Re: [Jmol-users] making jpg file from a molecule shown with jsmol
Addition to last post:
Server running and php running:
"Apache/2.2.14 (Win32) DAV/2 mod_ssl/2.2.14 OpenSSL/0.9.8l
mod_autoindex_color PHP/5.3.1"
From code of the Jsmol page which displays just fine:
var Info = {
width: 6000,
height: 3600,
color: "#00",
serverURL: "/jsmol/php/jsmol.php",
use: "HTML5",
j2sPath: "jsmol/j2s",}
The
serverURL
path and the
j2sPath
are correct.
Any ideas, why I can't get a jpg File from the displayed molecule?
Am 28.06.2014 09:39, schrieb Reinhold Störmann:
php is running with no problems.
Where can I find documentation for the use of "Info.serverURL"?
Am 28.06.2014 00:24, schrieb Robert Hanson:
This is a locally served page. I'm guessing your machine cannot run
PHP or you are not pointing to the correct file in Info.serverURL
Bob Hanson
On Fri, Jun 27, 2014 at 12:31 PM, Reinhold Störmann
mailto:rsto...@uni-bremen.de>> wrote:
Hi,
when I try to make a jpg file from a jsmol page using the menu
(File->Export JPG Image) instead of a file selector box I get a small
box "Save Image" with a preselected filename (identical to the
name of
the loaded model). Using these default values always gives me 404
error
after a while and I cannot find the presumably written file on my
computer .
The 404 error is related to not finding this url:
"http://localhost/jsmol/php/jsmol.php%20?841";
The
localhost/jsmol/php/jsmol.php
file is present.
And how can I change the directory where the jpg will be written?
Using windows 8.1
Firefox 30.0
local XAMPP system for running jsmol 14.1.2
Thanks for your help.
--
Dr. Reinhold Störmann
University of Bremen - Center for Environmental Research and
Sustainable
Technology
Leobener Str.
D-28359 Bremen
Germany
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Chair, Department 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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Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
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Re: [Jmol-users] making jpg file from a molecule shown with jsmol
php is running with no problems. Where can I find documentation for the use of "Info.serverURL"? Am 28.06.2014 00:24, schrieb Robert Hanson: This is a locally served page. I'm guessing your machine cannot run PHP or you are not pointing to the correct file in Info.serverURL Bob Hanson On Fri, Jun 27, 2014 at 12:31 PM, Reinhold Störmann mailto:rsto...@uni-bremen.de>> wrote: Hi, when I try to make a jpg file from a jsmol page using the menu (File->Export JPG Image) instead of a file selector box I get a small box "Save Image" with a preselected filename (identical to the name of the loaded model). Using these default values always gives me 404 error after a while and I cannot find the presumably written file on my computer . The 404 error is related to not finding this url: "http://localhost/jsmol/php/jsmol.php%20?841"; The localhost/jsmol/php/jsmol.php file is present. And how can I change the directory where the jpg will be written? Using windows 8.1 Firefox 30.0 local XAMPP system for running jsmol 14.1.2 Thanks for your help. ------ Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- - -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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 -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- - -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] making jpg file from a molecule shown with jsmol
Hi, when I try to make a jpg file from a jsmol page using the menu (File->Export JPG Image) instead of a file selector box I get a small box "Save Image" with a preselected filename (identical to the name of the loaded model). Using these default values always gives me 404 error after a while and I cannot find the presumably written file on my computer . The 404 error is related to not finding this url: "http://localhost/jsmol/php/jsmol.php%20?841"; The localhost/jsmol/php/jsmol.php file is present. And how can I change the directory where the jpg will be written? Using windows 8.1 Firefox 30.0 local XAMPP system for running jsmol 14.1.2 Thanks for your help. -- Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- - -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Highlight functional groups
Am 22.06.2013 13:56, schrieb Gudrun Colbow: > To whom it may concern, > > Jmol seems to have a feature that allows functional groups to be > highlighted. I am just building a web site that includes Jmol images. > Could you advise me how and where to introduce the highlight functional > groups function into my source so that I can choose a colour that > highlights the functional group(s) in my molecules? > > Thank you so much > > Gudrun Colbow > > -- > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > As far as I know, Jmol does not have the said feature to highlight functional groups by itself. Where have you seen this behavior? If you are referring to the site http://www.il-eco.uft.uni-bremen.de/ or http://oc-praktikum.de/ http://kriemhild.uft.uni-bremen.de/nop/ there I personally programmed this feature. But for it to work it requires a special - non-standard - version of pdb files, that include definitions of the functional groups for storing the molecules, and also some php-scripts. Other file formats than pdb do not have the necessary unused column to specify functional groups, so they won't work. Jmol does not know anything about which atoms belong to functional groups and which don't. If you are still interested in setting up a site that includes this feature, I can help you with the additions to the pdb files of the molecules and/or the php scripts needed. Dr. Reinhold Störmann -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol/JSpecView integration
28 -9.971 48 ##END= This format is usually NOT the one you get from an (13C NMR) instrument when you ask the software to output jcamp-dx! You'll probably get the x/y values in some kind of not human-readable binary format that can be read by some software that read jcamp-dx, but I haven't found a program that can interconvert these different jcamp-dx formats. There is a php script putting both, JMol view of the molecule and JSpecView of the spectrum - on the screen. You can find it attached to this mail. How many of these did you end up with? Might be a starting point. Only 4x 1H-NMR and 7x 13C-NMR (three of them may have a bug in the jcamp-format, they do not display correctly at the moment, but I haven't looked into it for a while, because I'm no longer employed at the university and there's NO budget for updating the site.) Hope that helps. I'm looking forward to a real integration of JMol + JSpecView to make all this easier. Greetings Reinhold -- Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany <<< text/html; name="interactive_spectrum.php": Unrecognized >>> -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol/JSpecView integration
> What we would like to do now is figure out a simple way to help users > quickly correlate peaks with atoms or vibfations. This is probably a > WebExport sort of functionality, I don't exactly know. All ideas are > welcome. The output would be a JCAMP-DX file. Looking for volunteers > for that. Should be a publication, I would think > Very nice idea, to make Jmol talk to Jspecview! In 2003 we tried to make this work for (then) MDL Chime and Jspecview with some success and transferred the files to work with Jmol now. First we had to convert the (so-called) jcampdx files (or the original file formats called "ASCI-Export") of the instruments involved in taking the spectra to jcampdx format (the hard part). This and annotating the spectra had to be done manually. So it was a tediuos work to do (not covered by the grant for our project) and we limited our efforts to very few examples. We did not use MOL files but PDB instead (because we tweaked the pdb specification to annotate 3D-models with a colour representation of molecular interaction potentials, which we could not do with MOL files), but you can see these files in Jmol / Jspecview (somewhat outdated versions I think) at http://www.oc-praktikum.de by selecting NOP-Nr.: 2003 or 1001, then Analytics -> 1H-NMR or 13C-NMR -> use the link on the right side called "interactive spectrum" Structures are geometrically optimized with MOPAC. Spectra are measured (not simulated) and not everything is correlated to the structure. If you are interested you can get the annotated jdx files and the pdb. There may be an easier and better way to do this all, if your plan works out. > In addition, if anyone already has correlated data -- NMR spectra in > JDX format with known mapping to atoms of a specific MOL file -- we'd > like to know about that. Does anybody have anything like that? We're > also looking for net-based applications that could, for example, be > sent a MOL file and have a simulated HNMR or CNMR spectrum returned, > packaged in JDX format, with the incorporated ##$Models and ##$Peaks > records. Any suggestions? > > Bob Hanson > > Reinhold Störmann ------ Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] new feature: Z-matrix reader
Am 20.11.2011 19:02, schrieb Angel Herráez: Info added to http://wiki.jmol.org/index.php/File_formats/Coordinates#Z-matrix and http://wiki.jmol.org/index.php/File_formats/Scripting#Script_inline_within_a_molecular_coordi nates_file Where is that format used? -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users This format is used by the MOPAC (Molecular Orbital PACkage) programs. (Good Idea to support that format, I use it a lot.) see: http://openmopac.net http://en.wikipedia.org/wiki/MOPAC Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to save a JMol script - and execute that script automatically on loading of the relevant page.
Solved at last! Thanks to all of you. It required some detective work on my side to get at the heart of the problem, so it might be helpful for you to know what went wrong. Yesterday I tested all available browsers (Firefox 5.0, IE 9, Chrome and Opera 11.50 with the Jmol page. All of them showed errors, but Opera was showing a different error than the other browsers. That seemed very strange to me. Opera said that the php script could not be found on localhost, while all other browsers had the java io error that Jmol could not be found. While all other browsers had no problem displaying "localhost/local/fernandez/external/jmol/LICENSE.TXT", Opera with "localhost/local/fernandez/external/jmol/LICENSE.TXT" gave: > HTTP ERROR: 404 > NOT_FOUND > > RequestURI=/local/fernandez/external/jmol/LICENSE.TXT > > Powered by jetty:// typing "http://localhost"; into Opera's address line showed me the root directory of a program I had to evaluate for work recently - instead of the root directory of my Apache installation! Jetty - according to its web site - is another http server, and was probably installed unknowingly together with the program. The program in question was not running. But after I deinstalled that program everything behaved normally again! Neither netstat -a nor an entry in "services" (on my windows vista machine) showed a process "jetty" or any process besides my local Apache using port 80. Of course I will give a report to the people who send me the program for evaluation. Greetings Reinhold -- FREE DOWNLOAD - uberSVN with Social Coding for Subversion. Subversion made easy with a complete admin console. Easy to use, easy to manage, easy to install, easy to extend. Get a Free download of the new open ALM Subversion platform now. http://p.sf.net/sfu/wandisco-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to save a JMol script - still not solved
Am 08.07.2011 18:31, schrieb Angel Herráez: > Oh, good for you, Reinhold! > That was a striking situation. > > Yes, 2nd calls of initialize are ignored by design in Jmol.js > > Is your popup menu now completely enabled? yes. I have to do all other things tomorrow. if any more problems turn up, I will inform you. thanks for all the help. > > All in all, I wouldn't expect the unsigned applet to offer any File> > Save options at all. For me (probably an older version of Jmol), the > whole File submenu is disabled > > > > -- > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to save a JMol script - still not solved
Am 08.07.2011 16:34, schrieb Rolf Huehne:
> On 07/08/2011 04:04 PM, Reinhold Störmann wrote:
>> Lets try to sort thesee things out correctly:
>>
>> 2. How can I verify that the signed applet is running and not the unsigned?
>>
> There are several indicators:
>
> 1) The first time you start the applet from a specific source there
> should pop up a security warning dialog. If you accept running the
> signed applet there it should run as a signed applet. If you don't
> accept it will still run but only like the unsigned applet.
>
> 2) The usual "Jmol" text at the bottom right of the applet frame (called
> "frank" within Jmol for some historical reason) is changed to a red
> "Jmol_S".
>
> 3) If you open the applet menu (e.g. with right-click) and go to "About
> Jmol" (or maybe it's translation to another language) then it is
> indicated behind the jmol version number:
> Jmol 11.6.8 (signed)
>
> (The "About Jmol" menu part changed in newer versions a little but I
> would expect that this information will still be there).
>
> You can try running the signed applet from this URL:
> http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&APPLET=signed
This url really starts the signed applet.
> There I invoke it explicitly:
> jmolInitialize("/ImgLibPDB/jmol/jmol-11.6.8", "JmolAppletSigned0.jar");
I changed my code to invoke the signed applet explicityl as you did, but
still the unsigned applet is loaded.
Cannot figure out why.
Closed all browser windows, and started the browser anew to remove
possible browser cache effects, still
jmolInitialize(\"external/jmol\",\"JmolAppletSigned0.jar\")
seems to load the unsigned applet.
Here is the content of the java console:
> Java Plug-in 1.6.0_25
> Verwendung der JRE-Version 1.6.0_25-b06 Java HotSpot(TM) Client VM
> Home-Verzeichnis des Benutzers = C:\Users\cheops
>
>
> c: Konsole löschen
> f: Objekte in Finalisierungswarteschlange finalisieren
> g: Speicherbereinigung
> h: Diese Hilfemeldung anzeigen
> l: ClassLoader-Liste ausgeben
> m: Speicherbelegung anzeigen
> o: Protokollierung auslösen
> q: Konsole ausblenden
> r: Richtlinien-Konfiguration neu laden
> s: System- und Bereitstellungseigenschaften ausgeben
> t: Threadliste ausgeben
> v: Thread-Stack ausgeben
> x: ClassLoader-Cache löschen
> 0-5: Trace-Stufe auf setzen
>
>
> security: property package.access value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.
> security: property package.access new value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.,com.sun.javaws
> security: property package.access value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.,com.sun.javaws
> security: property package.access new value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.,com.sun.javaws,com.sun.deploy
> security: property package.access value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.,com.sun.javaws,com.sun.deploy
> security: property package.access new value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.,com.sun.javaws,com.sun.deploy,com.sun.jnlp
> security: property package.definition value null
> security: property package.definition new value com.sun.javaws
> security: property package.definition value com.sun.javaws
> security: property package.definition new value
> com.sun.javaws,com.sun.deploy
> security: property package.definition value com.sun.javaws,com.sun.deploy
> security: property package.definition new value
> com.sun.javaws,com.sun.deploy,com.sun.jnlp
> security: property package.access value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.,com.sun.javaws,com.sun.deploy,com.sun.jnlp
> security: property package.access new value
> sun.,com.sun.xml.internal.ws.,com.sun.xml.internal.bind.,com.sun.imageio.,com.sun.javaws,com.sun.deploy,com.sun.jnlp,org.mozilla.jss
> security: property package.definition value
> com.sun.javaws,com.sun.deploy,com.sun.jnlp
> security: property package.definition new value
> com.sun.javaws,com.sun.deploy,com.sun.jnlp,org.mozilla.jss
> basic: Fortschritts-Listener hinzugefügt:
> sun.plugin.util.GrayBoxPainter$GrayBoxProgressListener@1d05c81
> basic: Plugin2ClassLoader.addURL parent called for
> http://localhost/local/fernandez/external/jmol/JmolApplet0.jar
> security: Blacklist-Revocation-Check ist aktiviert.
> security: Die Überprüfung der Liste vertrauenswürdiger Biblioth
Re: [Jmol-users] How to save a JMol script - still not solved
Lets try to sort thesee things out correctly:
1.
Is the script command
jmolInitialize("jmol/",true);
or more general
jmolInitialize("[Path to Jmoldirectory]/jmol/", true);
written correctly to initialize the signed applet?
(Or did I make a mistake here?)
2. How can I verify that the signed applet is running and not the unsigned?
Using the
File - Save script with state
still gives me the generated script in the JMol console and also in the
java console. (with the above invocation of the signed applet).
I DO NOT get a Save as Dialog.
So maybe the unsigned applet is running. If so, can you tell what went
wrong with invoking the signed applet?
I'm using php to generate the html, so the exact code I use is:
echo "
jmolInitialize(\"external/jmol/\",true);
jmolCheckBrowser(\"alert\", \"Your browser is incompatible. Please
upgrade your browser if possible.\", \"now\");
";
[backslashes are used as escapes for the double quotes)
Reinhold
Am 08.07.2011 14:46, schrieb Angel Herráez:
> Hi Reinhold
>
> I agree that this is becoming a big nuisance, but there's not much we
> can do on the Jmol side. It's a change in Java behaviour.
>
> Even though I posted about the select& drag method working in
> Windows (I was pretty sure it worked for me), just two days ago it
> has not worked for me, so I might be wrong at the time, or there are
> different circumstances, don't know. But I meant dragging from the
> script console, not the Java console. In this, Ctrl-C works, although
> if as you say the output is truncated, it's not going to be of much
> help.
>
> Let's keep searching for a trick, and listening.
>
> At least using the signed applet, can't you use the "write" command
> to save the script? Or even the popup menu, File> Save script with
> state. That should work (I am seeing it right now in a page of mine)
>
>
>> Using the
>> File - Save script with state
>> gives me the generated script in the JMol console and also in the java
>> console.
> That's not correct; it should open a Save As dialog. What version?
>
>
>
>
>
> --
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] How to save a JMol script - still not solved
> Having 3 different molecules in one JMol window, and after arranging
> them interactively to give the best representation of what I want to
> show, I stumbled upon the problem how to save this interactively
> generated script (on Windows Vista + Firefox 4.01 + JMol 12.0.39, if
> that matters).
>
> Using the
> File - Save script with state
> gives me the generated script in the JMol console and also in the java
> console.
>
> But I am unable to copy anything via CTRL-A, CTRL-C, CTRL-V into any
> editor program outside Java.
> Also it seems the consoles don't give me the option do save their
> contents ...
>
> So I' stuck (I dont want to copy the script by typing it symbol for
> symbol; it is quite long).
>
> Can anybody help?
>
> THanks
> Reinhold
>
I asked here above questions about a month ago, but unfortunately due to
lots of other work I had to do recently, I was unable to try out the
suggested solutions up to now.
1. Suggestion:
Using the signed applet
(
jmolInitialize("jmol/",true);
instead of
jmolInitialize("jmol/");
)
did not change anything. By the way I'm developing on localhost. So
there should be no issues with accessing URLs from anywhere else.
2. Suggestion (Angel Herráez)
Drag and drop the script from the jmol console to an editor (instead of
using CTRL-A, CTRL-C, CTRL-V)
does not work either. I always get the symbol that drag and drop is not
allowed
(no matter what editor I use, Windows Vista, JMol 12.0.39, Sun/Oracle
Java 1.6.0_25)
> Sorry to rescue this thread so late, but I found a fix.
>
> I've just found that, similar to what was described for MacOS, the cure for
> this limitation in
> Windows is to select the text in the Jmol script console and (rather than
> trying to copy it,
> which cannot be pasted outside Java) drag the selected text to a text editor.
> So, no need to open the Java console and copy from there. Just have a text
> editor at hand
> when you need to copy text that has been output to the Jmol script console.
>
> (Tested on WinXP, Sun/Oracle Java 1.6.0_25, Jmol 12.0.x)
Now I CAN copy Information from the JAVA console to an editor.
Unfortunately the Java console does not refelct all jmol commands,
especially the commands with coordinates are truncated:
> DATA "coord set"
> 119 ;
> Jmol Property Data Format 1 -- Jmol 12.0.39 2011-02-04 07:47;
> 1 C [LLW]0:A.C/1.1_#1 15.808979 12.575748 -1.9898928 ;
> 2 O [ZZZ]4:A.O/1.1_#2 1.9772998 18.798574 3.0733123 ;
> 3 C [LLW]0:A.C/1.1_#3 2.1830313 18.56621 1.7326368 ;
> 4 O [ZZZ]4:A.O/1.1_#4 1.6255851 19.29174 0.9535861 ;
> 5 N [LCW]446:A.N/1.1_#5 10.964918 14.905299 -2.3756077 ;
> 6 C [LCL]404:A.C/1.1_#6 9.894557 15.80536 -2.6844807 ;
> 7 C [LCL]404:A.C/1.1_#7 9.918614 16.426691 -3.9531403 ;
> 8 C [LCL]404:A.C/1.1_#8 8.856955 17.250237 -4.32592 ;
> 9 C [LCL]404:A.C/1.1_#9 7.7651854 17.454082 -3.4797227 ;
> 10 C [LCL]404:A.C/1.1_#10 7.762911 16.836826 -2.2138665 ;
> 11 C [LCL]404:A.C/1.1_#11 8.836377 16.036463 -1.7961241 ;
> 12 N [LCW]446:A.N/1.1_#12 6.5946965 16.979734 -1.3948852 ;
> 13 C [LLW]0:A.C/1.1_#13 6.5694203 16.79647 0.005976353 ;
> 14 O [ZZZ]446:A.O/1.1_#14 7.562506 16.774021 0.6928738 ;
> 15 C [LCL]404:A.C/1.1_#15 4.343219 17.670307 0.8542317 ;
> 16 C [LCL]404:A.C/1.1_#16 5.1769786 16.593086 0.5421457 ;
> 17 C [LCL]404:A.C/1.1_#17 4.7619824 15.277666 0.7813227 ;
> 18 C [LCL]404:A.C/1.1_#18 3.486769 15.038955 1.3139714 ;
> 19 C [LCL]404:A.C/1.1_#19 2.6473434 16.10605 1.6443704 ;
> 20 C [LCL]404:A.C/1.1_#20 3.0840995 17.417067 1.4142116 ;
> 21 C [LLW]0:A.C/1.1_#21 3.1124983 13.60282 1.5624653 ;
> 22 O [ZZZ]446:A.O/1.1_#22 3.803285 12.852937 2.214505 ;
> 23 N [LCW]446:A.N/1.1_#23 1.9148092 13.206674 0.92680573 ;
> 24 C [LCL]404:A.C/1.1_#24 1.4568963 11.855642 0.79157126 ;
> 25 C [LCL]404:A.C/1.1_#25 2.155736 10.77515 1.3444179 ;
> 26 C [LCL]404:A.C/1.1_#26 1.7208419 9.471325 1.0618236 ;
> 27 C [LCL]404:A.C/1.1_#27 0.56360507 9.242073 0.2919804 ;
> 28 C [LCL]404:A.C/1.1_#28 -0.14572828 10.338749 -0.20132324 ;
> 29 C [LCL]404:A.C/1.1_#29 0.28872105 11.644202 0.02622952 ;
> 30 N [LCW]446:A.N/1.1_#30 2.493695 8.337667 1.4737875 ;
> 31 C [LLW]0:A.C/1.1_#31 3.4159856 8.338484 2.5471625 ;
> 32 O [ZZZ]446:A.O/1.1_#32 3.4338934 9.187774 3.4046805 ;
> 33 C [LCL]404:A.C/1.1_#33 5.60258 7.4225307 1.8080117 ;
> 34 C [LCL]404:A.C/1.1_#34
> Trace message truncated for length over 10K
Only the Jmol console give the whole set of coordinates for my molecules.
So how I'm I supposed to get those new coordinates to disk?
(Making screenshots, saving them as jpg and submitting the 20-40 jpgs to
an OCR program?
There must be an easier way)
Greetings
Reinhold
-
[Jmol-users] How to save a JMol script
Having 3 different molecules in one JMol window, and after arranging them interactively to give the best representation of what I want to show, I stumbled upon the problem how to save this interactively generated script (on Windows Vista + Firefox 4.01 + JMol 12.0.39, if that matters). Using the File - Save script with state gives me the generated script in the JMol console and also in the java console. But I am unable to copy anything via CTRL-A, CTRL-C, CTRL-V into any editor program outside Java. Also it seems the consoles don't give me the option do save their contents ... So I' stuck (I dont want to copy the script by typing it symbol for symbol; it is quite long). Can anybody help? THanks Reinhold -- Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to "Load Append" in Jmol
Am 13.05.2011 19:03, schrieb Robert Hanson: right-click problem: We could put some debugging lines in if you want, but it will have to be for 12.1, not 12.0. Do you want me to do that? -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users If you could do that it would probably be helpful in finding the error. For my part I'm not a java expert. I'm doing programming in php. Just tell me what version of jmol I have to use then. Thanks Reinhold -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to "Load Append" in Jmol
Am 11.05.2011 19:08, schrieb Robert Hanson:
2011/5/11 Reinhold Störmann <mailto:rsto...@uni-bremen.de>>
But I still get some strange behavior of the jmol Applet that
doesn't necessarily have to be caused by my script:
After opening the jmol menue (right mouse button), a small warning
symbol appears to the right of the first menu entry ("all
molecules") and subsequently the menu doesn not open again on
klicking the right mouse button.
(jmol 12.0.39, java 1.6.0_25, Vista, FF 4.0 or Opera 10)
That would be a Java bug. I've worked with them before on this, and we
settled on the nuanced warning rather than a big bright frame or
something worse. Sounds like there may be an issue there. Lately I
haven't seen it, but that does sound like a problem. If you can report
back what is in the Java console (Java, not Jmol) after that, it would
be good to see. I doubt there is anything there, though. I'm using
1.6.0_24.
Any idea, why I can't open the menu again (e.g. to select another
molecule to rotate)?
Is something syntactically wrong in the commands?
Try opening the menu by clicking on the Jmol logo in the bottom right
corner.
Reinhold
--
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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I tried your suggested work-around for the supposed java bug to open the
jmol menu by clicking on the jmol logo. That works.
Also the java console does not give any hint about the bug that's
causing the problem.
Java Plug-in 1.6.0_25
Verwendung der JRE-Version 1.6.0_25-b06 Java HotSpot(TM) Client VM
Home-Verzeichnis des Benutzers = C:\Users\cheops
c: Konsole löschen
f: Objekte in Finalisierungswarteschlange finalisieren
g: Speicherbereinigung
h: Diese Hilfemeldung anzeigen
l: ClassLoader-Liste ausgeben
m: Speicherbelegung anzeigen
o: Protokollierung auslösen
q: Konsole ausblenden
r: Richtlinien-Konfiguration neu laden
s: System- und Bereitstellungseigenschaften ausgeben
t: Threadliste ausgeben
v: Thread-Stack ausgeben
x: ClassLoader-Cache löschen
0-5: Trace-Stufe auf setzen
The text above is the only thing in java console. There is a second java
console open, but that contains jmol commands and messages:
Java Plug-in 1.6.0_25
Verwendung der JRE-Version 1.6.0_25-b06 Java HotSpot(TM) Client VM
Home-Verzeichnis des Benutzers = C:\Users\cheops
c: Konsole löschen
f: Objekte in Finalisierungswarteschlange finalisieren
g: Speicherbereinigung
h: Diese Hilfemeldung anzeigen
l: ClassLoader-Liste ausgeben
m: Speicherbelegung anzeigen
o: Protokollierung auslösen
q: Konsole ausblenden
r: Richtlinien-Konfiguration neu laden
s: System- und Bereitstellungseigenschaften ausgeben
t: Threadliste ausgeben
v: Thread-Stack ausgeben
x: ClassLoader-Cache löschen
0-5: Trace-Stufe auf setzen
urlImage=jar:http://localhost/local/fernandez/external/jmol/JmolApplet0.jar!/jmol75x29x8.gif
Jmol applet jmolAppletcation__999342465799502__ initializing
AppletRegistry.checkIn(jmolAppletcation__999342465799502__)
1714 script command tokens
applet context: -applet
appletDocumentBase=http://localhost/local/fernandez/showmodel.php?model1=NF-270&model2=IM14&model3=%28CF3SO2%292N&wwidth=800&wheight=600
appletCodeBase=http://localhost/local/fernandez/external/jmol/
(C) 2009 Jmol Development
Jmol Version: 12
Re: [Jmol-users] Question to "Load Append" in Jmol
Hi,
first of all a lot of thanks to all of you for the help provided.
Hi,
http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#setmisc
There is a command for rotation and translation each:
set allowRotateSelected FALSE
When set TRUE, this parameter allows user rotation of the molecule
containing the selected atom using the mouse (holding ALT down while
dragging). The coordinates of the rotated molecule will be sightly
degraded
in this process.
set dragSelected OFF
When ON, allows the user to move selected atoms by pressing
ALT-SHIFT-LEFT
and dragging; when combined with set pickingstyle DRAG, just
LEFT-dragging
moves the atoms, and the ALT and SHIFT keys are not required.
Best
Alex
I tried to use the commands suggested by Alex to solve my problem.
The line (.php program) below successfully loads 3 molecules into one
jmolApplet, and after selecting one molecule, I can rotate it and
translate it with ALT and ALT-SHIFT-LEFT respectively.
*jmolApplet(size=[$wwidth, $wheight], script='load $pdb1; select all;
set ambient 45; wireframe 0.15; spacefill 20%; set bonds off; zoom 50;
set allowRotateSelected TRUE; set dragSelected TRUE; load append $pdb2;
load append $pdb3; frame *; display 1.1,2.1,3.1', 'cation');*
Variables are php-variable; $wwidth, $wheight are the dimensions of the
jmol applet; and $pdb1, $pdb2, $pdb3 are the .pdb files to load.
But I still get some strange behavior of the jmol Applet that doesn't
necessarily have to be caused by my script:
After opening the jmol menue (right mouse button), a small warning
symbol appears to the right of the first menu entry ("all molecules")
and subsequently the menu doesn not open again on klicking the right
mouse button.
(jmol 12.0.39, java 1.6.0_25, Vista, FF 4.0 or Opera 10)
Any idea, why I can't open the menu again (e.g. to select another
molecule to rotate)?
Is something syntactically wrong in the commands?
Reinhold
--
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What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
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[Jmol-users] Question to "Load Append" in Jmol
At the moment I'm trying to load more than one molecule from multiple pdb data files into one Jmol instance. It works fine using the load append command, and I can display any of the loaded molecules separately or all together. But I can't seem to find any function that allows me to manipulate (rotate, move) only one of the appended moleculesinteractively from the Jmol applet. I suppose there actually is such a function but I don't know how to activate it. Selecting only one out of two molecules and rotating it still rotates both molecules. Can anyone of you give me a hint how to move one molecule relative to the other interactively? Or, if this is only possible using script commands, where can I find a tutorial on that? thanks a lot in advance Reinhold Störmann -- Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
