
>
> This appears to work perfectly for the example file Aiden provided.
> It does connect the atoms properly in quartz.cif, but some bonds
> are missing, as
> noted above. It also fails to connect bonds properly in a test sample
> I have that involves a cif file with alternative locations but bonding
> only shown for one alternative. So there are definitely limitations,
> and I have set the default to be FALSE -- no change from previous
> behavior. You must explicitly include:
>
> applySymmetryToBonds = true
>
> prior to loading a file to instruct Jmol to carry out this bonding
> algorithm.
Bob, you are a pearl. Thanks heaps. I look forward to testing this out.
Cheers
Aidan
------------------------------
Message: 3
Date: Tue, 24 Apr 2007 12:02:10 +0200
From: "Angel Herraez" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] page design: flexible size, scrollable, no
frames
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Hello all
I have improved my layouts for automatically resizable Jmol and text
panels. Six different layouts are now available to see and to
download as templates with instructions.
As they are, they require at least Jmol 11.1.20 (because of
improvements in the associated Jmol.js). I will shortly be posting
patches for using them with 11.0.1 and with 10.2. This patch should
also be included in 11.0.2 when it is released.
As far as I can see, and based of testing of previous versions, these
layouts behave in all modern browsers and OSs. (Thanks to those who
tested the former versions). The myth about the need to use fixed-
pixel-size applets to avoid browser crash is definitely gone.
If anyone can think of or need a different layout, I will be glad to
implement it now that the method is fresh in my brain.
Everything is on http://biomodel.uah.es/Jmol/resizable/
and I will link to it from the Wiki, Recycling Corner.
I've put the templates under Creative Commons "by-sa", so please keep
the notices in the code when you use it. A mention in the
acknowledgments section of your pages is not compulsory, but will be
appreciated.
Enjoy amd make good use of it!
PS: anyone trying to run his/her pages in a UMPC at 800x480 pixels
screen resolution, or a PDA, or a mobile-whatever? Then this is for
you! --I don'tknow if there is a Java for those--.
?
Dr. Angel Herraez
Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
E-28871 Alcala de Henares (Madrid), Spain
------------------------------
Message: 4
Date: Tue, 24 Apr 2007 14:55:15 -0700 (PDT)
From: Harini Gopalakrishnan <[EMAIL PROTECTED]>
Subject: [Jmol-users] Class Not Found Exception while using the applet
tag
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=iso-8859-1
Hi,
I am trying to embed the applet tag in my html page
and I encounter the "Class not found Exception".
I have set the codebase to point to the URL where my
JmolApplet.jar resides and it still refuses to locate
the class. Can anyone help me figure as to what the
problem could be? The applet does load if I make use
of the Jmol.js script but for other reasons I would
want to embed the applet tag directly instead of
making a call to the javascript.
The snippet of the code I use to load my applet is a s
follows:
<body>
<applet code='JmolApplet.class'
codebase='http://rna.informatics.indiana.edu/cgi-bin/hgopalak/jmol'
archive='JmolApplet.jar' width='200' height='350'>
<param name='loadInline' value=''>
</applet>
</body></html>
The error thrown is as follows:
load: class JmolApplet.class not found.
java.lang.ClassNotFoundException: JmolApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown
Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown
Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown
Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown
Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: open HTTP connection
failed.
at sun.applet.AppletClassLoader.getBytes(Unknown
Source)
at sun.applet.AppletClassLoader.access$100(Unknown
Source)
at sun.applet.AppletClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native
Method)
... 10 more
Thanks,
Harini
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------------------------------
Message: 5
Date: Tue, 24 Apr 2007 20:59:26 -0500
From: Bob Hanson <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Class Not Found Exception while using the
applet tag
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Harini. You present yourself a challenge, since different browsers
require different configurations of these tags. Most likely some user
platforms will not load your page. But if you feel you really cannot use
Jmol.js, then at least use it once and have it display the proper tag
for you. Just use this once to see what it gives, then cut and paste::
Just from you hard drive -- just to see what the code is supposed to
look like:
<script src=Jmol.js></script>
<script>
jmolSetDocument(0)
s = jmolApplet(400)
document.write("<pre>"+s.replace(/\</g, "<")+"</pre>")
</script>
or, if you wish to force the <applet> tag instead of <object>:
<script src=Jmol.js></script>
<script>
jmolInitialize(".")
_jmol.useIEObject = false;
_jmol.useHtml4Object = false;
jmolSetDocument(0)
s = jmolApplet(400)
document.write("<pre>"+s.replace(/\</g, "<")+"</pre>")
</script>
Harini Gopalakrishnan wrote:
>Hi,
>
>I am trying to embed the applet tag in my html page
>and I encounter the "Class not found Exception".
>I have set the codebase to point to the URL where my
>JmolApplet.jar resides and it still refuses to locate
>the class. Can anyone help me figure as to what the
>problem could be? The applet does load if I make use
>of the Jmol.js script but for other reasons I would
>want to embed the applet tag directly instead of
>making a call to the javascript.
>
>The snippet of the code I use to load my applet is a s
>follows:
>
><body>
><applet code='JmolApplet.class'
>codebase='http://rna.informatics.indiana.edu/cgi-bin/hgopalak/jmol'
>archive='JmolApplet.jar' width='200' height='350'>
><param name='loadInline' value=''>
></applet>
></body></html>
>
>
>
With forcing, Jmol.js will produce this:
<applet name='jmolApplet0' id='jmolApplet0' code='JmolApplet'
archive='JmolApplet0.jar' codebase='.'
width='400' height='400' mayscript='true'>
<param name='progressbar' value='true' />
<param name='progresscolor' value='blue' />
<param name='boxbgcolor' value='black' />
<param name='boxfgcolor' value='white' />
<param name='boxmessage' value='Downloading JmolApplet ...' />
<param name='script' value='select *' />
<table bgcolor='yellow'><tr><td align='center' valign='middle'
width='400' height='400' >
You do not have the<br />
Java Runtime Environment<br />
installed for applet support.<br />
Visit <a
href='http://www.java.com'>www.java.com</a></td></tr></table></applet>
>The error thrown is as follows:
>
>load: class JmolApplet.class not found.
>java.lang.ClassNotFoundException: JmolApplet.class
>at sun.applet.AppletClassLoader.findClass(Unknown
>Source)
>at java.lang.ClassLoader.loadClass(Unknown Source)
>at sun.applet.AppletClassLoader.loadClass(Unknown
>Source)
>at java.lang.ClassLoader.loadClass(Unknown Source)
>at sun.applet.AppletClassLoader.loadCode(Unknown
>Source)
>at sun.applet.AppletPanel.createApplet(Unknown Source)
>at sun.plugin.AppletViewer.createApplet(Unknown
>Source)
>at sun.applet.AppletPanel.runLoader(Unknown Source)
>at sun.applet.AppletPanel.run(Unknown Source)
>at java.lang.Thread.run(Unknown Source)
>Caused by: java.io.IOException: open HTTP connection
>failed.
>at sun.applet.AppletClassLoader.getBytes(Unknown
>Source)
>at sun.applet.AppletClassLoader.access$100(Unknown
>Source)
>at sun.applet.AppletClassLoader$1.run(Unknown Source)
>at java.security.AccessController.doPrivileged(Native
>Method)
>... 10 more
>
>Thanks,
>Harini
>
>__________________________________________________
>Do You Yahoo!?
>Tired of spam? Yahoo! Mail has the best spam protection around
>http://mail.yahoo.com
>
>-----------------------------------------------------------------------
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>
------------------------------
Message: 6
Date: Wed, 25 Apr 2007 16:45:17 +0200
From: Alan Hewat <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] isosurface options POCKET, INTERIOR, MINSET
n
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"
At 17:40 18/04/2007, Bob Wrote:
>I saw the zeolite case as a nice opportunity to try a few new things.
The new features are indeed much better than what I previously used in
ICSD to represent cavities eg see:
http://icsd.ill.fr/icsd/cifdraw.php?&id[]=43790 But this brings us back
to a question from last August about "deleting" atoms.
Zeolites are often reported with their cavities full of other atoms (eg
water). To draw the cavities correctly you need to be able to select (eg
with the mouse) and hide/delete these junk atoms for the purpose of
constructing the cavities. (Yes I know you can't actually delete them
from the input file with Jmol; but you can already make them invisible
or of zero radius, though that doesn't seem to be sufficient for the
purpose of ignoring them for the construction of cavities).
I have other problems with zeolites in that the technique for
constructing coordination polyhedra from CIF files, which consists of
including all the surrounding cells but making them invisible, takes a
lot of time if the cell is large. I really don't need complete
surrounding cells to construct coordination polyhedra, just the
immediate surroundings would do, which should be faster for large
structures. (Yes, I can get around this by dumping just the atoms of
interest into a PDB or XYZ file, but that is ugly).
Alan.
BTW Christian, the new jmol drawings in your Zeolite Atlas look great.
Congrats to you and Bob.
_____________________________________________________________
Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48
+33.476.20.72.13 (.26 Mme Guillermet)
http://www.ill.fr/dif/people/hewat/
_____________________________________________________________
------------------------------
Message: 7
Date: Wed, 25 Apr 2007 10:03:56 -0500
From: Bob Hanson <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] isosurface options POCKET, INTERIOR, MINSET
n
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
If
isosurface ignore(xxxxx) ....
does not do the job for cavities, then that is a bug.
Alan Hewat wrote:
>At 17:40 18/04/2007, Bob Wrote:
>
>
>
>>I saw the zeolite case as a nice opportunity to try a few new things.
>>
>>
>
>The new features are indeed much better than what I previously used in
ICSD to represent cavities eg see:
http://icsd.ill.fr/icsd/cifdraw.php?&id[]=43790 But this brings us back
to a question from last August about "deleting" atoms.
>
>Zeolites are often reported with their cavities full of other atoms (eg
water). To draw the cavities correctly you need to be able to select (eg
with the mouse) and hide/delete these junk atoms for the purpose of
constructing the cavities. (Yes I know you can't actually delete them
from the input file with Jmol; but you can already make them invisible
or of zero radius, though that doesn't seem to be sufficient for the
purpose of ignoring them for the construction of cavities).
>
>I have other problems with zeolites in that the technique for
constructing coordination polyhedra from CIF files, which consists of
including all the surrounding cells but making them invisible, takes a
lot of time if the cell is large. I really don't need complete
surrounding cells to construct coordination polyhedra, just the
immediate surroundings would do, which should be faster for large
structures. (Yes, I can get around this by dumping just the atoms of
interest into a PDB or XYZ file, but that is ugly).
>
>
>
I understand. Let's see how this would work and see if there are any
major issues.
Four options:
a) the unwanted atoms are never delivered by the reader in the first
place.
b) the unwanted atoms are filtered out when the "real" atom set is
created from the set of atoms that were read.
c) user has a "delete atoms" option, and atoms are actually permanently
removed.
d) user has a "delete atoms" option, and deleted atoms are tagged but
still present.
Issues:
1) how to handles references to deleted atoms.
2) how to handle the "state" in order to preserve and reproduce the
changes.
If option a or b is chosen, it shouldn't be too difficult to do this.
Bob
>Alan.
>BTW Christian, the new jmol drawings in your Zeolite Atlas look great.
Congrats to you and Bob.
>
>_____________________________________________________________
>Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48
>+33.476.20.72.13 (.26 Mme Guillermet)
http://www.ill.fr/dif/people/hewat/
>_____________________________________________________________
>
>
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