[Jmol-users] Day of reckoning is today
ChemTube3D http://www.chemtube3d.com was ready for the day of reckoning and has migrated to JSmol. I would like to thank Bob Hanson and the rest of the community for their outstanding efforts to allow us to replicate the superb experience that was Jmol, but now miraculously without Java. I have a little survey running on ChemTube3D at present (Were you able to view the structure in 3D and interact with it?) and so far I have 100% Yes or Yes, eventually. I am also seeing traffic from mobile devices - they would have been disappointed before. We have added new sections on Inorganic Chemistry and a large collection of structures in the last few days. JSmol is a triumph! Best regards Nick -- Nick Greevesvia OS X Mail Director of Teaching and Learning Department of Chemistry University of Liverpool Donnan and Robert Robinson Laboratories Crown Street, LIVERPOOL L69 7ZD U.K. Email address:ngree...@liverpool.ac.ukmailto:ngree...@liverpool.ac.uk WWW Pages:http://www.chemtube3d.com Tel:+44 (0)151-794-3506 (3500 secretary) Dept Fax: +44 (0)151-794-3588 On 16 Jan 2014, at 07:22, jmol-users-requ...@lists.sourceforge.netmailto:jmol-users-requ...@lists.sourceforge.net wrote: Day of reckoning is today -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Day of reckoning is today
I've been trying my page today with both Java and JS versions of Jmol. While JS of course works fine, I get a weird problem with the Java version - the applet loads fine, but I can't seem to load files into it. Anyone has experience with this, or knows if it could be related with the changes in security policies? I know it was working until yesterday - but then again, I'm using a certified (14.0.2) version of Jmol. Maybe it's a matter of updating the JRE? Simone 2014/1/16 Greeves, Nick ngree...@liverpool.ac.uk ChemTube3D http://www.chemtube3d.com was ready for the day of reckoning and has migrated to JSmol. I would like to thank Bob Hanson and the rest of the community for their outstanding efforts to allow us to replicate the superb experience that was Jmol, but now miraculously without Java. I have a little survey running on ChemTube3D at present (Were you able to view the structure in 3D and interact with it?) and so far I have 100% Yes or Yes, eventually. I am also seeing traffic from mobile devices - they would have been disappointed before. We have added new sections on Inorganic Chemistry and a large collection of structures in the last few days. JSmol is a triumph! Best regards Nick -- Nick Greevesvia OS X Mail Director of Teaching and Learning Department of Chemistry University of Liverpool Donnan and Robert Robinson Laboratories Crown Street, LIVERPOOL L69 7ZD U.K. Email address:ngree...@liverpool.ac.uk WWW Pages:http://www.chemtube3d.com Tel:+44 (0)151-794-3506 (3500 secretary) Dept Fax: +44 (0)151-794-3588 On 16 Jan 2014, at 07:22, jmol-users-requ...@lists.sourceforge.net wrote: Day of reckoning is today -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Nuovo indirizzo e-mail: simonesturni...@gmail.com -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Day of reckoning is today
On 16 Jan 2014, at 09:43, Greeves, Nick ngree...@liverpool.ac.uk wrote: ChemTube3D http://www.chemtube3d.com was ready for the day of reckoning and has migrated to JSmol. I would like to thank Bob Hanson and the rest of the community for their outstanding efforts to allow us to replicate the superb experience that was Jmol, but now miraculously without Java. I have a little survey running on ChemTube3D at present (Were you able to view the structure in 3D and interact with it?) and so far I have 100% Yes or Yes, eventually. I am also seeing traffic from mobile devices - they would have been disappointed before. We have added new sections on Inorganic Chemistry and a large collection of structures in the last few days. JSmol is a triumph! Indeed it is! But we still need some progress on the speeds of surface rendering. Surfaces with lots of elements can render up to about 25 times slower than the equivalent Java does. The trick at the moment is to produce such surfaces are lower resolution than one normally would. I suppose in truth that the speed of the graphics components of tablets will erode some of that factor of 25, but I doubt it will suffice. I dont know if the eventual widespread support for WebGL on tablets might be what we are basing our hopes on? And to be fair, if you replace all old applet incarnations with the newly signed one from Bob, Java continues to work just fine even with the most recent update! This is what we did with instances of Java on the RSC and ACS journals sites, and they are now working just fine! signature.asc Description: Message signed with OpenPGP using GPGMail -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrate.htm for Gaussian output?
Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: jmolApplet0 = Jmol.getApplet(jmolApplet0, Info) Matt Kubasik From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thursday, January 16, 2014 2:22 AM To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] vibrate.htm for Gaussian output? We identified a problem with jmolGetPropertyAsArray today, and that may be the problem. Please try the version at http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.15.zip ___JmolVersion=14.1.6_dev_2014.01.15 bug fix: GETPROPERTY command and function can return SV.toString() rather than property escaped value bug fix: Jmol.getPropertyAsArray for certain arrays returns string [object Array] If that doesn't solve the problem, let me know. Bob On Wed, Jan 15, 2014 at 6:34 PM, Kubasik, Matt mkuba...@fairfield.edumailto:mkuba...@fairfield.edu wrote: Dear Bob and List, I've been trying to adapt Bob's vibrate.htm document to 1. read local Gaussian files (containing normal mode info) ; 2. Provide a drop-down menu of the normal modes. Non-working page is found here: www.neon22.com/jsmol/jsmol/jsmolvib700_e.htmhttp://www.neon22.com/jsmol/jsmol/jsmolvib700_e.htm I think my problem is with the syntax of jmol.getpropertyasarray. Using var InfoM = Jmol.GetPropertyAsArray(JmolApplet0,modelinfo.models.namehttp://modelinfo.models.name) Gives the following int the javascript console: Uncaught ReferenceError: JmolApplet0 is not defined Any ideas? Matt PS A more direct adaptation for Gaussian files for vibrate.htm is here: http://www.neon22.com/jsmol/jsmol/vibrateMKd_6.htm This version produces a drop down list as with Bob's original vibrate.htm. But for this version, the read button does not function. Hints for fixing either attempt would be appreciated. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
I am having trouble getting Jsmol to load gzipped files as well. Can someone
point me to the exact place to enter my server address in Jmol2.js? I’ve done
this for the two places where a search for “php” turned up.
Unzipped files are loading fine.
Thanks,
David
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From: Christopher Masi cm...@westfield.ma.edumailto:cm...@westfield.ma.edu
Reply-To:
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Friday, January 10, 2014 at 10:21 AM
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
Angel,
Thanks.
On Jan 10, 2014, at 10:28 AM, Angel Herráez
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:
Hello, Chris
A few things to check:
1- Have you pointed to the jmol.php file in your own server?
No, I hadn’t.
Now my header looks like this
script type=text/javascript src=../../reuse/JSmol.min.js/script
script type=text/javascript src=../../reuse/Jmol.js/script !--location
of renamed Jmol2.js library--
script type=text/javascript
var Info = {
j2sPath: ../../reuse/j2s”, //location of j2s directory on my server
use: HTML5,
serverURL: ../../reuse/php/jsmol.php” //location of jsmol.php on my server
};
/script
That is
specified in definition of the Info variable of J(S)mol, either in
your own page or in the Jmol2.js file. As far as I know, loading of
binary files relies of that php file and it must be in the same
server for full operation. The default Info points to StOlaf server,
so you need to set it properly.
It took me a little while to find how to set that setting in the “Info”
variable, but eventually I found it in one of the sample files and on the JSmol
wiki here
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#JSmol
2- I have also used Apache for running a local webserver, but I think
it may not include PHP. The other I have tested is EasyPHP which
indeed includes a PHP processor in addition to the web server.
In any case, in the end it will be the real online web server which
will have to provide PHP support.
I bought the “Server” app from the Apple app store (I think it was $20), and
there’s a checkbox that says “Enable PHP web applications”. I don’t know if the
server app is just a UI for configuring all the stuff that’s installed with
Mavericks, or if you get more server software when you buy the server app (I
suspect it’s the former). Downloading gzipped files works now, but the first
time a page loads a gzipped file I get the following error message,
JmolCore.js: synchronous binary file transfer is requested but not available”
but everything loads just fine after that error message is dismissed.
I just tested it on the campus server, and I get the same error the first time
a gzipped file is requested, but the file loads once the dialogue box is
dismissed.
Thanks for the help!
Chris
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Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
Hi David
Jmol2.js has this:
Jmol.Info = { // overrides jmolInitialize()
//jarPath: java,
//jarFile: JmolAppletSigned0.jar,
//j2sPath: j2s,
use: HTML5, // could be JAVA or HTML5
disableJ2SLoadMonitor: false,
disableInitialConsole: true
}
You need this:
[...]
use: HTML5,
serverURL: php/jsmol.php, //pointing to the correct folder in your
server
disableJ2SLoadMonitor: false,
disableInitialConsole: true
}
See e.g.
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Setting_paramete
rs
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Re: [Jmol-users] vibrate.htm for Gaussian output?
Matt, There was some list discussion of this a while back, and I'm still not sure what was recommended at the time. The discussion related to the use of the following in the head JavaScript prior to the body declaration: var jmolApplet0; I think the statement was made that this was no longer needed. I had some problems leaving it out, so I just continued to include it in my pages. If I have 10 JSmol objects in the body, I do 10 instantiations in the head. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 16, 2014, at 9:00 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: jmolApplet0 = Jmol.getApplet(jmolApplet0, Info) Matt Kubasik From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thursday, January 16, 2014 2:22 AM To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] vibrate.htm for Gaussian output? We identified a problem with jmolGetPropertyAsArray today, and that may be the problem. Please try the version at http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.15.zip ___JmolVersion=14.1.6_dev_2014.01.15 bug fix: GETPROPERTY command and function can return SV.toString() rather than property escaped value bug fix: Jmol.getPropertyAsArray for certain arrays returns string [object Array] If that doesn't solve the problem, let me know. Bob On Wed, Jan 15, 2014 at 6:34 PM, Kubasik, Matt mkuba...@fairfield.edumailto:mkuba...@fairfield.edu wrote: Dear Bob and List, I've been trying to adapt Bob's vibrate.htm document to 1. read local Gaussian files (containing normal mode info) ; 2. Provide a drop-down menu of the normal modes. Non-working page is found here: www.neon22.com/jsmol/jsmol/jsmolvib700_e.htmhttp://www.neon22.com/jsmol/jsmol/jsmolvib700_e.htm I think my problem is with the syntax of jmol.getpropertyasarray. Using var InfoM = Jmol.GetPropertyAsArray(JmolApplet0,modelinfo.models.namehttp://modelinfo.models.name) Gives the following int the javascript console: Uncaught ReferenceError: JmolApplet0 is not defined Any ideas? Matt PS A more direct adaptation for Gaussian files for vibrate.htm is here: http://www.neon22.com/jsmol/jsmol/vibrateMKd_6.htm This version produces a drop down list as with Bob's original vibrate.htm. But for this version, the read button does not function. Hints for fixing either attempt would be appreciated. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list
[Jmol-users] Applet white list
Robert Lancashire brought this to my attention: https://blogs.oracle.com/java-platform-group/entry/upcoming_exception_site_list_in?msgid=3-9509477622 The basic idea is that if you have unsigned applets -- older applets or ones that you are self-signing -- then you can test them on your own local site, and you can notify page visitors to (presumably temporarily) white-list your site if they want to view your older applets. Bob -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrate.htm for Gaussian output?
Thanks, Otis. Yes, the page has the var declaration in head. It seems the applet loads and all the other aspects of the page work properly. The error occurs when trying script containing jmol.getpropertyasarray. I tried w/ and w/o declaration in head, but it did not make a difference. Matt On 1/16/14 9:18 AM, Otis Rothenberger osrot...@chemagic.com wrote: Matt, There was some list discussion of this a while back, and I'm still not sure what was recommended at the time. The discussion related to the use of the following in the head JavaScript prior to the body declaration: var jmolApplet0; I think the statement was made that this was no longer needed. I had some problems leaving it out, so I just continued to include it in my pages. If I have 10 JSmol objects in the body, I do 10 instantiations in the head. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 16, 2014, at 9:00 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: jmolApplet0 = Jmol.getApplet(jmolApplet0, Info) Matt Kubasik From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thursday, January 16, 2014 2:22 AM To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] vibrate.htm for Gaussian output? We identified a problem with jmolGetPropertyAsArray today, and that may be the problem. Please try the version at http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.15.zip ___JmolVersion=14.1.6_dev_2014.01.15 bug fix: GETPROPERTY command and function can return SV.toString() rather than property escaped value bug fix: Jmol.getPropertyAsArray for certain arrays returns string [object Array] If that doesn't solve the problem, let me know. Bob On Wed, Jan 15, 2014 at 6:34 PM, Kubasik, Matt mkuba...@fairfield.edumailto:mkuba...@fairfield.edu wrote: Dear Bob and List, I've been trying to adapt Bob's vibrate.htm document to 1. read local Gaussian files (containing normal mode info) ; 2. Provide a drop-down menu of the normal modes. Non-working page is found here: www.neon22.com/jsmol/jsmol/jsmolvib700_e.htm http://www.neon22.com/jsmol/jsmol/jsmolvib700_e.htmhttp://www.neon22.com /jsmol/jsmol/jsmolvib700_e.htm I think my problem is with the syntax of jmol.getpropertyasarray. Using var InfoM = Jmol.GetPropertyAsArray(JmolApplet0,modelinfo.models.namehttp://modelinfo .models.name http://modelinfo.models.name/) Gives the following int the javascript console: Uncaught ReferenceError: JmolApplet0 is not defined Any ideas? Matt PS A more direct adaptation for Gaussian files for vibrate.htm is here: http://www.neon22.com/jsmol/jsmol/vibrateMKd_6.htm This version produces a drop down list as with Bob's original vibrate.htm. But for this version, the read button does not function. Hints for fixing either attempt would be appreciated. --- --- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktr k ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 --- --- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktr k ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Re: [Jmol-users] Day of reckoning is today
Simone, could you try Jmol 14.1.6_dev, please? See http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.15.zip That's the version with the fix for the [object Array] problem. On Thu, Jan 16, 2014 at 4:50 AM, Simone Sturniolo simonesturni...@gmail.com wrote: I've been trying my page today with both Java and JS versions of Jmol. While JS of course works fine, I get a weird problem with the Java version - the applet loads fine, but I can't seem to load files into it. Anyone has experience with this, or knows if it could be related with the changes in security policies? I know it was working until yesterday - but then again, I'm using a certified (14.0.2) version of Jmol. Maybe it's a matter of updating the JRE? Simone 2014/1/16 Greeves, Nick ngree...@liverpool.ac.uk ChemTube3D http://www.chemtube3d.com was ready for the day of reckoning and has migrated to JSmol. I would like to thank Bob Hanson and the rest of the community for their outstanding efforts to allow us to replicate the superb experience that was Jmol, but now miraculously without Java. I have a little survey running on ChemTube3D at present (Were you able to view the structure in 3D and interact with it?) and so far I have 100% Yes or Yes, eventually. I am also seeing traffic from mobile devices - they would have been disappointed before. We have added new sections on Inorganic Chemistry and a large collection of structures in the last few days. JSmol is a triumph! Best regards Nick -- Nick Greevesvia OS X Mail Director of Teaching and Learning Department of Chemistry University of Liverpool Donnan and Robert Robinson Laboratories Crown Street, LIVERPOOL L69 7ZD U.K. Email address:ngree...@liverpool.ac.uk WWW Pages:http://www.chemtube3d.com Tel:+44 (0)151-794-3506 (3500 secretary) Dept Fax: +44 (0)151-794-3588 On 16 Jan 2014, at 07:22, jmol-users-request@lists.sourceforge.netwrote: Day of reckoning is today -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Nuovo indirizzo e-mail: simonesturni...@gmail.com -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrate.htm for Gaussian output?
Capital J? Uncaught ReferenceError: JmolApplet0 is not defined. On Thu, Jan 16, 2014 at 9:00 AM, Kubasik, Matt mkuba...@fairfield.eduwrote: Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrate.htm for Gaussian output?
Wow! Good catch, Bob! But correcting to lowercase j in var InfoM = Jmol.GetPropertyAsArray(jmolApplet0,modelinfo.models.name) Now offers in Chrome's javasccript console: Uncaught TypeError: Object #Object has no method 'GetPropertyAsArray' Matt On 1/16/14 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Capital J? Uncaught ReferenceError: JmolApplet0 is not defined. On Thu, Jan 16, 2014 at 9:00 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Day of reckoning is today
Nah, now JSmol enters into some infinite or very long loop when loading the file and Firefox crashes (it happens on the line Script: file:///home/wml08325/Desktop/MagresViewHg/MagresView_1_2bis/jsmol/JSmol.min.js:331). Simone 2014/1/16 Robert Hanson hans...@stolaf.edu Right, the weak link now is surface creation. That is computationally expensive, and JavaScript is boarder-line acceptable in terms of doing it. Users needing relatively large or slow-to-render surfaces are STRONGLY encouraged to use the JVXL format. This is quite easy: 1) create your surface in a test environment, probably the free-standing Jmol application (Jmol.jar) 2) execute isosurface CACHE Your surface has just be replaced by a JVXL equivalent, and that has been cached in memory. You may see ever-so-slightly a change in the surface. If it is anything significant, I want to know about it. 3) write PNGJ xxx.png This saves a PNG+ZIP file format that contains all files necessary to reproduce the state, including the surface JVXL file. One file. Compressed. 4) load xxx.png or script xxx.png This tests the loading. You should see near-instantaneous surface creation, even with JavaScript. Bob On Thu, Jan 16, 2014 at 5:03 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: Indeed it is! But we still need some progress on the speeds of surface rendering. Surfaces with lots of elements can render up to about 25 times slower than the equivalent Java does. The trick at the moment is to produce such surfaces are lower resolution than one normally would. -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Nuovo indirizzo e-mail: simonesturni...@gmail.com -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-users Digest, Vol 92, Issue 7,Message 4
Jiayi, Yes, I fully appreciate the difficulty. Be sure to use Eclipse or, if you must, some other programming environment. Then you can follow function call links forwards and backwards, and walk through the code using breakpoints. If you don't have this capability, you will go crazy. The starting point for all scripting is in org.jmol.script.ScriptEvaluator. For example, there is a load() method there that is called from execution of the LOAD command. org.jmol.viewer.Viewer is the central processor. There is a somewhat-out-of-date graphic at http://chemapps.stolaf.edu/jmol/viewer.png that may be helpful. Beyond that, we are talking about hundreds of calls. The Jmol code consists of 474 classes and 3075 methods. Your questions: Q1. atom types are all determined in various readers found in org.jmol.adapter.readers. Not all readers generate atom types. Q2. structure comparisons are carried out using SMILES matching, with selective use of chirality. Search the code for enantiomer and you will see how that works. Bob On Thu, Jan 16, 2014 at 8:41 AM, jiayi.zhou jiayi.z...@mun.ca wrote: Hi, Robert: I know I have to look into the source code. I think you can understand it's really hard to read other's code. Is it possible for you to tell me some key functions' names or the entrance function names such as: 1. The function how Jmol get the atom types even the structure file only contains the atoms' coordinators when the user called load? 2. The function how Jmol know the two structures to be compared are isomers? Thank you. -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrate.htm for Gaussian output?
lower case g. :) On Thu, Jan 16, 2014 at 10:16 AM, Kubasik, Matt mkuba...@fairfield.eduwrote: Wow! Good catch, Bob! But correcting to lowercase j in var InfoM = Jmol.GetPropertyAsArray(jmolApplet0,modelinfo.models.name) Now offers in Chrome's javasccript console: Uncaught TypeError: Object #Object has no method 'GetPropertyAsArray' Matt On 1/16/14 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Capital J? Uncaught ReferenceError: JmolApplet0 is not defined. On Thu, Jan 16, 2014 at 9:00 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrate.htm for Gaussian output?
Unbelievable. Thanks! I'm sure I'll be back... On 1/16/14 10:28 AM, Robert Hanson hans...@stolaf.edu wrote: lower case g. :) On Thu, Jan 16, 2014 at 10:16 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Wow! Good catch, Bob! But correcting to lowercase j in var InfoM = Jmol.GetPropertyAsArray(jmolApplet0,modelinfo.models.name http://modelinfo.models.name) Now offers in Chrome's javasccript console: Uncaught TypeError: Object #Object has no method 'GetPropertyAsArray' Matt On 1/16/14 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Capital J? Uncaught ReferenceError: JmolApplet0 is not defined. On Thu, Jan 16, 2014 at 9:00 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: -- Robert M. Hanson Larson-Anderson 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 --- --- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktr k ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrate.htm for Gaussian output?
Thanks, Bob, Otis, and the list for your help. Still needing some cleaning up (especially wrt echoing frame names), the page is here: http://www.neon22.com/jsmol/jsmol/jsmolvib.htm Matt On 1/16/14 10:41 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Unbelievable. Thanks! I'm sure I'll be back... On 1/16/14 10:28 AM, Robert Hanson hans...@stolaf.edu wrote: lower case g. :) On Thu, Jan 16, 2014 at 10:16 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Wow! Good catch, Bob! But correcting to lowercase j in var InfoM = Jmol.GetPropertyAsArray(jmolApplet0,modelinfo.models.name http://modelinfo.models.name) Now offers in Chrome's javasccript console: Uncaught TypeError: Object #Object has no method 'GetPropertyAsArray' Matt On 1/16/14 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Capital J? Uncaught ReferenceError: JmolApplet0 is not defined. On Thu, Jan 16, 2014 at 9:00 AM, Kubasik, Matt mkuba...@fairfield.edu wrote: Bob, The previous problem persists. When I request the page to show a drop-down menu of frames/frame names, Chrome's javascript console still offers: Uncaught ReferenceError: JmolApplet0 is not defined. Initializing jsmol is new to me. Maybe I'm doing it wrong. I have var Info defined in the page's head tag and in body I have: -- Robert M. Hanson Larson-Anderson 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 --- --- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktr k ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 --- --- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktr k ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
David,
Found it…
Warning: I have no idea what I’m doing, and I could be breaking everything. By
trial and error I discovered the following:
I couldn’t get gz file download to work by putting anything in the jmol2.js
file. I thought the “serverURL belonged between lines 38 and 37, but that
didn’t work.
It occurred to me that the JSmol.min.js file was being called by my page, so I
decided to search the JSmol.min.js file. I found multiple occurrences for the
“serverURL” value. On line 269 I replaced the
“http://your.server.here/jsmol.php” with a path to my php file and it worked.
It worked when I used the complete URL, and it worked when I used a relative
path. However, it has occurred to me that the relative path will not always be
the same. The relative path that seems to matter here is not the path from
where the JSmol.min.js file resides to the Jmol.php file but the relative path
from where that file is being called from (the location of the html file) to
the Jmol.php file.
Since I test my pages on my personal computer before uploading them to a
server, I don’t want to hard code a URL (http://blah.blah.blah/php/jmol.php)
into this file. Since I may not always call JSmol from the directories that are
always at the same depth in my web pages, I think that I am going to keep
putting the “serverURL:” value in the header of the page that calls for JSmol.
That way I can use relative paths and I can get the pages to load regardless of
the server that is hosting them.
So in the headers of the pages that call JSmol I have this.
script type=text/javascript
var Info = {
j2sPath: ../../reuse/j2s,
use: HTML5,
serverURL: ../../reuse/php/jsmol.php
};
Jmol._alertNoBinary = false;
/script
The Jmol._alertNoBinary= false; was suggested to suppress and error message
that Safari keeps giving when it goes to download the file. The error still
shows up in Safari’s “Error Console” but it has no effect that I can see on the
loading of the page.
I haven’t finished switching everything over, but so far it has been working.
Chris
On Jan 16, 2014, at 8:47 AM, Marcey, David mar...@callutheran.edu wrote:
I am having trouble getting Jsmol to load gzipped files as well. Can someone
point me to the exact place to enter my server address in Jmol2.js? I’ve done
this for the two places where a search for “php” turned up.
Unzipped files are loading fine.
Thanks,
David
[…]
On Jan 10, 2014, at 10:28 AM, Angel Herráez angel.herr...@uah.es wrote:
Hello, Chris
A few things to check:
1- Have you pointed to the jmol.php file in your own server?
No, I hadn’t.
Now my header looks like this
script type=text/javascript src=../../reuse/JSmol.min.js/script
script type=text/javascript src=../../reuse/Jmol.js/script
!--location of renamed Jmol2.js library--
script type=text/javascript
var Info = {
j2sPath: ../../reuse/j2s”, //location of j2s directory on my server
use: HTML5,
serverURL: ../../reuse/php/jsmol.php” //location of jsmol.php on my server
};
/script
That is
specified in definition of the Info variable of J(S)mol, either in
your own page or in the Jmol2.js file. As far as I know, loading of
binary files relies of that php file and it must be in the same
server for full operation. The default Info points to StOlaf server,
so you need to set it properly.
It took me a little while to find how to set that setting in the “Info”
variable, but eventually I found it in one of the sample files and on the
JSmol wiki here
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#JSmol
[…]
Thanks for the help!
Chris
[…]
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Re: [Jmol-users] display echo while calculating
This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. set echo top center; echo Calculating surface...; refresh; isosurface mySurface molecular; echo; Jaim On Jan 15, 2014, at 7:03 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: echo and refresh will certainly work for this. But realize that there is no updating it, because the calculation is not interruptable at all, including updating any such message. On Wed, Jan 15, 2014 at 6:18 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: I would like to have a message “Working …” while Jmol is calculating and rendering. The following script displays the message only while rendering. There’s no message while calculating. I’ve added some refresh commands just in case, but same result. Tried with different representations instead of dots. Isosurface solvent is the worst example, where there seems to be no activity at all for a long time, then in a fast sequence I get the message, the rendering, and the message removed. select all; set echo middle center; echo Working ...|Please wait; font echo 20 ariel; color echo green; refresh; dots 100%; refresh; set echo OFF; Suggestions? On Jan 13, 2014, at 3:25 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: That's right, too. In this case you are putting a script into the queue and then immediately and independently firing the alert message. Your initial way is correct; just add a REFRESH command prior to that if you want the model to be displayed during the alert. On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Even if adding refresh to Jmol.script, the alert happens before the model gets loaded: Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;'); alert(“Back”); Jaim On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es wrote: I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk
Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
Chris, are you calling Jmol2.js before or after JSmol.min.js? That could be a reason for parameters not being applied. JSmol.min.js includes some defaults. I think you need Jmol2.js after it. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
Good sleuthing. I have added serverURL to the default Info block in Jmol2.js and added a comment about it there. If you can avoid making any changes to JSmol.min.js, that's wise. A real headache to maintain if you do. I don't recommend making this entry relative unless you are absolutely certain that all your files are all in the same relative position. It also will only work for creating PNG or PNGJ files if you have it on a server; PHP files won't be processed locally. As long as you local-test with FireFox, JSmol won't be calling that php file for file loading, only for file creation. Bob On Thu, Jan 16, 2014 at 12:13 PM, Christopher Masi cm...@westfield.ma.eduwrote: David, Found it… Warning: I have no idea what I’m doing, and I could be breaking everything. By trial and error I discovered the following: I couldn’t get gz file download to work by putting anything in the jmol2.js file. I thought the “serverURL belonged between lines 38 and 37, but that didn’t work. It occurred to me that the JSmol.min.js file was being called by my page, so I decided to search the JSmol.min.js file. I found multiple occurrences for the “serverURL” value. On line 269 I replaced the “ http://your.server.here/jsmol.php” with a path to my php file and it worked. It worked when I used the complete URL, and it worked when I used a relative path. However, it has occurred to me that the relative path will not always be the same. The relative path that seems to matter here is not the path from where the JSmol.min.js file resides to the Jmol.php file but the relative path from where that file is being called from (the location of the html file) to the Jmol.php file. Since I test my pages on my personal computer before uploading them to a server, I don’t want to hard code a URL ( http://blah.blah.blah/php/jmol.php) into this file. Since I may not always call JSmol from the directories that are always at the same depth in my web pages, I think that I am going to keep putting the “serverURL:” value in the header of the page that calls for JSmol. That way I can use relative paths and I can get the pages to load regardless of the server that is hosting them. - Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
then that's a bug. That should work perfectly. Bob -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
Yes, I think I found it. *delay 0.01 *should work even though *refresh *does not: *set echo top leftecho working...* *delay 0.01* *echo* Please try that; I'll also get *refresh *working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 ( http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5 ). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edu wrote: Yes, I think I found it. *delay 0.01 *should work even though *refresh *does not: *set echo top leftecho working...* *delay 0.01* *echo* Please try that; I'll also get *refresh *working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 ( http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5 ). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
Angel,
Yes, I think I’m calling the JSmol.min.js file first.
In the header of the html page, I’ve got this
script type=text/javascript src=../../reuse/JSmol.min.js/script
script type=text/javascript src=../../reuse/Jmol.js/script
!--location of renamed Jmol2.js library--
script type=text/javascript
var Info = {
j2sPath: ../../reuse/j2s,
use: HTML5
};
Jmol._alertNoBinary = false;
/script
If I put the Jmol.js call first, not surprisingly, nothing works (the
application doesn’t load).
In the body of the page I’ve got
script type=text/javascript
jmolHtml('center');
jmolInitialize(../../reuse); //required
jmolApplet(400, 'load o_atom_2s.cub.gz; spacefill .01;
bgcolor=255,255,255;','o_atom');
jmolHtml('br');
[…]
/script
When the serverURL is put between lines 38 and 47 of the jmol2.js file like this
Jmol.Info = {
jarPath: java,
jarFile: ,
j2sPath: j2s,
use: HTML5, // could be JAVA or HTML5
serverURL: http://wine-and-crackers.local/chem/reuse/php/jsmol.php;,
disableJ2SLoadMonitor: false,
disableInitialConsole: true
}
I get an error in a dialog box that says
Error connecting to server:
http://your.server.here/jsmol.php?call=getRawDataFromDatabasedatabase=_query=http%3A%2F%2Fwine-and-crackers.local%2Fchem%2Forganic%2Fmo_plain%2Fo_atom_2s.cub.gzencoding=base64”
The JSmol window shows an error that says “unrecognized file format for file
[…]cub.gz”
and the error console says
[Error] Failed to load resource: A server with the specified hostname could
not be found.” (There’s more if you want the whole list.)
Maybe I’ve screwed something up…
I was trying to go the minimal effort route, and since I call jmolInitialize
from my Jmol scripts I tried to follow these directions here
(http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#JSmol for using the
Jmol2.js method).
Previously, everything was stored in a directory I call “reuse” so I don’t have
to have multiple copies of the things I want to use on multiple pages.
The directory
/chem/reuse contains
renamed Jmol2.js file
jsmol.min.js file
j2s directory
php directory which contains the jsmol.php file
As long as it works when I include the “serverURL:” in each of the html file
that I create (and it does work) I’m ok with that.
Thanks,
Chris
On Jan 16, 2014, at 12:33 PM, Angel Herráez angel.herr...@uah.es wrote:
Chris, are you calling Jmol2.js before or after JSmol.min.js?
That could be a reason for parameters not being applied.
JSmol.min.js includes some defaults.
I think you need Jmol2.js after it.
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Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
Hi Chris
Uff that's complex to diagnose.
I'm not sure what is going wrong; it does sound reasonable.
I wold try to pool data and avoid defining Info values in two places. I.e.,
move
all declarattion into Jmol2.js or (less likely) into the page
Or, at least if unavoidable, don't declare var Jmol in the page but assign
values directly like
Jmol.Info.j2sPath = ../../reuse/j2s;
Jmol.Info.use = HTML5;
(anyway, those should not be needed at all since you have them in Jmol2
already)
It may happen that by using
var Info = { etc
in the page you are cancelling all that is done in the Jmol2 file --not sure
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Re: [Jmol-users] display echo while calculating
Thank you for the new version. I would say that now the sequence is as follows: it starts calculating the surface, freezing the browser then appears the message, draws, disappears the message. The message should appear before starting the long calculation time. Again, this is on Mac. Maybe other platforms behave better. Jaim On Jan 16, 2014, at 9:20 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, I think I found it. delay 0.01 should work even though refresh does not: set echo top left echo working... delay 0.01 echo Please try that; I'll also get refresh working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205tel:%2B49%203641%2065%206205 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210 E-Mail: rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/ Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 Larson-Anderson 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
Re: [Jmol-users] display echo while calculating
Dear Bob, On Safari Mac, with jsmol 14.1.6_dev_2014.01.16 , the notice while working performs great with delay 0.1 instead of refresh Thank you for the suggestion. Jaim On Jan 16, 2014, at 10:10 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you for the new version. I would say that now the sequence is as follows: it starts calculating the surface, freezing the browser then appears the message, draws, disappears the message. The message should appear before starting the long calculation time. Again, this is on Mac. Maybe other platforms behave better. Jaim On Jan 16, 2014, at 9:20 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, I think I found it. delay 0.01 should work even though refresh does not: set echo top left echo working... delay 0.01 echo Please try that; I'll also get refresh working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205tel:%2B49%203641%2065%206205 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210 E-Mail: rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/ Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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
[Jmol-users] Saving files to central server
Hi, If you have a central database of models located on a remote server (like the PDB), and you are using JSmol as a local viewer and editor, how would you save to the central server, rather than the local machine? I know Jmol 13+ could do this by sending the output of write to a URL, but I assume one should no longer be developing with Jmol. Or do I have this wrong, and both will be developed in parallel? Sincerely, James Ryley -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
Bob, Angel, Christopher, Thanks for all your help so far with the gzipped files. Still not working. Any advice would be GREATLY appreciated. Thanks in advance, David Here is what I’ve done (thanks Bob, for these instructions): 1. Opened JSmol.min.js and added js/Jmol2.js to it. 2. Saved that file as: Jmol.js and placed in directory above my jsmol exhibits 3. Also placed the folders “java” and “j2s” and “php” in the directory above the exhibits 4. Edited the new Jmol.js file (combined as above) to point to the http://[...]/jsmol.php file on our server (in the php directory) My exhibit files (e.g. molecule.html) have contain the following: script type=text/javascript // USER'S SETTINGS: var side = left var w = 60 var JmolPath = ../ //[…] //[…] script type=text/javascript jmolInitialize(JmolPath, JmolAppletSigned0.jar) jmolSetAppletColor(#ff) //same as page; you could choose another if you prefer jmolApplet(100%, 'background [xff]; load 1ehz.pdb; // […] So, my directory structure looks like: Jmol (folder) * j2s (folder) * Java (folder) * php (folder) * Jmol.js (file) * Some Exhibit (folder) * somemolecule.html (exhibit file) * .pbd Exhibits with .pdb unzipped load molecules well. Exhibits with .pdb gzipped yield an “unrecognized file format” error message. —— ~~~ ~~~ David J. Marcey Fletcher Jones Professor of Developmental Biology CLU, 60 West Olsen Road., MC#3700 Thousand Oaks, CA 91360 mar...@clunet.edu ph: 805-493-3263 fax: 805-493-3392 ~~ The Online Macromolecular Museum: www.clunet.edu/BioDev/omm/gallery.htm ~~ Cinelectures in Biology: www.youtube.com/user/dmflyboy ~~~ ~~~ -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
nah. impossible. I wonder if what you are seeing is the time it takes to load the modular components. If you have turned off the loading monitor, you may think nothing is happening -- or the calculation has started. I have a quite variable connection here in Jamaica (especially working through my VPN), and just now I saw very slow component loading while that command was processed. Take a look at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- middle column, half-way down: echo/surface test. I'm guessing the flash is the calculation. everything before that is file loading. Bob On Thu, Jan 16, 2014 at 3:10 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you for the new version. I would say that now the sequence is as follows: it starts calculating the surface, freezing the browser then appears the message, draws, disappears the message. The message should appear before starting the long calculation time. Again, this is on Mac. Maybe other platforms behave better. Jaim On Jan 16, 2014, at 9:20 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edu wrote: Yes, I think I found it. *delay 0.01 *should work even though *refresh *does not: *set echo top left echo working... * *delay 0.01 * *echo* Please try that; I'll also get *refresh *working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 ( http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5 ). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN
Re: [Jmol-users] Problem with JSmol 14.0.4 and gzipped files
You can only load binary files from your local machine if you are using
FireFox, I believe. And maybe just on a PC. I can't remember. Any chance
that is your problem?
What is happening is that your machine does not support asynchronous binary
file transfer using AJAX, so it has to go to a server and get the server to
convert that GZIP file to BASE64, transfer it, convert it back to GZIP,
then decode that. But it can't go to the server with a local call - or at
least that could never work (because it is a local file) and you get that
error message. So even if you had the right server call, this would not
work locally.
I need to get the newer Jmol2.js out there -- It should read:
Jmol.Info = {
//jarPath: java,
//jarFile: jmolAppletSigned.jar,
//signed: true,
//j2sPath: j2s,
use: HTML5, // could be JAVA or HTML5
serverURL: http://wine-and-crackers.local/chem/reuse/php/jsmol.php;,
disableJ2SLoadMonitor: false,
disableInitialConsole: true
}
Those lines need uncommenting only if your page doesn't call
jmolInitialize() or you want to override that call.
On Thu, Jan 16, 2014 at 2:23 PM, Christopher Masi cm...@westfield.ma.eduwrote:
Angel,
Yes, I think I’m calling the JSmol.min.js file first.
In the header of the html page, I’ve got this
script type=text/javascript src=../../reuse/JSmol.min.js/script
script type=text/javascript src=../../reuse/Jmol.js/script
!--location of renamed Jmol2.js library--
script type=text/javascript
var Info = {
j2sPath: ../../reuse/j2s,
use: HTML5
};
Jmol._alertNoBinary = false;
/script
If I put the Jmol.js call first, not surprisingly, nothing works (the
application doesn’t load).
In the body of the page I’ve got
script type=text/javascript
jmolHtml('center');
jmolInitialize(../../reuse); //required
jmolApplet(400, 'load o_atom_2s.cub.gz; spacefill .01;
bgcolor=255,255,255;','o_atom');
jmolHtml('br');
[…]
/script
When the serverURL is put between lines 38 and 47 of the jmol2.js file
like this
Jmol.Info = {
jarPath: java,
jarFile: ,
j2sPath: j2s,
use: HTML5, // could be JAVA or HTML5
serverURL: http://wine-and-crackers.local/chem/reuse/php/jsmol.php
,
disableJ2SLoadMonitor: false,
disableInitialConsole: true
}
I get an error in a dialog box that says
Error connecting to server:
http://your.server.here/jsmol.php?call=getRawDataFromDatabasedatabase=_query=http%3A%2F%2Fwine-and-crackers.local%2Fchem%2Forganic%2Fmo_plain%2Fo_atom_2s.cub.gzencoding=base64”
The JSmol window shows an error that says “unrecognized file format for
file […]cub.gz”
and the error console says
[Error] Failed to load resource: A server with the specified hostname
could not be found.” (There’s more if you want the whole list.)
Maybe I’ve screwed something up…
I was trying to go the minimal effort route, and since I call
jmolInitialize from my Jmol scripts I tried to follow these directions here
(http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#JSmol for using
the Jmol2.js method).
Previously, everything was stored in a directory I call “reuse” so I don’t
have to have multiple copies of the things I want to use on multiple pages.
The directory
/chem/reuse contains
renamed Jmol2.js file
jsmol.min.js file
j2s directory
php directory which contains the jsmol.php file
As long as it works when I include the “serverURL:” in each of the html
file that I create (and it does work) I’m ok with that.
Thanks,
Chris
On Jan 16, 2014, at 12:33 PM, Angel Herráez angel.herr...@uah.es wrote:
Chris, are you calling Jmol2.js before or after JSmol.min.js?
That could be a reason for parameters not being applied.
JSmol.min.js includes some defaults.
I think you need Jmol2.js after it.
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Re: [Jmol-users] Saving files to central server
Data is sent to a server via a simple http call, which can be a POST or not. This can be done with a WRITE command, but you can also just use the load() function. The key is to have ?POST? in the URL being loaded and then if you want specifically the PNGJ binary data sent, you add _PNGJBIN_ to that. x = load(http://myserver/myfile.php?POST?_PNGJBIN_name=testing;) If you want to say, send an XYZ file to the server, you might do this: print load(http://myserver?POST?name=t.xyzdata=; + write(xyz)) since that will POST name=t.xyzdata=[...xyz file data here...] to http://myserver (but I see there is a bug there preventing this working) Bob On Thu, Jan 16, 2014 at 3:42 PM, James ja...@ryley.com wrote: Hi, If you have a central database of models located on a remote server (like the PDB), and you are using JSmol as a local viewer and editor, how would you save to the central server, rather than the local machine? I know Jmol 13+ could do this by sending the output of write to a URL, but I assume one should no longer be developing with Jmol. Or do I have this wrong, and both will be developed in parallel? Sincerely, James Ryley -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
I would say that this is not a delay caused by loading, unless modules or model get unloaded in the middle. The Scene Authoring Tool in Proteopedia allows me to render and remove isosurface over and over again on the same loaded model with the click of a button. All components should be already available when requesting the same operation for a second or third time. Besides, only using 'delay 0.1' instead of 'refresh' allows for the working message to appear at the expected times in the same overall structure. This is good enough for the purpose of keeping the user aware that something's going on. Jaim On Jan 17, 2014, at 4:12 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: nah. impossible. I wonder if what you are seeing is the time it takes to load the modular components. If you have turned off the loading monitor, you may think nothing is happening -- or the calculation has started. I have a quite variable connection here in Jamaica (especially working through my VPN), and just now I saw very slow component loading while that command was processed. Take a look at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- middle column, half-way down: echo/surface test. I'm guessing the flash is the calculation. everything before that is file loading. Bob On Thu, Jan 16, 2014 at 3:10 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you for the new version. I would say that now the sequence is as follows: it starts calculating the surface, freezing the browser then appears the message, draws, disappears the message. The message should appear before starting the long calculation time. Again, this is on Mac. Maybe other platforms behave better. Jaim On Jan 16, 2014, at 9:20 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, I think I found it. delay 0.01 should work even though refresh does not: set echo top left echo working... delay 0.01 echo Please try that; I'll also get refresh working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205tel:%2B49%203641%2065%206205 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210 E-Mail: rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/ Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today.
