Re: [Jmol-users] Viewer.scriptWait(zoom 400;) hangs in 11.3.64
I will look at this, but I certainly have not observed it to date. I assume you are doing this from an application that has Jmol embedded in it? Are you sure you are starting a new thread and not using the main execution thread when executing viewer.scriptWait? This is necessary. On Tue, 25 Dec 2007 21:50:36 -0500, Golagani, Ravi [EMAIL PROTECTED] wrote: Hi The Viewer.scriptWait(zoom 400;) statement hangs java program forever in pre-release 11.3.64, other commands work fine in scriptWait(), the problem occurs only when we use zoom/zoomto commands. The same zoom command works fine with Viewer.scriptWait() in latest release 11.2.14. Are there any specific settings needed for using Viewer.scriptWait() in pre-release 11.3.64? thanks, Ravi Golagani - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Insertion code display problem in jmol-11.2.14
On Tue, 25 Dec 2007 21:20:05 -0500, Golagani, Ravi [EMAIL PROTECTED] wrote: Hi, I'm using the latest release jmol-11.2.14 (applet) in our project. When an atom consists PDB Insertion code as '100A' it shows it with some illegal character in tooltip. I'm passing the correct Insertion code in Jmol format (i.e '100^A'). Also it sends the same illegal character to JmolStatusListener.notifyAtomPicked(int atomIndex, String strInfo) method too. Please check the screenshot taken with Jmol application. http://img101.imageshack.us/my.php?image=jmolinscodeerrorex2.jpg It doesn't happen in old version latest pre-release 11.3.64. btw, The org.jmol.viewer.Viewer.getAtomSequenceCode() method is not a public method. Is there any way to get the atom's sequence code from Viewer class without parsing 'strInfo' in method? In 11.3.64 several more methods are public. Specifically, Viewer.getModelSet() and modelSet.getAtomAt() and getAtoms() These are in org.jmol.modelset.AtomCollection.java, but accessible via a modelSet. Once you have the atom, you can use org.jmol.modelset.Atom.getInsertionCode(), which is a public method. I remember fixing some bug like this, but it should all be right in 11.3.64. It probably was never fixed in 11.2. Since 11.4 is just around the corner, it may never be fixed in 11.2. thanks, Ravi Golagani - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Small buglet in saving graphics state (Jmol 11.4)
thank you - please enter as an official request for a bug fix.
Perhaps Egon can find that code in SelectionManager.java and fix it for us.
On Fri, 4 Jan 2008 15:50:11 +, Brian McMahon [EMAIL PROTECTED] wrote:
Hello
If one invokes the Jmol console (at least in 11.4RC1) and clicks the
State button, among the contents one finds
function _setSelectionState();
select ({0:48});
set hideNotSelected false;
end function
Note that the final end function does not have a closing semicolon.
This is legitimate; but if one then copies and pastes the graphics state
as an inline argument to jmolApplet() one must collapse the state
description into a single line, when the end function is no longer a
properly terminated statement.
For now I can workaround this by massaging the state as it is collapsed
into
a single line, but it would be good if this minor flaw were corrected in
future releases, and each statement were terminated with a semicolon.
Cheers
Brian
_
Brian McMahon tel: +44 1244 342878
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International Union of Crystallographye-mail: [EMAIL PROTECTED]
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Re: [Jmol-users] minimum Jmol download
On Wed, 2 Jan 2008 21:02:59 -0500, Frieda Reichsman [EMAIL PROTECTED] wrote: Bob, two part question: 1, Which component files of Jmol will download when a page has an applet displaying one structure (DNA only), in wireframe only, with NO buttons or other controls? (Assuming I am using the 'components' version of Jmol jar files). [ x ] JmolApplet0_Core.jar 30-Dec-2007 23:22 157K [ x ] JmolApplet0_Jars.jar 30-Dec-2007 23:23 55K [ ] JmolApplet0_Jvxl.jar 30-Dec-2007 23:23 79K [ x ] JmolApplet0_Main.jar 30-Dec-2007 23:23 36K [ x ] JmolApplet0_Popup.jar 30-Dec-2007 23:23 30K [ ] JmolApplet0_Quantum.jar30-Dec-2007 23:23 8.5K [ x ] JmolApplet0_ReadersCifPdb.jar 30-Dec-2007 23:23 15K [ x ] JmolApplet0_ReadersMolXyz.jar 30-Dec-2007 23:23 4.5K [ ] JmolApplet0_ReadersMore.jar30-Dec-2007 23:23 65K [ ] JmolApplet0_ReadersXml.jar 30-Dec-2007 23:23 22K [ x ] JmolApplet0_ShapeBio.jar 30-Dec-2007 23:23 50K [ ] JmolApplet0_ShapeSpecial.jar 30-Dec-2007 23:23 54K [ ] JmolApplet0_Smiles.jar 30-Dec-2007 23:23 7.8K [ x ] JmolApplet0_Viewer.jar 30-Dec-2007 23:23 384K [ x ] JmolApplet0_i18n.jar 30-Dec-2007 23:23 127K I think. 2, If there is a jvxl surface, would the only additional component be the JmolApplet0_Jvxl.jar file? also ShapeSpecial I'd like to be able to compare the file sizes for a user downloading an applet with a simple rotating structure vs. downloading various sizes of animated gifs. great. Thanks, Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] something broken in Jmol states (?)
looks like a missing semicolon after color selectionHalos none
If you can fix that manually for now, that will make it work.
[[Egon, can you fix this? It's in org/jmol/shapes/Halos.Java
62 public String getShapeState() {
63 return super.getShapeState()
64 + (colixSelection == Graphics3D.USE_PALETTE ?
65 : colixSelection == Graphics3D.INHERIT_ALL ? color
SelectionHalos NONE
66 : getColorCommand(selectionHalos, colixSelection) +
;\n);
line 65 should read:
65 : colixSelection == Graphics3D.INHERIT_ALL ? color
SelectionHalos NONE;\n
Bob
On Wed, 2 Jan 2008 19:08:30 +0100, Paul Pillot
[EMAIL PROTECTED] wrote:
I got this message runing a state from the applet with Jmol 11.3.63 :
script ERROR: bad argument count | line 12 command 11 of function
_setmodelstate file null: | color selectionHalos none select ({1189})
| line 6 command 6 of function _setstate file null: |
_setmodelstate | line 513 command 1 of file null: |
_setstate
the file is loaded but the complete view is not restored...
Paul
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Re: [Jmol-users] polyhedra bonds opaque broken
please enter as a request for a bug fix; in the mean time, please use color polyhedra opaque :) On Wed, 2 Jan 2008 19:05:49 +0100, Paul Pillot [EMAIL PROTECTED] wrote: Happy new year to all Jmolers ! I think there is something broken in respect with polyhedra translucency : polyhedra bonds (selected) translucent works fine polyhedra bonds (selected) opaque does not restore the default view whereas color polyhedra opaque does... Paul - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Testing 11.6.RC8
Thanks, Rolf. Yes, that's a bug introduced recently. It's the capital
letters.
That's checked in for 11.6.RC9.
On Tue, Aug 19, 2008 at 6:19 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Hi,
I tested Jmol 11.6.RC8 with our 'JenaLib Jmol Viewer' and noticed the
following problem:
Problem using draw object id within Jmol math calculation
(works with 11.5.35)
commands:
draw boundary_4_A PLANE PERP 100 (85:A.CA/1) (87:A.CA/1);
offset1 = $boundary_4_A - {86:A.CA/1}.xyz http://A.CA/1%7D.xyz;
error message:
script ERROR: draw object not defined: boundary_4_A
line 2 command 2 of file null:
offset1 = $ boundary_4_A - { 86 and *:A and *.ca
and */1 } . xyz
observations:
plane 'boundary_4_A' is visible;
plane 'boundary_4_A' can be switched off
URL:
http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1dehJMOLVERSION=11.6.RC8
No other problems detected (yet).
Test System
Java : 1.4.2_17
OS : Linux, OpenSuSE 10.2
Browser: Firefox 2.0.0.16
Regards,
Rolf
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Re: [Jmol-users] Testing 11.6.RC8
fixed and, sure, why not... getProperty pointGroupInfo print getProperty(pointgroupInfo.principalAxis) etc. On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote: Bob, write pointgroup draw gives the following error (for 11.6.RC8): Exception in thread QueueThread0 java.lang.NullPointerException at org.jmol.symmetry.PointGroup.getInfo(Unknown Source) at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source) at org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown Source) at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Eval.write(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)... Unrelated question: is there (or will there be) a getProperty command to retrieve information about symmetry elements? (I can grab them using show pointgroup, but getProperty would be nice). Dean - 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
Re: [Jmol-users] getting info from Jmol applet
Jeff,
The mistake here is timing. You cannot query an applet while the page is
loading (prior to /body and completion of applet initialization). In some
cases this crashes browsers; in others it just causes an error; in others it
permanently disables the applet communication.
The simple fix is to place the JavaScript code in a function defined in the
head block, and then add a JavaScript call to that function in the
start-up Jmol script, after the file is loaded. No need for form tags.
head
script type=text/javascript
function appletReady() {
var atomSetArray = jmolGetPropertyAsArray(atomInfo,atomno5);
alert (atomSetArray[0].info);
}
/script
/head
body
script type=text/javascript
jmolInitialize(jmol);
jmolApplet(500, load ../Jmol/jmol/models/1bf3.pdb;javascript
appletReady());
/script
/body
On Wed, Aug 20, 2008 at 2:29 PM, Jeff Hansen [EMAIL PROTECTED] wrote:
I'm having difficulty getting info from the Jmol applet. Here is my
code (basically copied from a post from Bob Hanson):
body
form
script type=text/javascript
jmolInitialize(jmol);
jmolApplet(500, load ../Jmol/jmol/models/1bf3.pdb);
var atomSet =
document
.getElementById(jmolApplet0).getProperty(atomInfo,atomno5);
alert (atomSet.get(0).get(info));
/script
/form
/body
This code displays the applet with the molecule loaded but does not
display the alert box at all. I must admit I am relatively new to
javascript. Any help getting started with this would be most
appreciated. Ultimately I am looking to get other types of info out
such as the energy of a molecule from a spartan file. Thought I would
start with something simple that has been done, but I'm having some
trouble with it.
Thanks in advance for any help you can give.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
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Re: [Jmol-users] a related popup window question....
ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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
Re: [Jmol-users] a related popup window question....
There's your answer. Out of memory. How big are these resizes? height/width? I wonder if a settable maximumWindowSize option might be in order here. Bob On Wed, Aug 20, 2008 at 3:00 PM, Thomas Stout [EMAIL PROTECTED]wrote: Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: Java heap space at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89) I see this behavior on both both WinXP and linux (CentOS) and both a pretty hefty machines (graphics and RAM-wise) -Tom On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote: ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 - 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
Re: [Jmol-users] Sync to separate window?
On Wed, Aug 20, 2008 at 11:53 AM, Eric Martz [EMAIL PROTECTED]wrote:
Dear Bob,
In Proteopedia.Org, Jaim Prilusky has implemented a popup button
under each Jmol that opens a new window containing only a Jmol. This
window can be made large and resized at will; resizing has been more
challenging to accomplish for Jmol within its Proteopedia structure
within MediaWiki.
Now we want scripts sent to the Jmol in the main Proteopedia page to
also be obeyed by the separate Jmol in the separate child window. How
best to do this?
I have tried sync * all. It works between two Jmols on the same
page (currently 11.5.51 in Proteopedia; update is planned soon), but
not to the Jmol in the child window.
sync * specifically syncs applets on the driver's page. Anything else would
be a nightmare in general. If you want to do it programmatically, I suggest
having your JavaScript get the property appletInfo.registry and from that
discern the FULL name of that popup applet. Give the popup applet a name
extension that the referring page can identify -- a random set of digits,
perhaps. You don't want to send this to the wrong popup in case the user has
two Protopedia pages up (which is a real possibility, of course).
Then use that FULL name in the sync. It looks something like this:
jmolAppletXXX__2923827392370230236823__
By giving that EXACT id, Jmol will send the message to that applet.
Alternatively, after the popup opens, an elegant way to do this would be to
have the created applet send back to the calling applet its id:
jmolApplet(.,'[state scripts here];myID =
getProperty(appletInfo,fullName);jsCall = opener.jmolScript(\'popupID =
\\ + myID + \\ \'); javaScript @jsCall'
I think that's the right number of escapes there! Text surrounded by single
quote needs \' inside...jmol command jsCall = ... + myID + ... needs to
end up in Jmol as
jsCall = opener.jmolScript('popupID = \ + myID + \ ');
so in the original we have to escape \ or it will be read as \ and change
to by the initial javaScript processing. Gotta love it.
The opener.jmolScript is a simple way to direct the message to the applet
on the page that opened the popup without knowing its applet id.
Bob
If we can get this to work, when there are more than one Jmol on the
initial page, we will want only one to send to the child window Jmol,
and none of the other Jmols on the page to receive. I suppose that
sync off may accomplish that.
(Yes, Bob, testing sync on 11.6.RCn is on my list for later today, I hope).
Thanks, -Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz
Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
Biochem 3D Education Resources http://MolviZ.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://workshops.proteinexplorer.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
http://bioinformatics.org/mailman/listinfo/molvis-list
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Re: [Jmol-users] Testing 11.6.RC8
found it -- Nico, let's get RC10 out so Dean can test it. Bob On Thu, Aug 21, 2008 at 11:21 PM, Dean Johnston [EMAIL PROTECTED]wrote: This (the write pointgroup draw command) still isn't working for me (RC9 and RC10). Not sure what is going on. Dean On Wed, Aug 20, 2008 at 2:18 AM, Robert Hanson [EMAIL PROTECTED] wrote: fixed and, sure, why not... getProperty pointGroupInfo print getProperty(pointgroupInfo.principalAxis) etc. On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote: Bob, write pointgroup draw gives the following error (for 11.6.RC8): Exception in thread QueueThread0 java.lang.NullPointerException at org.jmol.symmetry.PointGroup.getInfo(Unknown Source) at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source) at org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown Source) at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Eval.write(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)... Unrelated question: is there (or will there be) a getProperty command to retrieve information about symmetry elements? (I can grab them using show pointgroup, but getProperty would be nice). Dean - 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 - 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
Re: [Jmol-users] testing needed (point groups)
thanks -- RC9 is broken for pointgroups. (It can crash jmol when drawing) On Thu, Aug 21, 2008 at 11:22 AM, Xavier Prat-Resina [EMAIL PROTECTED]wrote: Bob, I finally had time to test the point groups in jmol. I used a set of structures included in Patchkovskii's code. They are not real molecules and atoms are quite close so I had to decrease the tolerance. As a result of that (I guess) some of the structures freeze jmol. I set up a web page where I tested that http://144.92.39.89/xavier/symmetry/index.php Would you mind to take a look at it? Thanks a lot!! This is the list of problems: C4h says it is C4 C7 says it is C1 C7h says it is Cs C7v says it is C1 (but finds all the planes) C8h doesnt find all elements for C8h Ci says it is C1 Cinfv doesnt find all elements for Cinfv D2 doesnt draw the right elements (D4?) D2d jmol freezes D2h says it is D2d D3 says it is C3 D3d jmol freezes D3h doesnt find all elements for D3h D4 says it is C4 D4d jmol freezes D4h says it is C4v D5 says it is C5 D5d jmol freezes D5h says it is C5v D6 says it is C6 D6h doesnt find all elements for D6h D6d jmol freezes D7 says it is C1 D7d says it is Ci D7h says it is C2h D8 says it is C8 D8d says it is C8v D8h says it is C8v Dinfh doesnt find all elements for Dinfh Ih says it is D5d Xavier (I'm included in the list of problems :) ) On Wed, Aug 13, 2008 at 6:48 AM, Bob Hanson [EMAIL PROTECTED] wrote: A chance to contribute! Nico has just released Jmol 11.6.RC6. This release needs serious testings in the next few days. Please check this in any way you can and get back to us. Refreshing -- Some core functionality was tweaked. Specifically, I reduced the number of times Jmol does refreshes. My first attempt at this (Jmol 11.5.RC5) was not successful, but I'm hoping 11.5.RC6 is better. These changes should significantly reduce the number of times Jmol tries to refresh, leading to smoother scripting. But it's also possible that I have removed a few too many of these. So the thing to look out for is odd refreshing behavior. Synchronization --- Eric Martz, I'm hoping you can check out synchronization issues, since you seem to be working on that. The changes I made should not affect synchronization, but they may. Documentation - Up to date? Working ok? Does the applet console Help menu item work? (I know there's a problem with the top item. Anybody care to fix that? What I'd like there is a Search item.) Point Groups Are we done? Images -- This is really incredible. Put an image anywhere using SET ECHO IMAGE, in 2D or 3D. Scale it anyway you want. Note that set fontScaling works the same as for 3D echo text as for echo images. Scaling can be accomplished right now using a not-so-obvious scaling factor in the FONT ECHO command. I would really appreciate someone doing some testing of this. Suggestions? Do we still need alpha translucency? -- That is, so that the applet can appear in a layer in front of an image? If so, please let me know how to do that. I think it's an easy addition. General --- So just a simple yes, this works on my site would be helpful. 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 -- Xavier Prat-Resina Research Associate Journal of Chemical Education and University of Wisconsin 209 N. Brooks St. Madison, WI 53715-1116 Tel: 608 8901702 // Fax: 608 2627145 e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat http://x.prat.resina.googlepages.com - 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
Re: [Jmol-users] Jmol-users Digest, Vol 27, Issue 24
oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands
include jmolEvaluate (my favorite), and jmolGetPropertyAsArray() or
jmolGetPropertyAsString()
On Thu, Aug 21, 2008 at 12:41 AM, Jeff Hansen [EMAIL PROTECTED] wrote:
Thanks Bob. That certainly works. So basically anytime I want to pull out
some info from the molecule file I need to do that in the jmolApplet
command. Or is there a way to do that prior to loading the molecule into
Jmol? I'm looking ahead to situations where I'll want to dynamically load a
structure into an applet, grab some data out of it and do some stuff with
it. Now I'm wondering how I'll be able to update other parts of the web
page based on this data if the applet hasn't finished loading the file yet.
Is there a way to find out what properties are accessible from the applet?
I'm looking at getting a protein's sequence into an array or a small
molecule's energy. If these aren't directly accessible can the entire file
be brought into a string variable and then dig the info out of it?
Thanks again.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 20, 2008, at 3:43 PM, [EMAIL PROTECTED]:
Message: 4
Date: Wed, 20 Aug 2008 14:42:00 -0500
From: Robert Hanson [EMAIL PROTECTED]
Subject: Re: [Jmol-users] getting info from Jmol applet
To: jmol-users@lists.sourceforge.net
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1
Jeff,
The mistake here is timing. You cannot query an applet while the page is
loading (prior to /body and completion of applet initialization). In some
cases this crashes browsers; in others it just causes an error; in others
it
permanently disables the applet communication.
The simple fix is to place the JavaScript code in a function defined in the
head block, and then add a JavaScript call to that function in the
start-up Jmol script, after the file is loaded. No need for form tags.
head
script type=text/javascript
function appletReady() {
var atomSetArray = jmolGetPropertyAsArray(atomInfo,atomno5);
alert (atomSetArray[0].info);
}
/script
/head
body
script type=text/javascript
jmolInitialize(jmol);
jmolApplet(500, load ../Jmol/jmol/models/1bf3.pdb;javascript
appletReady());
/script
/body
-
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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
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Re: [Jmol-users] a related popup window question....
You have total control over the popup characteristics -- it's your page! The only reason it's resizing is that you have percentages listed in the jmolApplet command, I think. Bob On Wed, Aug 20, 2008 at 4:30 PM, Thomas Stout [EMAIL PROTECTED]wrote: Yes: I've seen the users make the windows pretty big (especially when they hit the maximize window button in the upper right of the browser window -- the window then becomes as large as the monitor some of those are in the 2000 pixels dimensions now). I'd be interested in two possible solutions: i) be able to stipulate the size of the popup Applet and have it be a fixed size, or ii) your idea, to have an upper limit on how big it can get. Both have advantages: the fixed size popup Applet lets me have more control over layout and design, but the upper size limit is certainly much more flexible for the end user. -Tom On Wed, Aug 20, 2008 at 2:22 PM, Robert Hanson [EMAIL PROTECTED] wrote: There's your answer. Out of memory. How big are these resizes? height/width? I wonder if a settable maximumWindowSize option might be in order here. Bob On Wed, Aug 20, 2008 at 3:00 PM, Thomas Stout [EMAIL PROTECTED]wrote: Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: Java heap space at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89) I see this behavior on both both WinXP and linux (CentOS) and both a pretty hefty machines (graphics and RAM-wise) -Tom On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote: ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED] wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 - 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 - This SF.Net email is sponsored by the Moblin
Re: [Jmol-users] script in string
I guess I don't understand the context here. What is the addJmol command? Why is it being created as a script tag and not just as script addJmol() // whatever that may be /script Bob On Fri, Aug 22, 2008 at 2:22 PM, Matthew Zwier [EMAIL PROTECTED] wrote: If it's in the HTML page itself, wrapping the code in a CDATA section should help: script//![CDATA[ var loadJmol = script type='text/javascript'addJmol(molecule, divInc);/script; //]]/script Not sure on the compatibility factor for older browsers, but anything recent should digest it just fine. MZ On Fri, Aug 22, 2008 at 12:38 AM, Dean Johnston [EMAIL PROTECTED] wrote: I'm not sure of the context, but this should be OK if it's part of an external javascript file. If it's within an HTML page, the browser is interpreting the /script in your string as the closing tag of your script, thereby rendering everything that follows as HTML. Dean On Thu, Aug 21, 2008 at 11:20 PM, Jeff Hansen [EMAIL PROTECTED] wrote: Can anyone help me figure out what is wrong with this line of code? var loadJmol = script type='text/javascript'addJmol(molecule, divInc);/script; What is happening is the /script is not being recognized or something and everything from the closing quotation mark on, including the next several lines until the next /script, is being displayed as text on the web page. *** 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=/ ___ 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
Re: [Jmol-users] set picking spin
That's fixed. Thanks. Also, now you can still make double-click measurements while you have set picking spin The double click will stop any current spinning that might be happening. Bob On Fri, Aug 22, 2008 at 12:21 PM, rspinney [EMAIL PROTECTED] wrote: Set picking SPIN seems to be broken in 11.6-RC9 Rick Spinney - 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
Re: [Jmol-users] Jmol and MediaWiki Problem (jmolinitialize)
Steve, right -- it's simply a matter of the wiki not finding the path to Jmol.js. Nico or Angel can help you get that going. Bob Hanson On Fri, Aug 22, 2008 at 4:42 PM, Stephen Weppner [EMAIL PROTECTED]wrote: Hi, I have installed the JMol Mediawiki extension found at: http://wiki.jmol.org:81/index.php/MediaWiki but it is not working, the Wiki says it is installed: http://academics.eckerd.edu/facultywiki/index.php/Special:Version but it does not work with even a simple example http://academics.eckerd.edu/facultywiki/index.php/Jmol_Test The error console (firefox 3.01) gives me the following errors: -- Error: jmolInitialize is not defined Source File: http://academics.eckerd.edu/facultywiki/index.php/Jmol_Test Line: 60 Error: jmolCheckBrowser is not defined Source File: http://academics.eckerd.edu/facultywiki/index.php/Jmol_Test Line: 83 Error: jmolMenu is not defined Source File: http://academics.eckerd.edu/facultywiki/index.php/Jmol_Test Line: 85 Error: jmolButton is not defined Source File: http://academics.eckerd.edu/facultywiki/index.php/Jmol_Test Line: 88 -- like it is not able to load the Java script files?? I have made Jmol work embedded in a non-wiki web page and I have other applets running on this Wiki. So I know the Wiki can handle applets and the Jmol installation is OK. Any help would be appreciated... Cheers, Steve -- Stephen P. Weppner Associate Professor of Physics Natural Sciences Eckerd College 4200 54th Ave. S. St. Petersburg, FL 33711 727 864 8976 727 864 8382 (FAX) - 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
Re: [Jmol-users] unexpected image scaling
I cannot reproduce this problem. Are you sure you have not already defined mybackground PRIOR to the set fontscaling false command? set fontscaling only affects echos created after its invocation. On Mon, Aug 25, 2008 at 5:34 PM, Thomas Stout [EMAIL PROTECTED]wrote: Interesting. I have found today that set antialiasDisplay ON forces scaling of images even when set fontscaling false is set. Expected or no? I was surprised it took me a while to narrow it down to this one setting -Tom Here are some commands for testing: set antialiasDisplay ON; #ON results in scaling the star, OFF gives no scaling set echo none; set fontscaling false; set echo depth 0; set echo mybackground 50% 50%; set echo mybackground image star2.gif; PS -- This is all prior to loading a molecule. I am having the Applet come up with a logo and then urging the user to pick a structure for display - 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
Re: [Jmol-users] Jmol-users Digest, getting data from Jmol
The properties supported do depend upon the file type. What file type are you working with? Generally you can check this by using getproperty auxiliaryinfo which is a general holder for all sorts of molecular info. Bob On Mon, Aug 25, 2008 at 7:50 AM, Jeff Hansen [EMAIL PROTECTED] wrote: Bob, I've been looking through the documentation and trying to figure this out. I'm not having much success. I don't think I quite understand the syntax for doing this. I also don't understand what properties are available and where to find them and which file formats are supported. I'm not finding the help I need in the documentation or at least I'm not understanding well enough the help that is there. So lets say that I wanted to have a file with several related models and find the energy of the molecule in each model (actually that is what I want to do). I'm not looking for the code to do this, just another pointer in the right direction to move me in the right direction. Sorry if I'm too much of a bother. Robert Hanson Fri, 22 Aug 2008 07:22:24 -0700 oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands include jmolEvaluate (my favorite), and jmolGetPropertyAsArray() or jmolGetPropertyAsString() *** 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=/ ___ 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
Re: [Jmol-users] unexpected image scaling
yes, absolutely you must use the latest version if you are using any RC at all. On Tue, Aug 26, 2008 at 3:03 PM, Thomas Stout [EMAIL PROTECTED]wrote: I have a stripped down Jmol implementation that I am using for debugging. It contains nothing but the applet: !DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN html lang=en head meta http-equiv=Content-Type content=text/html; charset=utf-8 / meta http-equiv=content-language content=English / titleTesting Jmol/title script type=text/javascript src=Jmol.js/script script type=text/javascript src=new.js /script /head body script type=text/javascript mayscript=true jmolInitialize(./); jmolSetAppletColor(black); jmolApplet(512, script testecho.spt;, 0); /script br /body /html And the script testecho.spt contains the following: set antialiasdisplay ON; set echo none; set frank off; set fontscaling false; set echo depth 0; set echo mybackground 43% 83%; set echo mybackground image star2.gif; I am still using the applet of version 11.6RC7 -- perhaps I should download and test whatever the most current RC version is today. -Tom On Tue, Aug 26, 2008 at 8:56 AM, Robert Hanson [EMAIL PROTECTED] wrote: I cannot reproduce this problem. Are you sure you have not already defined mybackground PRIOR to the set fontscaling false command? set fontscaling only affects echos created after its invocation. On Mon, Aug 25, 2008 at 5:34 PM, Thomas Stout [EMAIL PROTECTED]wrote: Interesting. I have found today that set antialiasDisplay ON forces scaling of images even when set fontscaling false is set. Expected or no? I was surprised it took me a while to narrow it down to this one setting -Tom Here are some commands for testing: set antialiasDisplay ON; #ON results in scaling the star, OFF gives no scaling set echo none; set fontscaling false; set echo depth 0; set echo mybackground 50% 50%; set echo mybackground image star2.gif; PS -- This is all prior to loading a molecule. I am having the Applet come up with a logo and then urging the user to pick a structure for display - 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 - 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
Re: [Jmol-users] changing atom coordinates with {selected}.y
thanks for finding that, Angel. It's fixed for 11.6.RC11. Those files should
be available as
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip shortly
Bob
On Tue, Aug 26, 2008 at 2:25 PM, Angel Herráez [EMAIL PROTECTED] wrote:
Hello all
I had this script for getting a projection of certain (dummy) atoms onto
the
XZ plane:
{selected}.y=0
this works up to 11.5.41 but gives an error in 11.6.RC4 and RC10
Command expected
Is this intentional, and how can I achieve the result?
Thanks
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Re: [Jmol-users] Drawing individual symmetry elements
It's a bug I need to fix. Don't go back to RC9 -- that's broken for drawing pointgroups the second time. It's a problem with the caching I added in RC10. Jmol doesn't recalculate the point group or the draw set if it finds suitable ones already present. But I forgot to check for that axis number. Your workaround is fine. This is fixed for RC11. On Sun, Aug 24, 2008 at 10:18 PM, Dean Johnston [EMAIL PROTECTED]wrote: Dear All (but mostly Bob) - (Sorry about the duplicate message regarding echo - I thought my mail program never sent it out...) I'm having problems drawing individual symmetry elements (Jmol 11.6.RC11) using the format draw pointgroup c2 1 It correctly draws the first element, but then won't draw any other c2 axes. For example: draw delete; draw pointgroup c2 1; draw pointgroup c2 2 --- only draws one c2 axis draw delete; draw pointgroup c2 1; draw delete; draw pointgroup c2 2 --- draws the same c2 axis both times but draw delete; draw pointgroup c2 1; draw delete; draw pointgroup; draw delete; draw pointgroup c2 2 --- correct draws two different c2 axes I think this is recent, because the example on Bob's new pages (11.6.RC9) works just fine, but the same molecule won't work with 11.6.RC11. Can anyone else reproduce this? Dean - 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
Re: [Jmol-users] Testing 11.6.RC8
Dean, that fix is checked in -- problem for any case where there is no principal axis. On Fri, Aug 22, 2008 at 9:52 PM, Dean Johnston [EMAIL PROTECTED]wrote: OK, it's working much better, but a few obscure errors with my test set (this is with both 11.6.RC10-applet, and 11.6.RC11_dev-application). *D2* (twistane): correctly identifies point group, but crashes on write pointgroup draw *D2h* (N2O4): correctly identifies point group, but crashes on write pointgroup draw *D2h* (p-dibromobenzene): correctly identifies point group, but crashes on write pointgroup draw It must be a point group specific thing, because a lower symmetry (C2) version of my twistane structure works just fine. BTW, I love the getProperty pointGroupInfo. Thanks Bob! Dean On Fri, Aug 22, 2008 at 10:01 AM, Robert Hanson [EMAIL PROTECTED]wrote: found it -- Nico, let's get RC10 out so Dean can test it. Bob On Thu, Aug 21, 2008 at 11:21 PM, Dean Johnston [EMAIL PROTECTED]wrote: This (the write pointgroup draw command) still isn't working for me (RC9 and RC10). Not sure what is going on. Dean On Wed, Aug 20, 2008 at 2:18 AM, Robert Hanson [EMAIL PROTECTED]wrote: fixed and, sure, why not... getProperty pointGroupInfo print getProperty(pointgroupInfo.principalAxis) etc. On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote: Bob, write pointgroup draw gives the following error (for 11.6.RC8): Exception in thread QueueThread0 java.lang.NullPointerException at org.jmol.symmetry.PointGroup.getInfo(Unknown Source) at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source) at org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown Source) at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Eval.write(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)... Unrelated question: is there (or will there be) a getProperty command to retrieve information about symmetry elements? (I can grab them using show pointgroup, but getProperty would be nice). Dean - 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 -- 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
Re: [Jmol-users] problem in firefox
Right -- name attribute is quite problematical. In some browsers id is
accessible as name, but that's not acceptable. And in some browser
versions the name of an element in a form is under the form name rather than
the document.
Always use id and, as Dean points out, then access it only using
document.getElementById()
Most of us create a scrap of JavaScript that we put in all our pages that
provides us these services.
One I use is http://www.stolaf.edu/depts/chemistry/gca/divs.js
Bob
On Wed, Aug 27, 2008 at 10:19 AM, Dean Johnston [EMAIL PROTECTED]wrote:
Jeff,
No apologies needed. Giving an id to a div does not create a
Javascript object automatically (at least in Firefox). You will have to use
something like:
var myText = document.getElementById('jmolText');
and then say
myText.value = dump(_dataInfo);
It's interesting that it *does* work in Safari.
Dean
On Wed, Aug 27, 2008 at 11:05 AM, Jeff Hansen [EMAIL PROTECTED] wrote:
My apologies. This is really more of a javascript/html question but
it is on a Jmol project I am working on. Could someone explain to me
what is the problem with the following code? The appletReady()
function works just fine in Safari and the page validates as HTML 4.01
strict, but the appletReady() function doesn't work in Firefox.
Firebug reports an error and says jmolText is not defined.
function appletReady() {
var _dataInfo = jmolGetPropertyAsArray(auxiliaryInfo);
jmolText.value = dump(_dataInfo);
}
...
div id=textDiv
form action=
ptextarea cols=50 rows=50 id='jmolText'/textarea/p
/form
/div
The page is at http://web.mac.com/jhansen4/Jmol/NewJmolDiv.html if
that will help.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Echo with sub and sup tags
that's what I needed. Fixed. Vertical was off as well. On Wed, Aug 27, 2008 at 10:56 AM, Angel Herráez [EMAIL PROTECTED]wrote: On 27 Aug 2008 at 10:57, Dean Johnston wrote: OK, here is the state for ammonia, with a label of Point Group = Csub3v/sub at the bottom left. Without the tags the spacing is normal. Just typing it in the console of 11.6.RC10 app it looks Ok to me Maybe some combination with other scripts are doing it? - 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
Re: [Jmol-users] unexpected image scaling
Thanks. [States as attachments would be better] That's fixed for 11.6.RC11. On Tue, Aug 26, 2008 at 3:03 PM, Thomas Stout [EMAIL PROTECTED]wrote: I have a stripped down Jmol implementation that I am using for debugging. It contains nothing but the applet: !DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN html lang=en head meta http-equiv=Content-Type content=text/html; charset=utf-8 / meta http-equiv=content-language content=English / titleTesting Jmol/title script type=text/javascript src=Jmol.js/script script type=text/javascript src=new.js /script /head body script type=text/javascript mayscript=true jmolInitialize(./); jmolSetAppletColor(black); jmolApplet(512, script testecho.spt;, 0); /script br /body /html And the script testecho.spt contains the following: set antialiasdisplay ON; set echo none; set frank off; set fontscaling false; set echo depth 0; set echo mybackground 43% 83%; set echo mybackground image star2.gif; I am still using the applet of version 11.6RC7 -- perhaps I should download and test whatever the most current RC version is today. -Tom On Tue, Aug 26, 2008 at 8:56 AM, Robert Hanson [EMAIL PROTECTED] wrote: I cannot reproduce this problem. Are you sure you have not already defined mybackground PRIOR to the set fontscaling false command? set fontscaling only affects echos created after its invocation. On Mon, Aug 25, 2008 at 5:34 PM, Thomas Stout [EMAIL PROTECTED]wrote: Interesting. I have found today that set antialiasDisplay ON forces scaling of images even when set fontscaling false is set. Expected or no? I was surprised it took me a while to narrow it down to this one setting -Tom Here are some commands for testing: set antialiasDisplay ON; #ON results in scaling the star, OFF gives no scaling set echo none; set fontscaling false; set echo depth 0; set echo mybackground 50% 50%; set echo mybackground image star2.gif; PS -- This is all prior to loading a molecule. I am having the Applet come up with a logo and then urging the user to pick a structure for display - 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 - 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
Re: [Jmol-users] problem in firefox
I'm working towards my own at this point and I'm afraid looking at yours will just prevent my learning how to do it myself. Shame! NEVER say that! The way to learn this is by adapting anything you can find. That's the great thing about JavaScript. Learn how these code fragments work by testing it in your own application. You will learn lots. 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
Re: [Jmol-users] Hack to deal with Firefox 3 new behaviour regarding Files Input
yes, thanks, Paul, that's right. It's an interesting compromise. I had to
abandon the type=file in Jmol Protein Explorer for FireFox3 because of that.
If you can't get the actual path to the file, which I think is actually a
good security feature, you can't later reproduce the state, unless you want
to load the entire file as a DATA string. (Which may not be such a bad idea,
I guess.)
On 8/27/08, Paul Pillot [EMAIL PROTECTED] wrote:
This one might also be regarded as off topic, but as some you might
be stuck with the same problem, I thought it might be worth to share.
The issue is that starting from firefox 3.0, when using an input file
element in a form, you can't access to the full path of the file
chosen by the user, even if it's fully displayed in the form. e.g. : /
user/paul/3ert.pdb. From javascript, the file.value string would give
you only the file name (eg : 3ert.pdb).
I didn't find any way of getting the full path back. However one can
now access to the whole file content directly from javascript, using
the getAsText method. Coupled with the jmolLoadInline function, it
allows to load any local file into the Jmol applet. For example I
successfully used the following code :
input type=file id=loadname size=20 onchange=jmolLoadInline
(document.getElementById('loadname').files.item(0).getAsText(''));
return false;
It worked smoothly with any plain text file. It didn't work with a
gzipped file, giving back a unrecognized file format for file
string error message.
Paul
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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
My experience is the appendChild is overkill for what you generally need.
Just make sure you have
jmolSetDocument(0)
and then the applet you get from
var x = jmolApplet(.)
can be inserted into any div. HOWEVER, as I recall there are problems with
some browsers not being able to communicate properly with applets created
after the page is loaded. I could be wrong about that, but I think Opera is
the offender.
Here's a snippet from
http://www.stolaf.edu/people/hansonr/sudoku/sudoku3d.js that loads an applet
into a div after page load for
http://www.stolaf.edu/people/hansonr/sudoku/to show a 3D version of
the logical pathways of a Sudoku puzzle.
function createAppletInline(smodel,script){
if(isjmolinitialized !isjmolreset !isliveconnecterror){
isliveconnecterror=1
document.getElementById(jmolApplet0).script(script)
isliveconnecterror=0 //won't get here if we have a LiveConnect
error (Opera)
return
}
if(!isjmolinitialized)jmolInitialize(.)
isjmolinitialized=1
isjmolreset=0
jmolSetDocument(0)
var s=jmolApplet(450,set perspectivedepth OFF;+script,0)
s=addParam(s,loadInline,smodel.replace(/\n/g,|))
s=addParam(s,messageCallback,clickModel)
document.getElementById(apphere).innerHTML=s
}
were the addParam function inserts a parameter code into the HTML before it
is sent out. I'm pretty sure Opera doesn't allow this.
function addParam(sappcode,sname,svalue){
return sappcode.replace(/\param/,param name=\+sname+\
value=\+svalue+\ /\nparam)
}
Make sure you use () after any function call in JavaScript.
addParam
is the function contents -- as a string, as above
addParam()
executes the function.
On 8/27/08, Jeff Hansen [EMAIL PROTECTED] wrote:
Believe me I've been doing plenty of that, but I also have been finding
trial and error to be very instructive too. I did take a look at your
divs.js file. I don't yet understand all of it. I tried your divFind and
divWrite functions and I'm pretty sure I'm understanding what they do.
Unfortunately the divWrite doesn't do what I want. I want to put a Jmol
applet into the div and this function appears to only write text into a div.
I tried divWrite(jmolID, newJmol) and divWrite(jmolID, eval(newJmol) where
jmolID is a variable that holds the div's id and newJmol is a Jmol applet
object. Unfortunately both off these do the same thing which is to write
the function used to create the Jmol applet object into the into the div as
text.
I've also tried the following code:
document.getElementById(jmolID).appendChild(newJmol);
which produces the following error message in FireBug:
uncaught exception: Node cannot be inserted at the specified point in the
hierarchy (NS_ERROR_DOM_HIERARCHY_REQUEST_ERR)
document.getElementById(jmolID).update(newJmol);
gives the error: document.getElementById(jmolID).update is not a function
I've tried several variations. I got it to work once using:
newDiv.update(jmolApplet(400, eval(_jmolApplet.loadString))); where newDiv
was a reference to a div element, but this only worked in Safari and not
Firefox.
Unfortunately, everywhere I've read about adding something to a div element
the something being added is text. I can't find anywhere that gives an
example off adding some other kind of object.
Perhaps I should give it up. I thought it would be possible to create a
Jmol applet object and add it to the web page. Then I would be able to
include methods in the Jmol applet object constructor to change jmol
parameters and such. Obviously there are other ways to do that, but this
just seems an attractive way to me for some reason.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 27, 2008, at 2:14 PM, Robert Hanson wrote:
I'm working towards my own at this point and I'm afraid looking at yours
will just prevent my learning how to do it myself.
Shame! NEVER say that! The way to learn this is by adapting anything you
can find. That's the great thing about JavaScript. Learn how these code
fragments work by testing it in your own application. You will learn lots.
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
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Re: [Jmol-users] Testing 11.6.RC8
nah. It's fixed. On Thu, Aug 28, 2008 at 3:36 PM, Dean Johnston [EMAIL PROTECTED]wrote: Bob, Jmol still seems to crash with write pointgroup draw on these three examples (11.6.12_dev application): twistane, N2O4 and p-dibromobenzene. Other examples of D2h symmetry also give the same problem. Dean On Wed, Aug 27, 2008 at 10:41 AM, Robert Hanson [EMAIL PROTECTED]wrote: Dean, that fix is checked in -- problem for any case where there is no principal axis. On Fri, Aug 22, 2008 at 9:52 PM, Dean Johnston [EMAIL PROTECTED]wrote: OK, it's working much better, but a few obscure errors with my test set (this is with both 11.6.RC10-applet, and 11.6.RC11_dev-application). *D2* (twistane): correctly identifies point group, but crashes on write pointgroup draw *D2h* (N2O4): correctly identifies point group, but crashes on write pointgroup draw *D2h* (p-dibromobenzene): correctly identifies point group, but crashes on write pointgroup draw It must be a point group specific thing, because a lower symmetry (C2) version of my twistane structure works just fine. BTW, I love the getProperty pointGroupInfo. Thanks Bob! Dean On Fri, Aug 22, 2008 at 10:01 AM, Robert Hanson [EMAIL PROTECTED]wrote: found it -- Nico, let's get RC10 out so Dean can test it. Bob On Thu, Aug 21, 2008 at 11:21 PM, Dean Johnston [EMAIL PROTECTED]wrote: This (the write pointgroup draw command) still isn't working for me (RC9 and RC10). Not sure what is going on. Dean On Wed, Aug 20, 2008 at 2:18 AM, Robert Hanson [EMAIL PROTECTED]wrote: fixed and, sure, why not... getProperty pointGroupInfo print getProperty(pointgroupInfo.principalAxis) etc. On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED] wrote: Bob, write pointgroup draw gives the following error (for 11.6.RC8): Exception in thread QueueThread0 java.lang.NullPointerException at org.jmol.symmetry.PointGroup.getInfo(Unknown Source) at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source) at org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown Source) at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source) at org.jmol.viewer.Eval.write(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)... Unrelated question: is there (or will there be) a getPropertycommand to retrieve information about symmetry elements? (I can grab them using show pointgroup, but getProperty would be nice). Dean - 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 -- 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 - 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
Re: [Jmol-users] problem in firefox
remove the \ around the load command. It's just:
this.loadString = load ../Jmol/jmol/Models/ + molecule;
On Thu, Aug 28, 2008 at 2:59 PM, Jeff Hansen [EMAIL PROTECTED] wrote:
Thanks for your help Angel. This is getting me very nearly there. To
recap. I am trying to create a web page in which a div element is
created and a new Jmol applet is displayed in that new div. Your
suggestion to take a look at the Jmol homepage was very helpful. That
is essentially what I needed to do. Based on that I came up with the
following code. It creates the new div and puts a Jmol applet in it.
However, it does not load the molecule file into the the applet. The
message bar at the bottom of the window shows the following error
message: script compiler ERROR: command expectedload ../
Jmol/jmol/Models/benzene.smol;
Additionally, the alert(result1) (see code below) displays undefined
in the alert box and alert(result2) displays a blank alert box. So
I'm wondering what is going on with that.
Here is the code. molecule refers to a structure filename. Thanks to
Bob for the divFind and divWrite functions.
function divFind(name,issilent){
var d=document.getElementById(name);
// if(!d!issilentdebugPrint)debugPrint(couldn't find +name,1)
return d
}
function divWrite(name,what){
result1 = jmolGetStatus(scriptStatus);
alert(result1);
var d=divFind(name);
if(!d)return 0;
try{d.innerHTML=what}catch(error){alert(error)};
result2 = jmolGetStatus(scriptStatus,divInc);
alert(result2);
return d;
}
function jmolObject(molecule, divID){
jmolSetDocument(false);
this.loadString = \load ../Jmol/jmol/Models/ + molecule + ; +
\;
alert(this.loadString);
divWrite(divID,jmolApplet(400, this.loadString,divInc));
}
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
newDiv.id = 'Div' + (++divInc);
document.body.appendChild(newDiv);
jmolObject(molecule, newDiv.id);
}
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 2:41 PM, Angel Herráez wrote:
Hi Jeff
Not sure after the flurry of messages if you have solved your problem.
On 27 Aug 2008 at 16:21, Jeff Hansen wrote:
Unfortunately both off these do the same thing which is to write the
function used to create the Jmol applet object into the into the
div as text.
That may be due, as Bob has pointed out, to the need to use
jmolSetDocument(0)
being added is text. I can't find anywhere that gives an example
off adding some other kind of o
Have you checked out the method used in Jmol homepage? I'm not sure
if that's what you
are after. A similar solution is what I once called pop-in method
for inserting Jmol applet
upon user request. This is used in Jmol app Export to Web module
(Pop-in Template) and
in
I haven't tested those in Firefox 3 though (I'm yet sticking to 2.0
until my favorite add-ons
are updated).
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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] 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.
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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
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, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 5:41 PM, Angel Herráez wrote:
On 28 Aug 2008 at 15:59, Jeff Hansen wrote:
Additionally, the alert(result1) (see code below) displays undefined
in the alert box and alert(result2) displays a blank alert box. So
I'm wondering what is going on with that.
I would say that with result1 you are trying to read from the applet
before it has been
created, so it's not surprising thayt you get undefined.
As for result2, I'm not sure because I don't know the try/catch
command, but anyway it may
be too soon to have the applet ready. Javascript goes much faster
than loading Java +
Jmol.
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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] 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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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
Re: [Jmol-users] loading external files in the signed applet
Paul, check out this page to see how yours might be different.
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
It's using the signed applet and working just fine. Maybe has to be newer
than 11.6.RC8, but I don't think so. It should load files from the PDB using
load = and files from your hard drive using, for example:
load c:/temp/caffeine.xyz
Also, the Jmol Protein Explorer is using using the signed applet without a
hitch.
Bob
On Sat, Aug 30, 2008 at 7:32 AM, Paul Pillot
[EMAIL PROTECTED] wrote:
I am setting up a web page with the ability to load local files as
well as external files (for example, files coming from the pdb)
When I run the page locally, the applet is able to load any local
file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari):
java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms
eval ERROR: java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
line 1 command 1 of file null:
load http://www.rcsb.org/pdb/files/1gzx.pdb;
When the page is loaded from a webserver, the applet is unable to
load any local file, as well as remote files coming from elsewhere
than the webserver :
FileManager.openFile(''file:Users/paul/Desktop/
ac.pdb'') //''file:Users/paul/Desktop/ac.pdb''
FileManager opening
http://ordinateur-de-judith-ciosi.local/~paul/http://ordinateur-de-judith-ciosi.local/%7Epaul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
file ERROR:
http://ordinateur-de-judith-ciosi.local/~paul/http://ordinateur-de-judith-ciosi.local/%7Epaul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
java.io.FileNotFoundException: http://ordinateur-de-judith-
ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
openFile(''file:Users/paul/Desktop/ac.pdb''): 3 ms
eval ERROR: java.io.FileNotFoundException: http://ordinateur-de-
judith-ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
line 1 command 1 of file null:
load ''file:Users/paul/Desktop/ac.pdb''
I searched the mailing list archive for this issue and found a one
year old thread, which stated that this behavior is linked to the
inability to accept loading external files when the command is issued
by an unsigned javascript. A workaround is to reload the jmol applet
with the new file.
I would like to know if there is any other solution to make the
signed applet accept an external file ? I am also wondering at how
this problem has been dealt with in jmol protein explorer ?
Thanks in advance,
Paul
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Re: [Jmol-users] proposed change to Jmol.js
I'm working with them -- they are mostly waiting for 11.6 to be stable. Then they will go to that. Bob On Sat, Aug 30, 2008 at 7:29 AM, Angel Herráez [EMAIL PROTECTED] wrote: One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Assuming that they update their Jmol.js file!!! They are still using 10.2, and I think there have been requests for update already, to no avail - 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
Re: [Jmol-users] proposed change to Jmol.js
RCSB beta site is using Jmol 11.4. See for example: http://betastaging.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1O1I Current version there is 11.4.6, I think. On Sat, Aug 30, 2008 at 8:08 AM, Robert Hanson [EMAIL PROTECTED] wrote: I'm working with them -- they are mostly waiting for 11.6 to be stable. Then they will go to that. Bob On Sat, Aug 30, 2008 at 7:29 AM, Angel Herráez [EMAIL PROTECTED]wrote: One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Assuming that they update their Jmol.js file!!! They are still using 10.2, and I think there have been requests for update already, to no avail - 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 -- 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
Re: [Jmol-users] proposed change to Jmol.js
that's why I'm asking. Yes, I have tried this. We could make it only the applet from the server -- in other words not allow a new codebase -- if you think that is a major concern. How would you see the spoof working, Rolf? Bob On Sat, Aug 30, 2008 at 12:56 PM, [EMAIL PROTECTED] wrote: Quoting Robert Hanson [EMAIL PROTECTED]: One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Bob, have you tried that already? If this is allowed it would be exactly what should pe prevented within Jmol.js! It should only be allowed to load a different Jmol version from the same server! Otherwise anyone could use your/our service by 'URL Spoofing' to deliver an evil Jmol applet (or even a totally different applet) to the user!!! Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - 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
Re: [Jmol-users] New feature inquiry
Steve, there's probably not much sense in creating a generic bond-equivalent object like that. But you can do what you say yourself. For example, if a student is asked to click on a peptide bond, you know what bond it is, so you can create the link yourself and, like you say, make them transparent but still clickable. That you can do right now. But I see your point about lots of these. I don't see why we can't set up bond picking if that is what you are after. Wouldn't that be better? Bob On Sat, Aug 30, 2008 at 10:41 AM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: This is a preliminary inquiry about two feature requests. In my MolnIquiry site, I have imbedded line objects as bonds that can then be ?picked?; for example, students are asked to click on a peptide bond.). Creating these objects is a task, particularly if many are needed, and the lines can become visible if wireframe is turned off. Is it technically feasible that Jmol could: 1. generate a series of IDed objects between the connected atoms of an atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j? where j is incrementally increased with each line? 2. set the color of an object as ?transparent? (but still pickable). Does anyone see any other applications of these features? Thanks. Steve Dept of Biology and Environmental Science 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
Re: [Jmol-users] New feature inquiry
Jmol 11.6.RC12 now has
set atomPicking [default TRUE]
set bondPicking [default FALSE]
The report from the bond picking looks like this:
[bond,69 1 [GLY]37.C #263 -- [GLY]37.CA #262
1.5251089,21.2975,16.2235,6.473]
The First number is the bond ID. It is the number you would use to get the
bond properties:
print getProperty(BondInfo[69])
or
print getproperty(BondInfo, 69)
This number is also one more than the number you would use to specify that
bond using bond set notation (because in that case 0 is the first bond):
select [{68}]; color BOND white
The number 1 is the bond order; next are the identities of the two atoms and
the bond distance. The last three numbers are the coordinates of the center
of the bond.
That work for you, Steve?
Bob
On Sat, Aug 30, 2008 at 1:11 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Steve, there's probably not much sense in creating a generic
bond-equivalent object like that. But you can do what you say yourself. For
example, if a student is asked to click on a peptide bond, you know what
bond it is, so you can create the link yourself and, like you say, make them
transparent but still clickable. That you can do right now. But I see your
point about lots of these. I don't see why we can't set up bond picking if
that is what you are after. Wouldn't that be better?
Bob
On Sat, Aug 30, 2008 at 10:41 AM, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
This is a preliminary inquiry about two feature requests. In my
MolnIquiry site, I have imbedded line objects as bonds that can then be
?picked?; for example, students are asked to click on a peptide bond.).
Creating these objects is a task, particularly if many are needed, and the
lines can become visible if wireframe is turned off.
Is it technically feasible that Jmol could:
1. generate a series of IDed objects between the connected atoms of an
atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j?
where j is incrementally increased with each line?
2. set the color of an object as ?transparent? (but still pickable).
Does anyone see any other applications of these features?
Thanks.
Steve
Dept of Biology and Environmental Science
Marietta College
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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
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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] New feature inquiry
all three are independent: set atomPicking set bondPicking set drawPicking On Sat, Aug 30, 2008 at 2:49 PM, Angel Herráez [EMAIL PROTECTED] wrote: On 30 Aug 2008 at 14:20, Robert Hanson wrote: Jmol 11.6.RC12 now has set atomPicking [default TRUE] set bondPicking [default FALSE] Nice! and quick Are those 2 independently set, or are they alternative options? And, how does that combine with the different set picking variants? - 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
Re: [Jmol-users] The results of your email commands
Yes, this information comes back as a string in the pickCallback (second
parameter). The third parameter is an atom index:
0+ atom
-2 draw
-3 bond
Also, you can always check the most recent pick information using
var x = jmolEvaluate(_pickInfo)
or
var x = jmolEvaluate(_atomPicked)
You should be able to parse that as a JavaScript array directly:
var info = eval(jmolEvaluate(_pickInfo))
or from that second parameter, HOWEVER -- strings passed back to JavaScript
are Java strings, not JavaScript strings, so ALWAYS do
+ xxx
to turn them into JavaScript strings before you do anything with them. So in
a callback:
function myPickCallback(app, msg, atomIndex) {
var info = eval( + msg)
}
not just
function myPickCallback(app, msg, atomIndex) {
var info = eval(msg)
}
Bob
I've put sample JAR files up in
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.jar
(transferring now - takes a few minutes)
Bob
On Sat, Aug 30, 2008 at 3:09 PM, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
Bob,
(This seemed to have been bounced -- so I'm trying again)
I am trully overwelmed. This is great! It should work; I would like to
pass the ID of the 'picked' bond to a javascript variable. Is the report
returned to the pickCallback function as is atom picking, such that the ID
can be parsed out. Or is there another way (jmolEvaluate?) to pass the
report or ID to a javascript variable? I'll admit to confusion about
passing getProperty info to javascript.
Thanks.
Steve
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Re: [Jmol-users] Bond picking -- and getProperty in general
getProperty can be a very inefficient function. The algorithm is designed to
return the entire property set, then do the selections. So, for example, if
you say:
print getProperty(atomInfo[3])
and there are 3 atoms, then first a vector containing 3 elements is
produced and only after that is one selected.
I'm reminded that I thought of that and had a solution to it but forgot. The
alternative format:
print getProperty(atomInfo, {atomIndex=3})
is far more efficient, as it only creates a single atomInfo entry -- an
array with one element.
I've checked in code now that combines these:
print getProperty(atominfo[1].sym, {atomIndex=3})
creates only one entry and then selects the information about atom symbol
from that single entry. ([0] would work as well, because that means the
last entry, and there is only one)
In checking through the code, I also noticed that bondInfo works
similarly, but both atoms of the bond must be selected. I've now changed
that so that if you specify just one atom, then bondInfo gives you what
you think it would -- the bond info for that atom:
print getProperty(bondInfo, {atomno=2})
[[ information about all bonds to atom #2 are displayed ]]
Similarly,
print getProperty(bondInfo[1], {atomno=2})
give information about just the first bond to atom #2.
In addition, getProperty(modelInfo) was not allowing an atom expression,
but it seems to me that would make sense as well:
print getProperty(modelInfo, {atomIndex=2})
or perhaps
print getProperty(modelInfo, {1.3})
So I have added that.
Finally, getProperty(auxiliaryInfo) also could allow for specifying the
model, so I have added that as well:
print getProperty(auxiliaryInfo, {1.3})
These changes should make for much more efficient extraction of information.
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
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Re: [Jmol-users] loading external files in the signed applet
right, that actually makes sense. In communicating with the applet,
particularly the signed applet, you have to be very careful about threads.
When you use jmolScript() you pass the command to one of two free-running
script processors within Jmol. Commands involving the JavaScript command
must run on one thread; commands doing any sort of file opening from
restricted domains must run on a thread special thread created at the time
the applet was created. When you use jmolScriptWait() you use the thread
that gave the command, and since that is of browser origin it does not have
the security rights of the signed applet.
So the lesson here is that one cannot use jmolScriptWait() to open files
with the signed applet, and one should always use callbacks if further
processing in that case is required. The note I have in the code reads:
/*
* CommandWatcher thread handles processing of
* command scripts independently of the user thread.
* This is important for the signed applet, where the
* thread opening remote files cannot be the browser's,
* and commands that utilize JavaScript must be the browser's.
*
* We need two threads for the signed applet, because commands
* that involve JavaScript -- the javascript command or math
javascript() --
* must run on a thread created by the thread generating the applet call.
*
* This CommandWatcher thread, on the other hand, is created by the applet
at
* start up -- it can cross domains, but it can't run JavaScript.
*
*
*/
It's quite possible that there are methods of making all this work that I
just don't know of. But that's the way it is set up currently. I suspect
that someone with more Java experience could set this up so that the
JmolScriptWait() lets its thread sleep while the other processor is working.
Something like that.
Bob
On Sat, Aug 30, 2008 at 9:28 AM, Paul Pillot
[EMAIL PROTECTED] wrote:
Thanks Bob,I narrowed down the problem to the jmolScriptWaitAsArray()
function : surprisingly when I replace it by jmolScript(), I can load
whatever file I want. On the contrary jmolScriptWaitAsArray() gives me
access denial errors...
Paul
Le 30 août 08 à 15:07, Robert Hanson a écrit :
Paul, check out this page to see how yours might be different.
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
It's using the signed applet and working just fine. Maybe has to be newer
than 11.6.RC8, but I don't think so. It should load files from the PDB using
load = and files from your hard drive using, for example:
load c:/temp/caffeine.xyz
Also, the Jmol Protein Explorer is using using the signed applet without a
hitch.
Bob
On Sat, Aug 30, 2008 at 7:32 AM, Paul Pillot
[EMAIL PROTECTED] wrote:
I am setting up a web page with the ability to load local files as
well as external files (for example, files coming from the pdb)
When I run the page locally, the applet is able to load any local
file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari):
java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms
eval ERROR: java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
line 1 command 1 of file null:
load http://www.rcsb.org/pdb/files/1gzx.pdb;
When the page is loaded from a webserver, the applet is unable to
load any local file, as well as remote files coming from elsewhere
than the webserver :
FileManager.openFile(''file:Users/paul/Desktop/
ac.pdb'') //''file:Users/paul/Desktop/ac.pdb''
FileManager opening
http://ordinateur-de-judith-ciosi.local/~paul/http://ordinateur-de-judith-ciosi.local/%7Epaul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
file ERROR:
http://ordinateur-de-judith-ciosi.local/~paul/http://ordinateur-de-judith-ciosi.local/%7Epaul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
java.io.FileNotFoundException: http://ordinateur-de-judith-
ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
openFile(''file:Users/paul/Desktop/ac.pdb''): 3 ms
eval ERROR: java.io.FileNotFoundException: http://ordinateur-de-
judith-ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
line 1 command 1 of file null:
load ''file:Users/paul/Desktop/ac.pdb''
I searched the mailing list archive for this issue and found a one
year old thread, which stated that this behavior is linked to the
inability to accept loading external files when the command is issued
by an unsigned javascript. A workaround is to reload the jmol applet
with the new file.
I would like to know if there is any other solution to make the
signed applet accept an external file ? I am also wondering at how
this problem has been dealt with in jmol protein explorer ?
Thanks in advance,
Paul
Re: [Jmol-users] proposed change to Jmol.js
One more thought on this: What about an option that allows the replacement of the Jar file but first prompts the user for an OK (using JavaScript prompt() ) and explains why this might be an issue? If the user says it is OK, then the Jar file is used? Bob On Sat, Aug 30, 2008 at 2:43 PM, [EMAIL PROTECTED] wrote: Quoting Robert Hanson [EMAIL PROTECTED]: ok. Shucks. That's convincing. OK if it allows same-server jar changes? Yes, I think so. If the server is compromised then I guess it won't make much difference anyhow. Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - 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
Re: [Jmol-users] Bond picking -- and getProperty in general
almost. This of course depends upon the file format. But for auxiliaryInfo
the individual model data are under the vector models because there is
also auxiliaryInfo for the model set as a whole as well. {1.3} means the
third model of the first file, but that still returns a vector of models of
length 1.
var Energy = jmolEvaluate('getProperty(auxiliaryInfo.models[1].zeroPoint,
{1.3})', 1)
(I think)
On Sun, Aug 31, 2008 at 12:34 PM, Jeff Hansen [EMAIL PROTECTED] wrote:
So for example, could I use the following to get the zero point energy from
the third model in the first file loaded into the second applet of several
applets on a page?
var Energy = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint, {1.3},
1)')
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 30, 2008, at 11:45 PM, Robert Hanson wrote:
getProperty can be a very inefficient function. The algorithm is designed
to return the entire property set, then do the selections. So, for example,
if you say:
print getProperty(atomInfo[3])
and there are 3 atoms, then first a vector containing 3 elements is
produced and only after that is one selected.
I'm reminded that I thought of that and had a solution to it but forgot.
The alternative format:
print getProperty(atomInfo, {atomIndex=3})
is far more efficient, as it only creates a single atomInfo entry -- an
array with one element.
I've checked in code now that combines these:
print getProperty(atominfo[1].sym, {atomIndex=3})
creates only one entry and then selects the information about atom symbol
from that single entry. ([0] would work as well, because that means the
last entry, and there is only one)
In checking through the code, I also noticed that bondInfo works
similarly, but both atoms of the bond must be selected. I've now changed
that so that if you specify just one atom, then bondInfo gives you what
you think it would -- the bond info for that atom:
print getProperty(bondInfo, {atomno=2})
[[ information about all bonds to atom #2 are displayed ]]
Similarly,
print getProperty(bondInfo[1], {atomno=2})
give information about just the first bond to atom #2.
In addition, getProperty(modelInfo) was not allowing an atom expression,
but it seems to me that would make sense as well:
print getProperty(modelInfo, {atomIndex=2})
or perhaps
print getProperty(modelInfo, {1.3})
So I have added that.
Finally, getProperty(auxiliaryInfo) also could allow for specifying the
model, so I have added that as well:
print getProperty(auxiliaryInfo, {1.3})
These changes should make for much more efficient extraction of
information.
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
-
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challenge
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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
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Re: [Jmol-users] proposed change to Jmol.js
OK. Others have comments on this? Bob On Mon, Sep 1, 2008 at 9:58 AM, Rolf Huehne [EMAIL PROTECTED] wrote: Robert Hanson wrote: One more thought on this: What about an option that allows the replacement of the Jar file but first prompts the user for an OK (using JavaScript prompt() ) and explains why this might be an issue? If the user says it is OK, then the Jar file is used? Accepting should not be the default and then I think it should be ok. If it is integrated the possible consequences should be pointed out clearly in the documentation of 'Jmol.js'. And it should be easily removable by people who don't like to take the risk. 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 -- 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
Re: [Jmol-users] bug with echo?
On Wed, Sep 3, 2008 at 12:25 PM, rspinney [EMAIL PROTECTED] wrote: I am not sure if these are bugs are not, but I have a couple of problems with the echo command. First is set echo myecho hidden does not work, set echo hidden does, i.e. it does not like the echo name being used. Does seem odd. The following works: set echo myecho 30 30 echo testing set echo myecho hidden set echo myecho displayed The second one is based on the following code: x = Point Group = + script(calculate pointgroup); echo @x; How do I name is echo? echo myecho @x; does not work. x = Point Group = + script(calculate pointgroup); set echo myecho 50 50 echo @x Thanks, Rick -- Dr. Richard Spinney The Ohio State University Department of Chemistry 160 B Celeste Laboratory 120 West 18th Ave Columbus, Ohio 43210 email: [EMAIL PROTECTED] Phone: (614) 247 - 6847 Fax: (614) 292 - 1685 - 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
Re: [Jmol-users] bug with echo?
I consider the fact that hide $my* does not extend to ECHO to be a bug. Jmol 11.6.RC13 will have hide/display/color/delete $*xxx* implemented for ECHO Bob On Wed, Sep 3, 2008 at 1:14 PM, Robert Hanson [EMAIL PROTECTED] wrote: On Wed, Sep 3, 2008 at 12:25 PM, rspinney [EMAIL PROTECTED] wrote: I am not sure if these are bugs are not, but I have a couple of problems with the echo command. First is set echo myecho hidden does not work, set echo hidden does, i.e. it does not like the echo name being used. Does seem odd. The following works: set echo myecho 30 30 echo testing set echo myecho hidden set echo myecho displayed The second one is based on the following code: x = Point Group = + script(calculate pointgroup); echo @x; How do I name is echo? echo myecho @x; does not work. x = Point Group = + script(calculate pointgroup); set echo myecho 50 50 echo @x Thanks, Rick -- Dr. Richard Spinney The Ohio State University Department of Chemistry 160 B Celeste Laboratory 120 West 18th Ave Columbus, Ohio 43210 email: [EMAIL PROTECTED] Phone: (614) 247 - 6847 Fax: (614) 292 - 1685 - 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 -- 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
Re: [Jmol-users] New browser Chrome from Google
It's saying LiveConnect is not working. On Thu, Sep 4, 2008 at 2:30 PM, Angel Herráez [EMAIL PROTECTED] wrote: (Well, this reply to Henry's posts has become long, so I'm splitting it into this Chrome- related part and another Java 6u10 post) So I've just installed the new Java 6u10RC (1.6.0_10-rc) required for Google Chrome It runs. Bad news: I cannot make any javascript-to-applet work in Chrome These are example errors: Uncaught TypeError: Object #an HTMLAppletElement has no method 'script' http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.js (line 354) Uncaught TypeError: Object #an HTMLAppletElement has no method 'script' http://biomodel.uah.es/Jmol.js (line 354) sounds like some weird incompatibility in Jmol.js code, maybe around the applet object in this browser. - 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
Re: [Jmol-users] beyond a limitation of JMOL: TiBS article on publication-integrated 3D models in PDFs
fascinating. So one would simply need to write a U3D file format exporter. Very good project for someone. But of course, one would lose much of the richness of the Jmol experience. Still On Thu, Sep 4, 2008 at 4:58 PM, Wayne Decatur [EMAIL PROTECTED] wrote: Thought people might be interested in a new article in Trends in Biochemical Sciences by Pravin Kumar, Alexander Ziegler, Julian Ziegler, Barbara Uchanska-Ziegler, and Andreas Ziegler entitled Grasping molecular structures through publication-integrated 3D models. They detail using Pymol and Adobe Acrobat 3D toolkit to describe how an interactive 3D model of a molecular complex can be embedded directly into a PDF, thus providing readers with important and educational visual information that would otherwise be more difficult to disseminate. Article can be accessed at: http://www.sciencedirect.com/science/journal/09680004 - 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
Re: [Jmol-users] Problems with echo images image buttons
definitely needs fixing. (1) antialiasdisplay is doubling the image size. (2) vertical centering is not quite right, I think. Bob On Fri, Sep 5, 2008 at 4:25 PM, Eric Martz [EMAIL PROTECTED]wrote: Hi, Bob, This does not have to work in 11.6 (final release). On April 13, 2007, you announced that echos can be made into buttons that, when clicked, execute a specified script, giving this example: http://chemapps.stolaf.edu/jmol/docs/examples-11/buttons.htm This works fine for me. I can use this for now. The manual states that an image file can be displayed as an echo. I am trying to combine the two: display an image of a button, and have it respond to a click by executing a specified script. Because it will look like a button, I can avoid the long label that I might think best with a text echo Click Here to Center All, just labeling the button Center All. Plus, it will be more intuitive -- and COOL! I am having several problems displaying the image correctly, and these also keep the portion of the image that is clickable to be very tiny. I have placed a demo listing the issues here: http://www.bioinformatics.org/jmol-tutorials/jtat_2008_08_05/jtatdemo/test1/contents.htm Thanks, -Eric - 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
Re: [Jmol-users] Getting a complete history/historyLevel
set historylevel 2 works fine for me. It should work as you expected. But history was recording full scripts, not individual commands, so commands were out of order. This might have thrown you off. That's corrected now. On Sat, Sep 6, 2008 at 9:12 AM, Eric Martz [EMAIL PROTECTED]wrote: It is often useful to be able to see the complete command history in Jmol applet's console, including all commands in scripts and scripts called from scripts (second level). After trying a few ideas yesterday, I decided that set historyLevel 1 was the best I hit upon. (Are there other methods?) It appeared that this must be issued before the first script file is called. If it is issued within a script file, the subsequent commands seemed not to be reported. Not surprisingly, I notice that set historyLevel 1 gives the commands in script files only one level down, plus the commands at the top level (level 0 I guess). If a script file contains a script command invoking a second level script file, the commands in that second level script are not reported. So I tried set historyLevel 2. Now I get the commands in the second level script ONLY. The entire remainder of the history before and after (levels 0 and 1) is missing. Is there a set historyLevel setting that will report the entire command history at all levels? What are the possible values for set historyLevel N and what do they mean? Bob, it would be great to clarify the documentation on set historyLevel about the range of legal values, what they mean, how to get the entire history for all levels all at once, and that the set historyLevel command must be issued before the first script command is encountered -- or whatever is correct if I have it wrong. Thanks very much, -Eric - 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
Re: [Jmol-users] javascript command fails in Safari?
better to fix that. On Fri, Sep 5, 2008 at 8:18 PM, Eric Martz [EMAIL PROTECTED]wrote: It appears to me that the javascript command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: javascript alert(hi) or javascript alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the javascript command in the Jmol reference manual. Thanks, Eric - 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
Re: [Jmol-users] javascript command fails in Safari?
sorry - missed some of those messages. OK, I'll assume the javascript command is working ok. As for pause -- that would be a threading issue. But pause is working fine for me on Mac OS-X. Bob On Sat, Sep 6, 2008 at 10:00 AM, Robert Hanson [EMAIL PROTECTED] wrote: better to fix that. On Fri, Sep 5, 2008 at 8:18 PM, Eric Martz [EMAIL PROTECTED]wrote: It appears to me that the javascript command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: javascript alert(hi) or javascript alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the javascript command in the Jmol reference manual. Thanks, Eric - 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 -- 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
Re: [Jmol-users] javascript command fails in Safari?
yes, that's a far better solution anyway. The javascript command cannot be used with the signed applet in any command that also accesses files -- script, load, echo IMAGE. I had to do something like that in Jmol Protein Explorer as well. You have to be very careful with more complex scripts that you aren't mixing these two modes -- javascript commands and file reading -- in the same script thread. That's one of the reasons I implement the change that # comments are not simply ignored but instead processed as commands and sent to the script callback function. That's definitely the way to go with complex scripts like yours, Eric. Eric, are you using the signed or unsigned applet? Bob On Sat, Sep 6, 2008 at 10:45 AM, Eric Martz [EMAIL PROTECTED]wrote: In my previous message on this thread, I agreed that Jmol's javascript command was working in Safari on OS X. However, as I continue to test this code today, sometimes it stops working for no apparent reason. Once it stops, it seems to fail repeatably until I quit and restart Safari. When it stops working, if the Jmol console is open and debugscript is on, the javascript command appears in the console, but the results of that javascript do not occur. I have not managed to examine the Java console when this is happening. So I am getting intermittant failures. So I have decided not to rely on Jmol's javascript command. Instead I use Jmol's message command to send a unique message, trap that in messageCallback, and use that to trigger the desired javascript code. I have used messageCallback extensively and have never found any issues with it. If anyone else observes this intermittant failure of Jmol's javascript command in Safari, I suggest that this be mentioned as a caution in the Jmol documentation entry on javascript. My OS X and Safari are up to date: 10.5.4 and 3.1.2 respectively. I am using Jmol applet 11.6.RC12. -Eric At 9/6/08, Dean Johnston wrote: I can't reproduce this - the javascript command works just fine from the Jmol console for me on both Firefox and Safari for OS X. Dean On Fri, Sep 5, 2008 at 6:18 PM, Eric Martz mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] wrote: It appears to me that the javascript command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: javascript alert(hi) or javascript alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the javascript command in the Jmol reference manual. Thanks, Eric - 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=/ http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list mailto:Jmol-users@lists.sourceforge.netJmol-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 - 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 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Re: [Jmol-users] Problems with echo images image buttons
Eric, That script is way too complex for me to reproduce here, but I did fix the echo alignment. There were a couple of bugs there, particularly with the y-offset of centered echos. All should be fixed. I'll see if we can get RC13 out this weekend so you can check it. Anything else you are finding? Bob On Fri, Sep 5, 2008 at 4:25 PM, Eric Martz [EMAIL PROTECTED]wrote: Hi, Bob, This does not have to work in 11.6 (final release). On April 13, 2007, you announced that echos can be made into buttons that, when clicked, execute a specified script, giving this example: http://chemapps.stolaf.edu/jmol/docs/examples-11/buttons.htm This works fine for me. I can use this for now. The manual states that an image file can be displayed as an echo. I am trying to combine the two: display an image of a button, and have it respond to a click by executing a specified script. Because it will look like a button, I can avoid the long label that I might think best with a text echo Click Here to Center All, just labeling the button Center All. Plus, it will be more intuitive -- and COOL! I am having several problems displaying the image correctly, and these also keep the portion of the image that is clickable to be very tiny. I have placed a demo listing the issues here: http://www.bioinformatics.org/jmol-tutorials/jtat_2008_08_05/jtatdemo/test1/contents.htm Thanks, -Eric - 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
Re: [Jmol-users] cgi and Jmol
Dear Avenha, there is absolutely nothing special about cgi output. Hard to say what you mean by a Jmol java script inside an HTML document. pasted the code to what? Can you send an example or point us to a page? The main thing is to have Jmol.js in the right place and have Jar and model files appropriately placed as well. Also, a common error is capitalization. On your hard drive capitalization of file names doesn't matter; on the server it will. First thing is to find the Java console on your client and see what it is telling you. Clip that message and send it by email to this list. Bob Hanson On Sat, Sep 6, 2008 at 5:21 PM, avehna [EMAIL PROTECTED] wrote: Hello: I just tried to run a Jmol java script inside a html document from a cgi output, but I got an error (Exec format error). I pasted the same html code generated from cgi output and it works perfectly, so it seems I should take another thing into account trying to invoke a java script from the cgi output and dont have any idea what it is. It will be very helpful to me if any of you can help me. Thank you A. - 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
Re: [Jmol-users] Dynamic base64 decoding
I don't think you can put that many bytes on a URL line. Better would be to
put the base64 data into a textarea in a form and submit it using
method=post. Even that might have some limitations.
Bob
On Sat, Sep 6, 2008 at 12:19 PM, [EMAIL PROTECTED] wrote:
Hi Bob,
Aha, jmolScriptwait ? that?s the ticket!
Yeah, I know about the MSIE issue, and I?m trying to deal with that now.
Here?s
the issue: I'm adding the jmol applet images dynamically to the open
webpage, as opposed to exporting to another window as does Angel?s code (and
very nicely too).
My code for MSEI looks like this:
if (nav64=='nocomp'){
var testimg=document.getElementById(SnpShtImg)
var imgB64 = image/jpeg;base64, + jmolGetPropertyAsString('image');
var B64path=base64.php
testimg.src = B64path + ? + imgB64;
}
Which calls Dean Edwards original base64.php code.
It doesn?t work; the img appears empty.
Yet if I manually feed a base64-encoded image (such as this from Dean
Edwards web page), it does work.
imgB64=data:image/gif;base64,R0lGODlhDwAPAKECzMzM/wAAACwADwAPAAACIISPeQHsrZ5ModrLlN48CXF8m2iQ3YmmKqVlRtW4MLwWACH+H09wdGltaXplZCBieSBVbGVhZCBTbWFydFNhdmVyIQAAOw==;
Could the issue be the size of the jmol-derived image?
Thinking about this from another angle? is there a technical reason why
jmol cannot deliver a non-base64 encoded image that could be dynamically
added to the open web page: something like testimg.src=jmolGetImage
(?jpeg?)?
(Have I just fully revealed my lack of understanding of JAVA, or, is this
already possible and I have once again missed it in the documentation?)
Steve
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Steven R. Spilatro
Dept of Biology and Environmental Science
Marietta College
Marietta, OH
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Re: [Jmol-users] echo vs. hover?
Eric, No, it just means they are related. That's all. Nico has released 11.6.RC13, so please check out my bug fixes. Thanks, Nico! Bob On Sat, Sep 6, 2008 at 11:42 AM, Eric Martz [EMAIL PROTECTED]wrote: In the documentation, the sections on echo and set echo say See also: hover. At the section on hover, I don't see anything about echo, except See also: echo. Can echos have hovers? How? -Eric - 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
Re: [Jmol-users] Dynamic base64 decoding -- legible
On Sun, Sep 7, 2008 at 9:48 AM, Steven R. Spilatro [EMAIL PROTECTED]wrote: Could the issue be the size of the jmol-derived image? Yes, I'm pretty sure that's it. The way to test, of course, is to use the same base64 info from Jmol in an img data: - aware browser. There's a link under the applet at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htmthat does this. You can always view source for that popup and send it to see what happens. But most browsers place a severe restriction on GET length -- something like 2K total for the URL line. You just have to do it with a form and textarea. Thinking about this from another angle; is there a technical reason why jmol cannot deliver a non-base64 encoded image that could be dynamically added to the open web page: something like: testimg.src=jmolGetImage (jpeg)? just not supported by any browser. (Have I just fully revealed my lack of understanding of JAVA, or, is this already possible and I have once again missed it in the documentation?) it's just that browsers aren't set up to handle binary image data like that. Thanks! 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 -- 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
Re: [Jmol-users] javascript command fails in Safari?
then for that I'm not aware of any threading issues. But in general, be careful that you are not cycling one thread around and around JavaScript--Jmol--JavaScript--Jmol--... That could be a potential problem. It's good to do some setTimeout() calls just to get a new thread periodically. Otherwise you might get some sort of lock-up. That's a guess. I make it a habit of not sending calls to Jmol from threads that are calling JavaScript from Jmol. And to have, for example, a callback function calling Jmol so that Jmol can call JavaScript... I think you are asking for trouble there. Bob On Sun, Sep 7, 2008 at 10:46 AM, Eric Martz [EMAIL PROTECTED]wrote: On 9/6/08, Bob Hanson asked: Eric, are you using the signed or unsigned applet? Jmol Tutorial-Authoring Template (JTAT): unsigned only. FirstGlance in Jmol: unsigned 99.9% of the time. There is code to detect installations and situations where the signed applet will be needed to access the PDB file from a different server, and then the user is notified that s/he will have to approve the applet. -Eric - 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
Re: [Jmol-users] Placing Jmol image in same web page
works for me -- once I figured out I needed to click a radio button. A default there would be nice. Most impressive is that by using a base tag and my own signed applet I can even make it work in MSIE from a version saved to my hard drive. Good job! Bob On Tue, Sep 9, 2008 at 1:34 PM, Steven R. Spilatro [EMAIL PROTECTED]wrote: Hi everyone, I've created a demo page for placing images of the Jmol model into the same web page, drawing upon some ideas and code from Angel Herráez and Dean Edwards. For compliant browsers, the base64-encoded Jmol image is simply directly to an image element; for non-base64 compliant browsers, the decoded image is targeted to an Iframe. I've tested in several browsers (but not Chrome); while the image can be copied and pasted from either type of element; I find that a saved file from the Iframe does not open in Photoshop. . I welcome comments and feedback. The page is at: http://www.marietta.edu/~spilatrs/MnQuiry/JmolDemo/jmolImgCopy.htmlhttp://www.marietta.edu/%7Espilatrs/MnQuiry/JmolDemo/jmolImgCopy.html (Also; for some reason our server sometimes sends a 'java.security.AccessControlException: access denied ' warning when a Jmol applet page is opened, which goes away with a page refresh) 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 -- 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
Re: [Jmol-users] Dynamic base64 decoding
Well, if you want, give it a try. You will have to use the latest version of
Jmol -- http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolApplet.jar
Just issue
var x = jmolGetPropertyAsJavaObject(image)
That AsJavaObject ensures that the image created is returned as a byte
array -- the actual JPEG code -- rather than as a Base64-encoded string.
That return value is a Java byte[] object, not a JavaScript object. There is
no such thing as a byte array in JavaScript.
Good luck!
Bob
On Tue, Sep 9, 2008 at 4:01 PM, Steven R. Spilatro [EMAIL PROTECTED]wrote:
Bob,
Well, I'm not sure... In the demo web page I sent earlier I assign
the base64-encoded Jmol image, to a image element in the same page:
var jmlImgB64 = jmolGetPropertyAsString('image');
document.getElementById(jmlImage).innerHTML = 'img
width='+imgWd+' height='+imgHt+' src=data:image/jpeg;base64,' +
jmlImgB64 + '';
I'm wondering if Jmol could deliver a non-base64 encoded image (e.g.,
jpg) that could be assigned to a image element in a similar way? (and
therefore eliminate the need for php decoding!)
Steve
The feature just doesn't exist for browsers. You can set a JavaScript
variable to any memory-constrained length, but you are asking for
something
different, I think.
Bob
Would a feature like testimg.src=jmolGetImage (jpeg) involve
similar contraints?
Steve
Dr. Steven R. Spilatro
Department of Biology and Environmental Science
Marietta College
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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] Intermittent loading error
Any chance these are pages that involve more than one applet? In any case,
it's some sort of caching problem with that browser version.
You might get around it by adding a random search to the URL:
test/advanced/ReO3.cif?23023789234
where that number changes each time so that it forces an update from the
server. Something to test, anyway.
Bob
On Tue, Sep 9, 2008 at 3:34 PM, Nick Greeves [EMAIL PROTECTED]wrote:
Hi Steve,I've also had complaints from IE users (particularly) about this
with my site. Today I managed to duplicate the problem and capture the log
with IE7/XP.
FileManager.openFile(test/advanced/ReO3.cif) //test/advanced/ReO3.cif
FileManager opening
http://www.chemtube3d.com/solidstate/test/advanced/ReO3.cif
file ERROR: http://www.chemtube3d.com/solidstate/test/advanced/ReO3.cif
java.security.AccessControlException: access denied (java.io.FilePermission
C:\Documents and Settings\ngreeves.livad\Application
Data\Sun\Java\Deployment\cache\6.0\56\245680b8-446c7509.idx read)
openFile(test/advanced/ReO3.cif): 63 ms
eval ERROR: java.security.AccessControlException: access denied
(java.io.FilePermission C:\Documents and Settings\ngreeves.livad\Application
Data\Sun\Java\Deployment\cache\6.0\56\245680b8-446c7509.idx read)
line 1 command 1 of file null:
load test/advanced/ReO3.cif { 3 3 3 }
I know nothing about WIndows but it looks as if some setting in Documents
and Settings may be implicated? Could this be the explanation?
The html file is
http://www.chemtube3d.com/solidstate/_ReO3(final).htmhttp://www.chemtube3d.com/solidstate/_ReO3%28final%29.htmand
it loads just fine for me.
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)
On 9 Sep 2008, at 19:55, [EMAIL PROTECTED] wrote:
(Also; for some reason our server sometimes sends
a 'java.security.AccessControlException: access
denied ' warning when a Jmol applet page is
opened, which goes away with a page refresh)
Steve
Dr. Steven R. Spilatro
Department of Biology and Environmental Science
Marietta College
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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] Jmol Tutorial-Authoring Template Released
http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents/contents.htm Jmol Version 11.3.13 2007-08-28 16:07 really? Bob On Mon, Sep 8, 2008 at 10:15 PM, Eric Martz [EMAIL PROTECTED]wrote: At long last, I have completed a version of the Jmol Tutorial-Authoring Template (JTAT) that I believe to be adequately documented, and fully functional (http://bioinformatics.org/jmol-tutorials). Improvements since I last put up a pre-release version (July 2008): - Documentation on how to use the template, color key functions, etc. to author a tutorial has been completed. - A new chapter on DRuMS Color Schemes has been added to the JTAT Demonostration Tutorial. - The chapter on Animations and Movies in the JTAT Demonstration Tutorial has been clarified. - Functions are provided to easily generate standard color keys, and scripts are provided to apply the standard color schemes to molecular views. A Quick Reference page for color HTML is provided. - Support for checkboxes that modify the molecular view. Example: View 1 in the Demo Tutorial chapter on Color Schemes. - After centering an atom by clicking on it, the next time Center Clicked is checked, a new button appears for re-centering the entire molecule. - The links (at the bottom of every page in a tutorial) for further exploration of the molecules in the tutorial now support links to FirstGlance in Jmol that display modified or customized PDB files included in the tutorial, as well as the usual published PDB codes. - Jmol applet has been updated to the current version (11.6.RC12). Of course, the entire template and website is downloadable in a single file, jtat.zip. Caveat: I will be away from email until after September 20. Any questions, feedback, or things that I botched up will have to wait till after I get back. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ - 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
Re: [Jmol-users] identifying proteins in mol2 files
no. not that I know of. Only PDB and CIF support for that. Is there some sort of MOL2 designation that would suggest otherwise? On Wed, Sep 10, 2008 at 8:22 AM, Reichsman Frieda [EMAIL PROTECTED] wrote: Hi Bob et al., If a mol2 file is correctly formated, should Jmol be able to recognize protein (as in 'select protein') and residue names? Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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
Re: [Jmol-users] identifying proteins in mol2 files
We could set up the mol2 reader to do this. BUT I have to be convinced first that it's a real standard. What programs write these? Is it just totally arbitrary what these IDs are? Are the names standard? Try some more unusual structures, like DNA, RNA, nonstandard amino acids, 1BLU with its FeS4 sites. Hemoglobin. On Wed, Sep 10, 2008 at 8:51 AM, Angel Herraez [EMAIL PROTECTED] wrote: Dear Frieda I've never tried that. From the doc http://www.tripos.com/data/support/mol2.pdf it seems that atoms can have IDs and residue IDs; they quote an example: 1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000 BACKBONE|DICT|DIRECT 1 CA -0.149 0.299 0.000 C.3 [...] the atom is named CA and is [...] It belongs to the substructure with ID 1 which is named ALA1. So, Jmol should be able to interpret that, but maybe the file reader has not been set for that. As far as I know, the protein is determined based on bonding and key atom names (N, CA, C) within the same residue. Similarly for residue names. A quick test with a pdb file read into Accelrys DS Viewer 1.7 and saved into mol2 shows that the atom IDs are read in Jmol (example: select *.CA works), but not recognized as protein. select ala doesn't work either. So maybe it's just the residue ID part that is not being interpreted. Notably, that goes after the coordinates, rather than before them as in pdb. - 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
Re: [Jmol-users] Placing Jmol image in same web page
On Wed, Sep 10, 2008 at 9:33 AM, Steven R. Spilatro [EMAIL PROTECTED]wrote: Thanks to everyone for the feedback on the 'Placing Jmol image in same web page' which I've updated. http://www.marietta.edu/~spilatrs/MnQuiry/JmolDemo/jmolImgCopy.htmlhttp://www.marietta.edu/%7Espilatrs/MnQuiry/JmolDemo/jmolImgCopy.html 'Output size' now shows a default (Lesson of the Night: do not put radio buttons in a table if you want to set the checked property). nah. huh? must be something else. Of course you can put a checkbox in a table and have it checked Bob, I played around with jmolGetPropertyAsJavaObject(image), but no luck yet. ;) 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 -- 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] Jmol signed applet
Soon Nico will be releasing 11.6.RC14. I think this will be one of our last releases prior to Jmol 1.6.0. Something I'm very interested in people trying out is the signed applet. You can do that at http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm The cool thing there is that the signed applet basically does everything Chime could do in terms of reading local files *and writing them*, and all the new things that Jmol does such as reading files from any web domain, producing JPG, PNG, and (now) GIF files, POV-Ray and Maya output, and JVXL surface files, writing variable and coordinate data to files, etc., etc. I'm hoping some people will explore this more either at that simple.htm site or at http://Jmol.ProteinExplorer.org, where i I think I'd like to get this into the menuing system. Perhaps -- 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] Jmol signed applet
[still catching on to Google Mail...] Soon Nico will be releasing 11.6.RC14. I think this will be one of our last releases prior to Jmol 1.6.0. Something I'm very interested in people trying out is the signed applet. You can do that at http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm The cool thing there is that the signed applet basically does everything Chime could do in terms of reading local files *and writing them*, and all the new things that Jmol does such as reading files from any web domain, producing JPG, PNG, and (now) GIF files, POV-Ray and Maya output, and JVXL surface files, writing variable and coordinate data to files, etc., etc. I'm hoping some people will explore this more either at that simple.htm site or at http://Jmol.ProteinExplorer.org, where it is now implemented as well. Try creating JPEGs, scripts, whatever suits you. Let me know what you think the menu should look like, and we will get that in for 1.6. Bob I think I'd like to get this into the menuing system. Perhaps -- 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 -- 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
Re: [Jmol-users] Jmol app - size of start-up window
There's help available for the command line, but to see it on a Windows machine you have to use java -jar jmol.jar -h not just jmol.jar -h java -jar jmol.jar -h usage: Jmol -o,--noconsole no console -- all output to sysout -q,--quality JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compres sion 9) -g,--geometrywindow width x height, e.g. -g500x500 -x,--exitexit after script (implicit with -n) -D property=value supported options are given below -b,--backgroundtransparent transparent background -c,--check check script syntax only -h,--helpgive this help page -i,--silent silent startup operation -l,--listlist commands during script execution -m,--menumenu file to use -n,--nodisplay no display (and also exit when done) -s,--script script file to execute -t,--threadedindependent commmand thread -w,--write CLIP or GIF|JPG|JPG64|PNG|PPM:filename For example: Jmol -ions myscript.spt -w JPEG:myfile.jpg output.txt The -D options are as follows (defaults in parathesis): cdk.debugging=[true|false] (false) cdk.debug.stdout=[true|false] (false) display.speed=[fps|ms] (ms) JmolConsole=[true|false] (true) jmol.logger.debug=[true|false] (false) jmol.logger.error=[true|false] (true) jmol.logger.fatal=[true|false] (true) jmol.logger.info=[true|false] (true) jmol.logger.logLevel=[true|false] (false) jmol.logger.warn=[true|false] (true) plugin.dir (unset) user.language=[CA|CS|DE|EN|ES|FR|NL|PT|TR] (EN) On Fri, Sep 12, 2008 at 3:05 PM, Reichsman Frieda [EMAIL PROTECTED] wrote: Hi, can someone remind me of how to tell the Jmol app to open its display window to a certain width and height? All I can find in the archives is the following post, which seems no longer to have an effect, and the scripting documentation is still unavailable (and I'm not too hopeful it would be in there)... Tim wrote: By the way is there a command-line option for adjusting the window size at start-up? No, but that is a very good idea. I just checked in code to allow one to set the window size on the Jmol application command-line: -g WIDTHxHEIGHT or --geometry WIDTHxHEIGHT Where WIDTHxHEIGHT is the width and the height in pixels separated by a lower case 'x' 500x550 (the current default) 300x350 (something smaller) 800x850 (something larger) These examples all have a larger height in order to account for the space of the button bar, menus, and status bar. Note that I did not do any work in the area of saving the size as a user preference. Miguel Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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
Re: [Jmol-users] Jmol app - size of start-up window
Someone more familiar with Macs help me out here You need a terminal window and a prompt. At the prompt, on a PC at least, you type java -jar jmol.jar -h That starts the program and assumes that the path to java.exe is known to the system. If you can get that working, then you start Jmol using java -jar jmol.jar -g600x600 and you should be good to go. Bob On Fri, Sep 12, 2008 at 3:29 PM, Reichsman Frieda [EMAIL PROTECTED] wrote: On Sep 12, 2008, at 4:12 PM, Robert Hanson wrote: There's help available for the command line, but to see it on a Windows machine you have to use java -jar jmol.jar -h not just jmol.jar -h In Jmol app on my MacBook Pro, each of these gives an error. java -jar jmol.jar -h usage: Jmol -o,--noconsole no console -- all output to sysout -q,--quality JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compres sion 9) -g,--geometrywindow width x height, e.g. -g500x500 when I type -g500x500 into the command line of Jmol, I get script compiler error: command expected. Same with -g 500x500 --geometry500x500 --geometry 500x500 What am I missing? Thanks, -Frieda -x,--exitexit after script (implicit with -n) -D property=value supported options are given below -b,--backgroundtransparent transparent background -c,--check check script syntax only -h,--helpgive this help page -i,--silent silent startup operation -l,--listlist commands during script execution -m,--menumenu file to use -n,--nodisplay no display (and also exit when done) -s,--script script file to execute -t,--threadedindependent commmand thread -w,--write CLIP or GIF|JPG|JPG64|PNG|PPM:filename For example: Jmol -ions myscript.spt -w JPEG:myfile.jpg output.txt The -D options are as follows (defaults in parathesis): cdk.debugging=[true|false] (false) cdk.debug.stdout=[true|false] (false) display.speed=[fps|ms] (ms) JmolConsole=[true|false] (true) jmol.logger.debug=[true|false] (false) jmol.logger.error=[true|false] (true) jmol.logger.fatal=[true|false] (true) jmol.logger.info=[true|false] (true) jmol.logger.logLevel=[true|false] (false) jmol.logger.warn=[true|false] (true) plugin.dir (unset) user.language=[CA|CS|DE|EN|ES|FR|NL|PT|TR] (EN) On Fri, Sep 12, 2008 at 3:05 PM, Reichsman Frieda [EMAIL PROTECTED]wrote: Hi, can someone remind me of how to tell the Jmol app to open its display window to a certain width and height? All I can find in the archives is the following post, which seems no longer to have an effect, and the scripting documentation is still unavailable (and I'm not too hopeful it would be in there)... Tim wrote: By the way is there a command-line option for adjusting the window size at start-up? No, but that is a very good idea. I just checked in code to allow one to set the window size on the Jmol application command-line: -g WIDTHxHEIGHT or --geometry WIDTHxHEIGHT Where WIDTHxHEIGHT is the width and the height in pixels separated by a lower case 'x' 500x550 (the current default) 300x350 (something smaller) 800x850 (something larger) These examples all have a larger height in order to account for the space of the button bar, menus, and status bar. Note that I did not do any work in the area of saving the size as a user preference. Miguel Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - 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
[Jmol-users] big step for Jmol 11.6
We are almost there! I think I made some work for the translators, but in general we have an amazing signed applet. Here's the scoop: Basically the signed applet and the application now allow you to script user-prompted file input and saving. All you do is use a question mark in the script: load ? script ?.spt write file ? write ?.jpg write ?.png write POVRAY ? The question mark indicates that Jmol should put up a dialog box that allows you do browse your file system. There are three basic dialogs -- file open, file save, and image write. These are all slightly different -- open has the very cool preview capability of the Jmol application; save is a standard save dialog, with confirmation if this will overwrite a file, and image write has extra controls for quality of JPG and PNG images. This works anywhere a file name might be used. For example: isosurface ?.jvxl lets you choose which surface to display if there are several. In addition, the file open dialog box has a special feature you will really like: You can use it to point to files on your hard drive, of course, but also you can enter a URL there to get a file off the web, and you can enter the abbreviated form = to get a PDB file directly from the Protein Data Bank. There are some threading issues there. I might need help from Charles and Nico on that 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
Re: [Jmol-users] big step for Jmol 11.6
Oh, I see now that Java on the Mac doesn't allow entry of filenames by keyboard typing in file-open dialog boxes. That's unfortunate. It boggles my mind why Apple hasn't caught on to the fact that maybe a file-open box could also be used for input from the web. Sure works nicely on the PC. If someone knows how to coerce Java on the Mac to display a file name entry box, let me know. Othewise I'll have to put up something different for web-based file entry. I suppose it could be added as a separate text box. Bob On Tue, Sep 16, 2008 at 12:42 AM, Robert Hanson [EMAIL PROTECTED] wrote: Jmol users, good news! The signed new applet load/save menu items have been checked successfully now on Windows XP/Firefox,MSIE and Mac OS-X/Safari,Firefox. This is a whole new age for the applet. Specifically the signed applet menu adds these two items near the top: Load Load PDB Load file or URL Load full unit cell Save File [filename here] SPT State SPT History --- JPG Image PNG Image POV-Ray --- JVXL Isosurface VRML 3D Model Maya 3D Model Really these are just scripts that employ the new capability to throw up a file open/save dialog box anyplace in a script where a filename is appropriate. Just prepend the filename with a question mark: load ? script ?.spt write image 500 500 ?1crn.jpg isosurface ?.jvxl In addition, load ? has the interesting capability of allowing Jmol preview of the model prior to full loading -- even of remote web-based models. It's that simple. The ? syntax works also in the Jmol application, since the two code segments were merged in the process of development. As currently implemented, if the user clicks [cancel], then any further script processing within that running script is canceled --- same as a quit command. The logic there is that if a file wasn't loaded, probably one should not continue to the next line of the script. The revision is 11.6.RC15. You can see it in action at http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?1blu (or your choice of any four-digit PDB code) and http://Jmol.ProteinExplorer.org I'm sure there are some interface glitches here, so please check these capabilities out and send your feedback. I think a reasonable estimate of release of 1.6 should be Oct. 1. If people can get testing on this, I should be able to have a final release candidate soon, and then two weeks of stability testing should do it. Enjoy! Bob ps - It turns out there was a GIF encoder hiding in the Jmol code all along, so I activated that as well. You can now save GIF images, but frankly they look terrible because (I believe) GIF is limited to 256 colors. So I didn't add that possibility to the menu. On Mon, Sep 15, 2008 at 4:26 PM, Robert Hanson [EMAIL PROTECTED] wrote: OK, I'll check out Mac OS tonight. Not surprised, really. http://chemapps.stolaf.edu/Users/paul/Documents/Bob On Mon, Sep 15, 2008 at 3:46 PM, Paul Pillot [EMAIL PROTECTED] wrote: Bob, this is GREAT ! I specially appreciate that the snapshot taken is with antialiasdisplay on even if the original image hasn't got this setting. Would it be possible to add a dialog with the image size as well, if one wants to increase (or decrease!) the resolution ? Unfortunately loading models from my hard drive did not work so well, I ran into a bug with MacOSX 10.4, using Safari with your simple page: FileManager opening http://chemapps.stolaf.edu/Users/paul/Documents/ 1HSW.pdb file ERROR: http://chemapps.stolaf.edu/Users/paul/Documents/1HSW.pdb java.io.FileNotFoundException: http://chemapps.stolaf.edu/Users/paul/ Documents/1HSW.pdb openFile(?): 1428 ms eval ERROR: java.io.FileNotFoundException: http://chemapps.stolaf.edu/ Users/paul/Documents/1HSW.pdb line 1 command 1 of file null: load ? This makes clear that the path has gone wrong due to the concatenation of the actual page base location, with the desired local file path... Paul - 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 -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr
Re: [Jmol-users] big step for Jmol 11.6
Jmol users, good news! The signed new applet load/save menu items have been checked successfully now on Windows XP/Firefox,MSIE and Mac OS-X/Safari,Firefox. This is a whole new age for the applet. Specifically the signed applet menu adds these two items near the top: Load Load PDB Load file or URL Load full unit cell Save File [filename here] SPT State SPT History --- JPG Image PNG Image POV-Ray --- JVXL Isosurface VRML 3D Model Maya 3D Model Really these are just scripts that employ the new capability to throw up a file open/save dialog box anyplace in a script where a filename is appropriate. Just prepend the filename with a question mark: load ? script ?.spt write image 500 500 ?1crn.jpg isosurface ?.jvxl In addition, load ? has the interesting capability of allowing Jmol preview of the model prior to full loading -- even of remote web-based models. It's that simple. The ? syntax works also in the Jmol application, since the two code segments were merged in the process of development. As currently implemented, if the user clicks [cancel], then any further script processing within that running script is canceled --- same as a quit command. The logic there is that if a file wasn't loaded, probably one should not continue to the next line of the script. The revision is 11.6.RC15. You can see it in action at http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?1blu (or your choice of any four-digit PDB code) and http://Jmol.ProteinExplorer.org I'm sure there are some interface glitches here, so please check these capabilities out and send your feedback. I think a reasonable estimate of release of 1.6 should be Oct. 1. If people can get testing on this, I should be able to have a final release candidate soon, and then two weeks of stability testing should do it. Enjoy! Bob ps - It turns out there was a GIF encoder hiding in the Jmol code all along, so I activated that as well. You can now save GIF images, but frankly they look terrible because (I believe) GIF is limited to 256 colors. So I didn't add that possibility to the menu. On Mon, Sep 15, 2008 at 4:26 PM, Robert Hanson [EMAIL PROTECTED] wrote: OK, I'll check out Mac OS tonight. Not surprised, really. http://chemapps.stolaf.edu/Users/paul/Documents/Bob On Mon, Sep 15, 2008 at 3:46 PM, Paul Pillot [EMAIL PROTECTED] wrote: Bob, this is GREAT ! I specially appreciate that the snapshot taken is with antialiasdisplay on even if the original image hasn't got this setting. Would it be possible to add a dialog with the image size as well, if one wants to increase (or decrease!) the resolution ? Unfortunately loading models from my hard drive did not work so well, I ran into a bug with MacOSX 10.4, using Safari with your simple page: FileManager opening http://chemapps.stolaf.edu/Users/paul/Documents/ 1HSW.pdb file ERROR: http://chemapps.stolaf.edu/Users/paul/Documents/1HSW.pdb java.io.FileNotFoundException: http://chemapps.stolaf.edu/Users/paul/ Documents/1HSW.pdb openFile(?): 1428 ms eval ERROR: java.io.FileNotFoundException: http://chemapps.stolaf.edu/ Users/paul/Documents/1HSW.pdb line 1 command 1 of file null: load ? This makes clear that the path has gone wrong due to the concatenation of the actual page base location, with the desired local file path... Paul - 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 -- 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
Re: [Jmol-users] big step for Jmol 11.6
Sorry -- a fix I made did not make it into the package. Standby On Tue, Sep 16, 2008 at 2:36 AM, Paul Pillot [EMAIL PROTECTED] wrote: Bob,I am still experiencing the same bug with MacOs X.4, Safari : from your simple page, I can't load any local file. Preview works fine, but the final path provided to the applet is not correct (relative to the webpage and not absolute): FileManager opening http://chemapps.stolaf.edu/Users/paul/Desktop/1F58.pdb file ERROR: http://chemapps.stolaf.edu/Users/paul/Desktop/1F58.pdb java.io.FileNotFoundException: http://chemapps.stolaf.edu/Users/paul/Desktop/1F58.pdb openFile(?=1crn): 14076 ms eval ERROR: java.io.FileNotFoundException: http://chemapps.stolaf.edu/Users/paul/Desktop/1F58.pdb line 1 command 1 of file null: load ?=1crn Also, after not having been able to load a file, the applet completely stops working : no more command can be issued... Paul Le 16 sept. 08 à 07:51, Robert Hanson a écrit : Oh, I see now that Java on the Mac doesn't allow entry of filenames by keyboard typing in file-open dialog boxes. That's unfortunate. It boggles my mind why Apple hasn't caught on to the fact that maybe a file-open box could also be used for input from the web. Sure works nicely on the PC. If someone knows how to coerce Java on the Mac to display a file name entry box, let me know. Othewise I'll have to put up something different for web-based file entry. I suppose it could be added as a separate text box. Bob On Tue, Sep 16, 2008 at 12:42 AM, Robert Hanson [EMAIL PROTECTED]wrote: Jmol users, good news! The signed new applet load/save menu items have been checked successfully now on Windows XP/Firefox,MSIE and Mac OS-X/Safari,Firefox. This is a whole new age for the applet. Specifically the signed applet menu adds these two items near the top: Load Load PDB Load file or URL Load full unit cell Save File [filename here] SPT State SPT History --- JPG Image PNG Image POV-Ray --- JVXL Isosurface VRML 3D Model Maya 3D Model Really these are just scripts that employ the new capability to throw up a file open/save dialog box anyplace in a script where a filename is appropriate. Just prepend the filename with a question mark: load ? script ?.spt write image 500 500 ?1crn.jpg isosurface ?.jvxl In addition, load ? has the interesting capability of allowing Jmol preview of the model prior to full loading -- even of remote web-based models. It's that simple. The ? syntax works also in the Jmol application, since the two code segments were merged in the process of development. As currently implemented, if the user clicks [cancel], then any further script processing within that running script is canceled --- same as a quit command. The logic there is that if a file wasn't loaded, probably one should not continue to the next line of the script. The revision is 11.6.RC15. You can see it in action at http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?1blu (or your choice of any four-digit PDB code) and http://Jmol.ProteinExplorer.org I'm sure there are some interface glitches here, so please check these capabilities out and send your feedback. I think a reasonable estimate of release of 1.6 should be Oct. 1. If people can get testing on this, I should be able to have a final release candidate soon, and then two weeks of stability testing should do it. Enjoy! Bob ps - It turns out there was a GIF encoder hiding in the Jmol code all along, so I activated that as well. You can now save GIF images, but frankly they look terrible because (I believe) GIF is limited to 256 colors. So I didn't add that possibility to the menu. On Mon, Sep 15, 2008 at 4:26 PM, Robert Hanson [EMAIL PROTECTED]wrote: OK, I'll check out Mac OS tonight. Not surprised, really. http://chemapps.stolaf.edu/Users/paul/Documents/Bob On Mon, Sep 15, 2008 at 3:46 PM, Paul Pillot [EMAIL PROTECTED] wrote: Bob, this is GREAT ! I specially appreciate that the snapshot taken is with antialiasdisplay on even if the original image hasn't got this setting. Would it be possible to add a dialog with the image size as well, if one wants to increase (or decrease!) the resolution ? Unfortunately loading models from my hard drive did not work so well, I ran into a bug with MacOSX 10.4, using Safari with your simple page: FileManager opening http://chemapps.stolaf.edu/Users/paul/Documents/ 1HSW.pdb file ERROR: http://chemapps.stolaf.edu/Users/paul/Documents/1HSW.pdb java.io.FileNotFoundException: http://chemapps.stolaf.edu/Users/paul/ Documents/1HSW.pdb openFile(?): 1428 ms eval ERROR: java.io.FileNotFoundException: http://chemapps.stolaf.edu/ Users/paul/Documents/1HSW.pdb line 1 command 1 of file null: load ? This makes clear that the path has gone wrong due to the concatenation of the actual page
Re: [Jmol-users] big step for Jmol 11.6 MacOS
Hmm. Could be a Java version issue. I definitely see what is shown at http://developer.apple.com/releasenotes/Java/Java142RN/WhatsNew/chapter_2_section_5.html You don't? I don't think I did anything to modify that, and the Java documentation supports the idea that there is no such box in Mac Java. In any case, I think I have to get rid of that idea and allow URL entry elsewhere in that dialog. On Tue, Sep 16, 2008 at 7:56 AM, Jonathan Gutow [EMAIL PROTECTED] wrote: Is this an applet only issue? I can definitely type the filename into the open dialog in the application version. Jmol 11.4.6, MacOS 10.4.11 Jonathan On Sep 16, 2008, at 2:37 AM, [EMAIL PROTECTED] wrote: Message: 1 Date: Tue, 16 Sep 2008 00:51:03 -0500 From: Robert Hanson [EMAIL PROTECTED] Subject: Re: [Jmol-users] big step for Jmol 11.6 To: jmol-users@lists.sourceforge.net Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Oh, I see now that Java on the Mac doesn't allow entry of filenames by keyboard typing in file-open dialog boxes. That's unfortunate. It boggles my mind why Apple hasn't caught on to the fact that maybe a file-open box could also be used for input from the web. Sure works nicely on the PC. If someone knows how to coerce Java on the Mac to display a file name entry box, let me know. Othewise I'll have to put up something different for web-based file entry. I suppose it could be added as a separate text box. Bob Dr. Jonathan H. Gutow Chemistry Department [EMAIL PROTECTED] UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/faculty_staff/gutow/ - 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
Re: [Jmol-users] big step for Jmol 11.6
On Tue, Sep 16, 2008 at 7:30 AM, Rolf Huehne [EMAIL PROTECTED] wrote: There is usually no drastic quality difference. It depends of course of the specific rendering and larger images might also be more problematic. If file size matters in my experience the quality of GIF images of PDB structures compared to JPEG images of similar size is often better. Therefore I didn't switch to JPEG images after implementing the automatic image generation with Jmol in the JenaLib. If there is a much higher quality loss with Jmol generated GIF images it might be due to an unfavourable mechanism to map the colors in the image to 256 colors. If this is not the case I would vote to include GIF in the menu and let the user decide to use it or not. There's probably some simple algorithm that I don't know about that makes this possible. Until I find it, though, I'd rather leave the GIF option off the menu (but it is available with the WRITE IMAGE command). It really looks bad right now. 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 -- 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] help needed -- bonding radii of anions
Jmol has some very odd bonding radii for unusual anions. Note the numbers: (8 4) + (-2 + 4), 1320, // O-2 (8 4) + (-1 + 4), 1760, // O-1 // WAY too large? (14 4) + (-4 + 4), 2710, // Si-4 (14 4) + (-1 + 4), 3840, // Si-1 // same problem here? (34 4) + (-2 + 4), 1910, // Se-2 (34 4) + (-1 + 4), 2320, // Se-1 // same problem here? (50 4) + (-4 + 4), 2940, // Sn-4 (50 4) + (-1 + 4), 3700, // Sn-1 // same problem here? (52 4) + (-2 + 4), 2110, // Te-2 (52 4) + (-1 + 4), 2500, // Te-1 // same problem here? My question is, why would it be that the X(1-) numbers are way larger than the X(2-) numbers? I'm guessing O(1-) is for something like Na2O2, sodium peroxide. But still, that makes no sense whatsoever. The reference reads: * This data is from * Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143 * (scanned for Jmol by Phillip Barak, Jan 2004) Can someone look that up, please? Where are these numbers really from? The problem is that carboxylic acid salts are given a way too large maximum bonding radius for their oxygen atoms. I've temporarily set the O- bonding radius to 1000, but still 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
Re: [Jmol-users] big step for Jmol 11.6
Thanks, I'll take a look at that, but more important things to do now. On Wed, Sep 17, 2008 at 5:01 AM, Rolf Huehne [EMAIL PROTECTED] wrote: Robert Hanson wrote: On Tue, Sep 16, 2008 at 7:30 AM, Rolf Huehne [EMAIL PROTECTED] wrote: There is usually no drastic quality difference. It depends of course of the specific rendering and larger images might also be more problematic. If file size matters in my experience the quality of GIF images of PDB structures compared to JPEG images of similar size is often better. Therefore I didn't switch to JPEG images after implementing the automatic image generation with Jmol in the JenaLib. If there is a much higher quality loss with Jmol generated GIF images it might be due to an unfavourable mechanism to map the colors in the image to 256 colors. If this is not the case I would vote to include GIF in the menu and let the user decide to use it or not. There's probably some simple algorithm that I don't know about that makes this possible. Until I find it, though, I'd rather leave the GIF option off the menu (but it is available with the WRITE IMAGE command). It really looks bad right now. I am using the open source package ImageMagick for the conversion: http://www.imagemagick.org 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 -- 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
Re: [Jmol-users] New browser Chrome from Google
good news -- Jmol is working perfectly, including liveConnect, with a recent fix to Chrome. Info on this fix and relevant Chrome release: http://code.google.com/p/chromium/issues/detail?id=580#c30 Bob On Thu, Sep 4, 2008 at 4:24 PM, Robert Hanson [EMAIL PROTECTED] wrote: It's saying LiveConnect is not working. On Thu, Sep 4, 2008 at 2:30 PM, Angel Herráez [EMAIL PROTECTED]wrote: (Well, this reply to Henry's posts has become long, so I'm splitting it into this Chrome- related part and another Java 6u10 post) So I've just installed the new Java 6u10RC (1.6.0_10-rc) required for Google Chrome It runs. Bad news: I cannot make any javascript-to-applet work in Chrome These are example errors: Uncaught TypeError: Object #an HTMLAppletElement has no method 'script' http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.js (line 354) Uncaught TypeError: Object #an HTMLAppletElement has no method 'script' http://biomodel.uah.es/Jmol.js (line 354) sounds like some weird incompatibility in Jmol.js code, maybe around the applet object in this browser. - 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 -- 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] partial charges
Frieda, that's fixed.
The way to get partial charge data into .pdb files is to put it in the
temperature field. You can do that with:
{*}.temperature = {*}.partialcharge.all
Which will work on the revised Jmol that I haven't uploaded yet.
Which suggests to me that you might also try this in the version you have:
{*}.partialcharge = {*}.property_partialcharge.all
That copies all the property_partialcharge data into the real partialcharge
field of the atoms.
Then do the isosurface MEP business.
Bob
On Fri, Sep 19, 2008 at 4:32 PM, Reichsman Frieda [EMAIL PROTECTED] wrote:
Hi Bob,
Finally have my machine back and am catching up.
The script below works for coloring the atoms by partial charge (very cool
that Jmol can do that from two files!) but not for creating an isosurface
that colors by mep. How can I get at the partial charges for that purpose?
I tried the usual isosurface commands, but Jmol says it needs partial
charges, so I would like to word the command to tell Jmol where to find
them.
Also tried to write the pdb file with the partial charges in it:
write coords pdb myfile.pdb
but no partial charges appear in the file.
Frieda
On Sep 13, 2008, at 1:00 PM, Robert Hanson wrote:
If that's all you want to do, try this:
load .pdb
set propertydatafield 9
x = load(.mol2)
data property_partialcharge @x
color property_partialcharge
On Sat, Sep 13, 2008 at 8:22 AM, Reichsman Frieda [EMAIL PROTECTED]wrote:
That sounds very interesting. Yes, if I could take the partial charges
from the mol2 file and put them in the pdb file inside Jmol, that would do
the trick!
In doing this, I do not usually need to remove atoms. While it might be
useful to be able to do so, removing atoms is done so easily by editing the
pdb file that I usually go that route, either deleting or just commenting
them out.
I am not sure if mol2 files that are saved from pdb files have their atoms
in exactly the same order. I guess this would be important? Certainly I can
test this. Another issue is, if one has a mol2 file and no exact duplicate
pdb file. If the mol2 file did have residue names, numbers, and atom names
that included the .CA etc, perhaps one could tell Jmol where exactly to
find these items in this file?
Frieda
On Sep 13, 2008, at 5:48 AM, Robert Hanson wrote:
Frieda, I'm working on a new system that will allow you to merge file
formats -- take the PDB/bonding information from one file and combine it
with the coordinate data from another file. This sounds to me like it might
be exactly what you are after.
Question: in doing this, do you reduce the number of atoms from what they
were in the original PDB file?
Bob
On Fri, Sep 12, 2008 at 3:45 PM, Reichsman Frieda [EMAIL PROTECTED]wrote:
The program I am using at present is AtomSmith, but many other programs
also apparently write mol2 files. Would that be a problem, since they may
not all write them correctly? Or can we focus on the mol2 files written by
AtomSmith?
Some mol2 files are supplied with the AtomSmith program, but yes,
starting with a pdb file I can save it as a mol2 file. I generally do this
after creating an electrostatic potential surface so that the partial
charges get saved there, so then I can display it in Jmol, and this is my
primary motivation for making this request.
For the amino acids page that I think you saw, I had to define every
backbone atom in every file (there was no real pattern to the atomno
designations) in order to make certain displays.
Just yesterday I learned how to use python to extract characters from
text files so theoretically I could soon take the partial charges out of a
mol2 file and put them in the temperature field of a pdb file. And I am very
willing to go that route if this mol2 thing is not worth the effort.
I can send you a few files that are supplied as well as some that are
exported form pdbs, if this makes sense to pursue.
-Frieda
On Sep 12, 2008, at 4:30 PM, Robert Hanson wrote:
On Fri, Sep 12, 2008 at 3:21 PM, Reichsman Frieda [EMAIL PROTECTED]wrote:
On Sep 12, 2008, at 4:04 PM, Robert Hanson wrote:
Well, what about the documentation at
http://www.tripos.com/data/support/mol2.pdf
I was assuming that this document is of no use in this regard, since you
seemed to know of this documentation already. It states at the beginning,
Mol2 files are written out in a *free format *to avoid the restrictions
created by
fixed format files.
To me, this sounds like a definitive statement that, forget it, anybody
can write anything they want in a mol2 file. But, then on page 12 the
document does lay out what the atom records can or should contain. I do not
understand from the language of this documentation, whether these are
considered recommendations or are a more hard-and-fast thing. Do you?
free format just means space characters separate fields rather than
designated columns where one number can abut
Re: [Jmol-users] proposed change to Jmol.js
I've put up a proposed change to Jmol.js. Please check it out. The idea is that we would be able to test sites using different Jar files. The comment in the Jar file reads: // Note added 12:41 PM 9/21/2008 by Bob Hanson, [EMAIL PROTECTED]: // JMOLJAR=x.jar on the URL for this page will override // the JAR file specified in the jmolInitialize() call. // The idea is that it can be very useful to test a web page with different JAR files // Or for an expert user to substitute a signed applet for an unsigned one // so as to use a broader range of models or to create JPEG files, for example. // If the JAR file is not in the current directory (has any sort of / in its name) // then the user is presented with a warning and asked whether it is OK to change Jar files. // The default action, if the user just presses OK is to NOT allow the change. // The user must type the word yes in the prompt box for the change to be approved. // If you don't want people to be able to switch in their own JAR file on your page, // simply set this next line to read var allowJMOLJAR = false. You can try it out using URLs such as these: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolApplet.jar http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar Bob On Mon, Sep 1, 2008 at 10:03 AM, Robert Hanson [EMAIL PROTECTED] wrote: OK. Others have comments on this? Bob On Mon, Sep 1, 2008 at 9:58 AM, Rolf Huehne [EMAIL PROTECTED]wrote: Robert Hanson wrote: One more thought on this: What about an option that allows the replacement of the Jar file but first prompts the user for an OK (using JavaScript prompt() ) and explains why this might be an issue? If the user says it is OK, then the Jar file is used? Accepting should not be the default and then I think it should be ok. If it is integrated the possible consequences should be pointed out clearly in the documentation of 'Jmol.js'. And it should be easily removable by people who don't like to take the risk. 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 -- 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 -- 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
Re: [Jmol-users] two issues
From the documentation: *[radius option] Addition of the keyword radius followed by a distance in angstroms allows definition of the radius of a modified or newly created bond. If the modify/create option is absent, then modify is assumed; if the bond type is absent, then bonds of any type are set, but their bond type is not changed. *Key there is that MODIFY is assumed. So you need: connect (atomno=70) (atomno=111) hbond orange radius 0.05 CREATE instead. Bob On Sun, Sep 21, 2008 at 6:56 AM, Volker Blum [EMAIL PROTECTED] wrote: Dear all, using the latest prerelease version of jmol,prerelease 11.6.RC15, I have questions on two issues that I've found difficult for a while: 1) (minor) For two initially unconnected atoms, connect (atomno=70) (atomno=111) hbond orange radius 0.05 does not work. Doing first connect (atomno=70) (atomno=111) hbond and then connect (atomno=70) (atomno=111) hbond orange radius 0.05 produces the desired result. Any reason why the original command does not work out of the box? 2) Regarding cartoons (ribbons etc) - I have found it excessively tedious to get a ribbon into what is obviously a helix in a structure of mine. Doing this based on an xyz file is obviously impossible. Converting first to a .pdb file, then hand-editing the pdb file to get CA's and CB's right gets the ribbon for me correctly in one structure, but not in another (exactly same procedure). Questions: What exact information does jmol even require to safely produce a ribbon? For me, this was a rather frustrating guessing in the dark experience. Empirically, it's - a pdb file - numbered residues, perhaps their names - correctly specified CA's and CB's - ??? what else? Is there any reason why a ribbon should not be producable by simply specifying the atoms to be connected from within jmol itself? Having such a feature available would be a great help thanks best wishes V. Blum - 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
Re: [Jmol-users] two issues
That's a bug. Fixed for the next version. Workaround is to open the console and type write image ?.jpg Bob On Sun, Sep 21, 2008 at 7:36 AM, Volker Blum [EMAIL PROTECTED] wrote: Hi again, - The Export - image menu as well as the Save current view as an image button do not function in the prerelease 11.6.RC15 version downloaded by me today (I downloaded the binaries package, not the source). This used to work without problems in 11.2.x (which I used before). -- 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
Re: [Jmol-users] two issues
I certainly see your point. Once defaults are in, though, that's pretty much a done deal. The idea in this case was that this is the only mechanism for changing the radii of specific bonds that already exist. So it is conservative -- with modify as the default you can always undo it; with create as a default, that's trickier. On Sun, Sep 21, 2008 at 1:25 PM, Volker Blum [EMAIL PROTECTED] wrote: Thanks again! I could not try yet but am sure it'll solve the issue. I did read the documentation on atomExpression and could not figure out the exact syntax from there - what I was missing was a few examples like yours. Would it make sense to put some examples there, or did I miss that, too? (possible!) So noted. Atom expressions can be incredibly complex. I don't know how much could be added to the documentation in that regard. Maybe you can suggest some very specific (few) examples. Better to get Angel's book! :) Bob best Volker On Sep 21, 2008, at 5:14 PM, Angel Herráez wrote: On 21 Sep 2008 at 15:50, Volker Blum wrote: - the sequence of commands structure HELIX (atomno=17,18,19,27,28,29,37,38,39,47,48,49); ribbon on does nothing at all in my case (those are the numbers of the backbone ...-CCN-CCN-...'s . The whole thing is clearly helical - what am I missing?) It's just that you cannot specify atom numbers that way. structure HELIX (atomno=17, atomno=18, atomno=19,etc or structure HELIX (atomno=17 and atomno=19, atomno=27 and atomno=29, etc Thanks for your help, and sorry about the perhaps silly follow-up questions. No problem, we are here to learn and to help - 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 -- Dr. Volker Blum Fritz-Haber-Institut der MPG Abteilung Theorie Faradayweg 4-6 D-14195 Berlin, Germany phone +49 30 8413 4846 fax +49 30 8413 4701 [EMAIL PROTECTED] ---key:1-0.0735-11600-23.05:fhi--- - 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
Re: [Jmol-users] partial charges
one last thing -- with the latest Jmol you can do:
load .pdb
{*}.partialcharge = data(load(whatever.mol2),9,0,9)
All in one swoop, you have your partial charges.
That loads file whatever.mol2 into a temporary variable, then takes the 9th
field* starting at the 9th line. Using 9,0,1 there would also work,
because there are fewer than 9 fields in all the lines preceding the atom
lines, but it's better, I think, to indicate the true starting line in case
some file has a long title.
*The 0 there indicates this is a free-format file and we are indicating the
9th white-space-separated field on the line; if it had been a fixed-format
file, then the first numeric parameter would indicate a column number, and
the 0 would be replaced with the number of columns for this field.
Bob
On Sun, Sep 21, 2008 at 10:17 AM, Reichsman Frieda [EMAIL PROTECTED]wrote:
On Sep 19, 2008, at 10:12 PM, Robert Hanson wrote:
The way to get partial charge data into .pdb files is to put it in
the temperature field. You can do that with:
{*}.temperature = {*}.partialcharge.all
Which will work on the revised Jmol that I haven't uploaded yet.
Which suggests to me that you might also try this in the version you
have:
{*}.partialcharge = {*}.property_partialcharge.all
That copies all the property_partialcharge data into the real
partialcharge field of the atoms.
Then do the isosurface MEP business.
Yes, this works perfectly for displaying the mep surface- beautiful!
And being able to get the values into the pdb file will be terrific.
Thanks,
Frieda
On Sep 13, 2008, at 1:00 PM, Robert Hanson wrote:
If that's all you want to do, try this:
load .pdb
set propertydatafield 9
x = load(.mol2)
data property_partialcharge @x
color property_partialcharge
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Jmol-users] Jmol 11.6.RC15 image write workaround
Sorry, I broke the menu/toolbar buttons for writing images in Jmol 11.6.RC15. The workaround is to open the console and type write image ?.jpg This will open up the dialog box. -- 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] final testing appreciated
Final testing appreciated for Jmol 11.6. Anything you can do to try to break it would be great. One bug I know about seems to be that the applet stalls if a file load error occurs. I'm onto that one. 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
Re: [Jmol-users] final testing appreciated
(That's the SIGNED applet...) On Mon, Sep 22, 2008 at 6:14 PM, Robert Hanson [EMAIL PROTECTED] wrote: One bug I know about seems to be that the applet stalls if a file load error occurs. I'm onto that one. Bob - 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] JS code snippet to display PDB TITLE information in Jmol Applet
Nice. You can save yourself a little trouble with:
var title = jmolEvaluate('getProperty(fileHeader).split().find(TITLE)')
Also, realize that this goes back and retrieves the file again from its
source. If you know you want to use the file header this way, it's more
efficient to use
set pdbGetHeader TRUE
(uh, undocumented, I see...)
This setting instructs Jmol to preserve the file header in memory when the
file is loaded. It is used in Jmol Protein Explorer.
Since you are really wanting to display this in Jmol, you might consider
something like the following Jmol script, which requires no JavaScript:
function getHeader()
var titleLines = getProperty(fileHeader).split().find(TITLE).split()
for (var i = 1; i = titleLines.size;i = i + 1)
titleLines[i] = (titleLines[i])[11][0].trim()
end for
return titleLines.join(|)
end function
set echo bottom left
echo @{getheader()}
Something like that
Bob
On Mon, Sep 22, 2008 at 3:50 PM, Thomas Stout [EMAIL PROTECTED]wrote:
Here, then -- with my thanks for all the help -- is a working method to
pull the TITLE lines from a PDB file and echo it to the bottom of the Jmol
Applet window:
var headerInfo = jmolGetPropertyAsString(fileHeader);
var cutUp = headerInfo.split(\n);
var headerstring=;
for (l=0;lcutUp.length;l++) {
var regexp = new RegExp(TITLE.{5}(.*)\s*);
var temp = cutUp[l];
if (temp.search(regexp) == 0) {
temp2 = RegExp.$1;
temp2.replace(/^\s+|\s+$/g, ).replace(/\s+/g, );
temp2 = temp2 + |;
headerstring += temp2;
}
}
headerstring.replace(/TITLE/, );
jmolScript(set echo depth 0; set echo headerecho 2% 2%;
font echo 12 sanserif bolditalic; color echo green);
jmolScript('echo ' + headerstring + '');
Cheers,
Tom
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If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Best way to output results of script using Jmol application
Dean,
Fun! Yes,
write VAR
is a great way to go. Signed applet or Jmol application will do that.
Bob
On Tue, Sep 23, 2008 at 12:48 PM, Dean Johnston [EMAIL PROTECTED]wrote:
Dear All,
I've been playing around with some of the molecular math features of
Jmol - it's truly amazing how easy it is to analyze a large number of
structures. My only difficulty has been getting the results out to a simple
text file.
At first I tried copying the text from the console - doesn't seem to work
(at least on OS X).
For simple scripts I was able to say:
output = script(echo hello world); write VAR output output.txt;
But this is cumbersome with longer scripts or with scripts that have quotes
in them.
The following seems to work (I just figured this out...):
output = script(script \myscript.spt\); write VAR output output.txt;
Am I missing an easier (cleaner?) way to do this? I guess I'd like to be
able to tell the script(...) command that what is in the quotes is a
path to a file.
Just FYI, here is a bit of what I'm doing with this (the file is the
results of a search on the Cambridge Structure Database with about 100
structures). The structures are all metal clusters and I'm calculating the
average distance from the center of the cluster to each of the bridging
ligands in the structure. Pretty cool...
nModel = getProperty(modelInfo, modelCount);
for (x = 1; x = nModel; x = x+1);
name = getProperty(modelInfo, models, @x, name).trim(CSD_CIF);
model @x;
print Model # + x + : + name;
bridging = (connected(3,{molybdenum}) {model = @x});
moly = ({molybdenum} {model = @x});
print Bridging atoms: + bridging.label(%e).join( );
print Bridging distance = + bridging.distance(moly);
print ;
end for;
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] final testing appreciated
I'll check into that. On Wed, Sep 24, 2008 at 12:16 PM, Thomas Stout [EMAIL PROTECTED]wrote: One oddity that I've just noticed: I downloaded 11.6.RC16 (several times in the last 24 hours) and find that if I run the stand alone or load the signed applet, they report version 11.6.RC16. However, if I run the un-signed Applet, it is still reporting version 11.6.RC14 -- is this known and/or intentional? Cheers, Tom On Mon, Sep 22, 2008 at 4:14 PM, Robert Hanson [EMAIL PROTECTED] wrote: Final testing appreciated for Jmol 11.6. Anything you can do to try to break it would be great. One bug I know about seems to be that the applet stalls if a file load error occurs. I'm onto that one. 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 - 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
