[Jmol-users] How to save to JVXL both surface and structure
Dear Jmol, Is there a way to save Jmol state with the pre-calculated surface? We can save the Jmol state, and render the structure with the same look, orientation, etc. However, if the state contains a surface calculation, the surface is recalculated again on load. On the other side, I can save to .jvxl the surface alone ... Can we combine both? Or the option is to reload state and then load jvxl? Thanks, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] error with jmolColorPickerBox
yes you are right -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456 --- From: Jonathan Gutow [gu...@uwosh.edu] Sent: Sunday, August 15, 2010 4:28 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] error with jmolColorPickerBox Angel, I think Piero and I straightened this out. Piero, correct me if I'm wrong...:). Angel is correct that the second array must be a JavaScript array, not a string. Angel, Just so you know, I did modify JmolColorPicker.js to accept the same kind of array structure as most Jmol.js command in place of a script. This was specifically for Piero's application. See the advanced usage section of the documentation in the current version (1.2). Jonathan On Aug 15, 2010, at 3:31 AM, jmol-users-requ...@lists.sourceforge.netmailto:jmol-users-requ...@lists.sourceforge.net wrote: Message: 1 Date: Sat, 14 Aug 2010 11:23:25 +0200 From: Angel Herr?ez angel.herr...@uah.esmailto:angel.herr...@uah.es Subject: Re: [Jmol-users] error with jmolColorPickerBox To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Message-ID: 4c66608d.23204.5593...@angel.herraez.uah.esmailto:4c66608d.23204.5593...@angel.herraez.uah.es Content-Type: text/plain; charset=us-ascii Piero, I think your problem may have originated in some mismatch that existed between instructions and the actual functions in JmolColorPicker.js. var colorScript = [setAtomColor, 'atomColor']; I'm not sure why you have that. it should be a string with a Jmol script, not an array. jmolColorPickerBox(colorScript, '[100,100,100]'); Here you need to remove the quotes. The 2nd parameter must be a javascript array: jmolColorPickerBox(colorScript, [100,100,100]); (this is the piece that was wrong in the doc) If that fails, get the updated version from http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/openscience/jmol/app/webexp ort/html/JmolColorPicker.js Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edumailto:gu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?
Hi, does someone else experience painfully slow callbacks in firefox on mac osx? http://weirdbyte.de/jmol-test/html/slow_callbacks.html I did some measurements. The numbers do very, but there is always a huge difference between callbacks registered and not. Best Alexander The numbers: * Firefox 2.6.8 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:10:09.660 END load pdb: 3:10:10.155 DURATION [495 ms]load pdb START load append pdb: 3:10:10.158 END load append pdb: 3:10:10.510 DURATION [352 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:10:10.652 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 null 3 1.1 jmol_load_struct_callback: 3:10:19.638 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:10:19.705 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:10:19.763 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:19.821 END load pdb: 3:10:19.857 DURATION [9205 ms]load pdb START load append pdb: 3:10:19.862 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:24.416 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) null 3 1.1 jmol_load_struct_callback: 3:10:24.420 END load append pdb: 3:10:24.423 DURATION [4561 ms]load append pdb * Safari 5.0.1 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:45:35.845 END load pdb: 3:45:36.496 DURATION [651 ms]load pdb START load append pdb: 3:45:36.497 END load append pdb: 3:45:36.734 DURATION [237 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:45:36.782 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:36.801 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:45:36.935 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:45:36.989 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 3 1.1 1.1 jmol_load_struct_callback: 3:45:37.000 END load pdb: 3:45:37.161 DURATION [379 ms]load pdb START load append pdb: 3:45:37.161 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) 3 1.1 2.1 jmol_load_struct_callback: 3:45:37.230 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.360 END load append pdb: 3:45:37.408 DURATION [247 ms]load append pdb jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.430 jmol_anim_frame_callback: jmolApplet0 -1 0 0 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.437 -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?
Seconded. I thought this would be fixed back when the 200 ms issue was fixed, but I'm still experiencing slow callbacks. On Mon, Aug 16, 2010 at 8:50 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, does someone else experience painfully slow callbacks in firefox on mac osx? http://weirdbyte.de/jmol-test/html/slow_callbacks.html I did some measurements. The numbers do very, but there is always a huge difference between callbacks registered and not. Best Alexander The numbers: * Firefox 2.6.8 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:10:09.660 END load pdb: 3:10:10.155 DURATION [495 ms]load pdb START load append pdb: 3:10:10.158 END load append pdb: 3:10:10.510 DURATION [352 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:10:10.652 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 null 3 1.1 jmol_load_struct_callback: 3:10:19.638 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:10:19.705 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:10:19.763 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:19.821 END load pdb: 3:10:19.857 DURATION [9205 ms]load pdb START load append pdb: 3:10:19.862 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:24.416 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) null 3 1.1 jmol_load_struct_callback: 3:10:24.420 END load append pdb: 3:10:24.423 DURATION [4561 ms]load append pdb * Safari 5.0.1 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:45:35.845 END load pdb: 3:45:36.496 DURATION [651 ms]load pdb START load append pdb: 3:45:36.497 END load append pdb: 3:45:36.734 DURATION [237 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:45:36.782 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:36.801 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:45:36.935 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:45:36.989 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 3 1.1 1.1 jmol_load_struct_callback: 3:45:37.000 END load pdb: 3:45:37.161 DURATION [379 ms]load pdb START load append pdb: 3:45:37.161 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) 3 1.1 2.1 jmol_load_struct_callback: 3:45:37.230 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.360 END load append pdb: 3:45:37.408 DURATION [247 ms]load append pdb jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.430 jmol_anim_frame_callback: jmolApplet0 -1 0 0 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.437 -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Mike Evans Organic Chemistry Graduate Student Moore Group University of Illinois, Urbana-Champaign -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?
This seems to be another example of Mac Firefox (and I suspect Camino and SeaMonkey) behaving differently. I would be interested in the results of the following three experiments: 1. What happens if you use the signed rather than the unsigned applet? 2. What happens if you remove the javaembedding plugin files (FirefoxcontentsMacOSPlugins)? There are two: JavaEmbeddingPlugin and MRJplugin. Don't throw them away, since once removed manipulating the structure in the applet will be disabled. But does it affect the callback speed. 3. What happens if you use Firefox 4.0b3 to open the page? Phil Bays On Aug 16, 2010, at 9:50 AM, Alexander Rose wrote: Hi, does someone else experience painfully slow callbacks in firefox on mac osx? http://weirdbyte.de/jmol-test/html/slow_callbacks.html I did some measurements. The numbers do very, but there is always a huge difference between callbacks registered and not. Best Alexander The numbers: * Firefox 2.6.8 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:10:09.660 END load pdb: 3:10:10.155 DURATION [495 ms]load pdb START load append pdb: 3:10:10.158 END load append pdb: 3:10:10.510 DURATION [352 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:10:10.652 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 null 3 1.1 jmol_load_struct_callback: 3:10:19.638 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:10:19.705 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:10:19.763 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:19.821 END load pdb: 3:10:19.857 DURATION [9205 ms]load pdb START load append pdb: 3:10:19.862 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:24.416 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) null 3 1.1 jmol_load_struct_callback: 3:10:24.420 END load append pdb: 3:10:24.423 DURATION [4561 ms]load append pdb * Safari 5.0.1 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:45:35.845 END load pdb: 3:45:36.496 DURATION [651 ms]load pdb START load append pdb: 3:45:36.497 END load append pdb: 3:45:36.734 DURATION [237 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:45:36.782 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:36.801 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:45:36.935 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:45:36.989 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 3 1.1 1.1 jmol_load_struct_callback: 3:45:37.000 END load pdb: 3:45:37.161 DURATION [379 ms]load pdb START load append pdb: 3:45:37.161 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) 3 1.1 2.1 jmol_load_struct_callback: 3:45:37.230 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.360 END load append pdb: 3:45:37.408 DURATION [247 ms]load append pdb jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.430 jmol_anim_frame_callback: jmolApplet0 -1 0 0 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.437 -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users J. Philip Bays Professor of Chemistry Department of Chemistry and Physics Saint Mary's College Notre Dame, IN 46556 (574) 284-4663 pb...@saintmarys.edu -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] change the visible part of an isosurface without reloading
Hi, Am 11.08.2010 um 17:51 schrieb Robert Hanson: I think you mean that you want to be able to set the cutoff or sigma value on the fly. you're right That's not going to happen. Jmol doesn't save the entire cube file or map data -- and doesn't generally have the memory available to do that. You will just need to reload the map for that. Easy enough to save a couple of JVXL files for each sigma of interest if there are only a few and it isn't a general file load. Of course, also such a divide and conquer approach is especially good when working online with the applet. Alex -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] change the visible part of an isosurface without reloading
Hi,
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 10. August 2010 14:48:50
Betreff: Re: [Jmol-users] change the visible part of an isosurface without
reloading
On Tue, Aug 10, 2010 at 7:33 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
It's certainly an interesting idea, though. Sort of a hide selected
triangles option, I think. Hmm. We have:
isosurface ID foo show
isosurface ID foo hide
maybe
isosurface ID foo show within 2.0 {atomset}
isosurface ID foo show all
thanks for implementing it as 'isosurface display within 2.0 {atomset}'
Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html
One minor thing: When changing the display params via a jmolscript PickCallback
(see below), I get a loading indicator which stays until a mouseclick. However
it works. (Tested on Linux/Firefox, Mac/Firefox/Safari)
Alex
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[Jmol-users] set memory for the applet on Firefox/Mac OSX
Hi, i can't set the memory for the applet (jmolSetMemoryMb(512);) on Firefox/Mac OSX, but it works on Safari/Mac and Firefox/Ubuntu. Any Ideas? I also set the memory Java-Preferences app on mac, but no change. Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html Alex -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] disable 'mouse down zoom area' on the right
Hi, Is there a way to disable the 'mouse down zoom area' on the right side of the applet? Alex -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] change the visible part of an isosurface without reloading
Alex,
I'm not sure what you are doing on your web page, but it is causing some
strange behavior for me on Safari 5.0 on OS X 10.6.4. Several times it crashed
the browser. It seems to be opening the page and somehow automatically opening
what looks like Firebug, but it is behind the applets so I can't see it well
except for when scrolling.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 12:14 PM, Alexander Rose wrote:
Hi,
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 10. August 2010 14:48:50
Betreff: Re: [Jmol-users] change the visible part of an isosurface without
reloading
On Tue, Aug 10, 2010 at 7:33 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
It's certainly an interesting idea, though. Sort of a hide selected
triangles option, I think. Hmm. We have:
isosurface ID foo show
isosurface ID foo hide
maybe
isosurface ID foo show within 2.0 {atomset}
isosurface ID foo show all
thanks for implementing it as 'isosurface display within 2.0 {atomset}'
Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html
One minor thing: When changing the display params via a jmolscript
PickCallback (see below), I get a loading indicator which stays until a
mouseclick. However it works. (Tested on Linux/Firefox, Mac/Firefox/Safari)
Alex
--
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Re: [Jmol-users] change the visible part of an isosurface without reloading
Hi,
Am 16.08.2010 um 20:58 schrieb Jeff Hansen:
Alex,
I'm not sure what you are doing on your web page, but it is causing some
strange behavior for me on Safari 5.0 on OS X 10.6.4. Several times it
crashed the browser. It seems to be opening the page and somehow
automatically opening what looks like Firebug, but it is behind the applets
so I can't see it well except for when scrolling.
I'm sorry, forgot about smaller monitors, made the applet smaller.
It was opening FirebugLite, I removed it, wasn't need here.
I also removed one of the applets, the remaining one is enough to make my point.
Your browser was probably crashing, because the applet did not had enough
memory, 512M should be enough
(http://wiki.jmol.org/index.php?title=Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with).
I thought stating 'jmolSetMemoryMb(512);' would do the trick, but it it
seems not to work, neither for the signed nor the unsigned applet.
Sorry for the inconvenience
Alex
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 12:14 PM, Alexander Rose wrote:
Hi,
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 10. August 2010 14:48:50
Betreff: Re: [Jmol-users] change the visible part of an isosurface without
reloading
On Tue, Aug 10, 2010 at 7:33 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
It's certainly an interesting idea, though. Sort of a hide selected
triangles option, I think. Hmm. We have:
isosurface ID foo show
isosurface ID foo hide
maybe
isosurface ID foo show within 2.0 {atomset}
isosurface ID foo show all
thanks for implementing it as 'isosurface display within 2.0 {atomset}'
Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html
One minor thing: When changing the display params via a jmolscript
PickCallback (see below), I get a loading indicator which stays until a
mouseclick. However it works. (Tested on Linux/Firefox, Mac/Firefox/Safari)
Alex
--
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Re: [Jmol-users] change the visible part of an isosurface without reloading
Yes, upping the memory given to java seems to have helped. I think in the
process of editing the page you may have messed something else up since the
following is showing at the bottom of the page.
function klick(){
isosurface display within 5.0 ({atomIndex = _atomPicked});
center {atomIndex = _atomPicked};
}
set PickCallback jmolscript:klick();;
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 4:20 PM, Alexander Rose wrote:
Hi,
Am 16.08.2010 um 20:58 schrieb Jeff Hansen:
Alex,
I'm not sure what you are doing on your web page, but it is causing some
strange behavior for me on Safari 5.0 on OS X 10.6.4. Several times it
crashed the browser. It seems to be opening the page and somehow
automatically opening what looks like Firebug, but it is behind the applets
so I can't see it well except for when scrolling.
I'm sorry, forgot about smaller monitors, made the applet smaller.
It was opening FirebugLite, I removed it, wasn't need here.
I also removed one of the applets, the remaining one is enough to make my
point.
Your browser was probably crashing, because the applet did not had enough
memory, 512M should be enough
(http://wiki.jmol.org/index.php?title=Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with).
I thought stating 'jmolSetMemoryMb(512);' would do the trick, but it it
seems not to work, neither for the signed nor the unsigned applet.
Sorry for the inconvenience
Alex
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 12:14 PM, Alexander Rose wrote:
Hi,
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 10. August 2010 14:48:50
Betreff: Re: [Jmol-users] change the visible part of an isosurface without
reloading
On Tue, Aug 10, 2010 at 7:33 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
It's certainly an interesting idea, though. Sort of a hide selected
triangles option, I think. Hmm. We have:
isosurface ID foo show
isosurface ID foo hide
maybe
isosurface ID foo show within 2.0 {atomset}
isosurface ID foo show all
thanks for implementing it as 'isosurface display within 2.0 {atomset}'
Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html
One minor thing: When changing the display params via a jmolscript
PickCallback (see below), I get a loading indicator which stays until a
mouseclick. However it works. (Tested on Linux/Firefox, Mac/Firefox/Safari)
Alex
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Re: [Jmol-users] set memory for the applet on Firefox/Mac OSX
Hi, I looked into it some more and it seems that 'jmolSetMemoryMb(512);' is also not working for Safari/Mac. I was previously mistaken, because I hadn't taken the effect of the Java-Preferences app into account. Signed and unsigned Applet Safari 5.0.1/Mac: Java-Preferences app -Xmx512 - works jmolSetMemoryMb(512); - doesn't work Firefox 3.6.8/Mac: Java-Preferences app -Xmx512 - doesn't work jmolSetMemoryMb(512); - doesn't work Chrome 5/Mac: Java-Preferences app -Xmx1024 - doesn't work jmolSetMemoryMb(1024); - works - note that chrome/mac seems to have a higher default, 512 instead of 96 (?) Alex Am 16.08.2010 um 18:17 schrieb Alexander Rose: Hi, i can't set the memory for the applet (jmolSetMemoryMb(512);) on Firefox/Mac OSX, but it works on Safari/Mac and Firefox/Ubuntu. Any Ideas? I also set the memory Java-Preferences app on mac, but no change. Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html Alex -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] change the visible part of an isosurface without reloading
hi,
that's allright, its some jmolscript, just to show you what is supposed to
happen when you click on an atom
alex
Am 16.08.2010 um 22:56 schrieb Jeff Hansen:
Yes, upping the memory given to java seems to have helped. I think in the
process of editing the page you may have messed something else up since the
following is showing at the bottom of the page.
function klick(){
isosurface display within 5.0 ({atomIndex = _atomPicked});
center {atomIndex = _atomPicked};
}
set PickCallback jmolscript:klick();;
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 4:20 PM, Alexander Rose wrote:
Hi,
Am 16.08.2010 um 20:58 schrieb Jeff Hansen:
Alex,
I'm not sure what you are doing on your web page, but it is causing some
strange behavior for me on Safari 5.0 on OS X 10.6.4. Several times it
crashed the browser. It seems to be opening the page and somehow
automatically opening what looks like Firebug, but it is behind the applets
so I can't see it well except for when scrolling.
I'm sorry, forgot about smaller monitors, made the applet smaller.
It was opening FirebugLite, I removed it, wasn't need here.
I also removed one of the applets, the remaining one is enough to make my
point.
Your browser was probably crashing, because the applet did not had enough
memory, 512M should be enough
(http://wiki.jmol.org/index.php?title=Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with).
I thought stating 'jmolSetMemoryMb(512);' would do the trick, but it it
seems not to work, neither for the signed nor the unsigned applet.
Sorry for the inconvenience
Alex
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 12:14 PM, Alexander Rose wrote:
Hi,
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 10. August 2010 14:48:50
Betreff: Re: [Jmol-users] change the visible part of an isosurface
without reloading
On Tue, Aug 10, 2010 at 7:33 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
It's certainly an interesting idea, though. Sort of a hide selected
triangles option, I think. Hmm. We have:
isosurface ID foo show
isosurface ID foo hide
maybe
isosurface ID foo show within 2.0 {atomset}
isosurface ID foo show all
thanks for implementing it as 'isosurface display within 2.0 {atomset}'
Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html
One minor thing: When changing the display params via a jmolscript
PickCallback (see below), I get a loading indicator which stays until a
mouseclick. However it works. (Tested on Linux/Firefox, Mac/Firefox/Safari)
Alex
--
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Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?
Hi, Am 16.08.2010 um 17:48 schrieb Philip Bays: This seems to be another example of Mac Firefox (and I suspect Camino and SeaMonkey) behaving differently. I would be interested in the results of the following three experiments: 1. What happens if you use the signed rather than the unsigned applet? still slow: http://weirdbyte.de/jmol-test/html/slow_callbacks_signed.html 2. What happens if you remove the javaembedding plugin files (FirefoxcontentsMacOSPlugins)? There are two: JavaEmbeddingPlugin and MRJplugin. Don't throw them away, since once removed manipulating the structure in the applet will be disabled. But does it affect the callback speed. both removed: fast, but callbacks seem to be ignored, no messages JavaEmbeddingPlugin removed: Error _jmolSetCodebase is not defined MRJplugin removed: 1st load opens a program called Java Applet Host, fast, but callbacks seem to be ignored, 2nd subsequent loads (with Java Applet Host program open), fast callbacks with messages 3. What happens if you use Firefox 4.0b3 to open the page? first, there is a warning the browser would not be fully compatible with jmol, but nevermind, because... ... the slow callbacks are gone :-) Alex Phil Bays On Aug 16, 2010, at 9:50 AM, Alexander Rose wrote: Hi, does someone else experience painfully slow callbacks in firefox on mac osx? http://weirdbyte.de/jmol-test/html/slow_callbacks.html I did some measurements. The numbers do very, but there is always a huge difference between callbacks registered and not. Best Alexander The numbers: * Firefox 2.6.8 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:10:09.660 END load pdb: 3:10:10.155 DURATION [495 ms]load pdb START load append pdb: 3:10:10.158 END load append pdb: 3:10:10.510 DURATION [352 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:10:10.652 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 null 3 1.1 jmol_load_struct_callback: 3:10:19.638 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:10:19.705 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:10:19.763 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:19.821 END load pdb: 3:10:19.857 DURATION [9205 ms]load pdb START load append pdb: 3:10:19.862 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:24.416 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) null 3 1.1 jmol_load_struct_callback: 3:10:24.420 END load append pdb: 3:10:24.423 DURATION [4561 ms]load append pdb * Safari 5.0.1 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:45:35.845 END load pdb: 3:45:36.496 DURATION [651 ms]load pdb START load append pdb: 3:45:36.497 END load append pdb: 3:45:36.734 DURATION [237 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:45:36.782 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:36.801 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:45:36.935 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:45:36.989 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 3 1.1 1.1 jmol_load_struct_callback: 3:45:37.000 END load pdb: 3:45:37.161 DURATION [379 ms]load pdb START load append pdb: 3:45:37.161 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) 3 1.1 2.1 jmol_load_struct_callback: 3:45:37.230 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.360 END load append pdb: 3:45:37.408 DURATION [247 ms]load append pdb jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.430 jmol_anim_frame_callback: jmolApplet0 -1 0 0 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.437 -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users J. Philip Bays Professor of Chemistry Department of Chemistry and Physics Saint Mary's College Notre Dame, IN 46556 (574) 284-4663 pb...@saintmarys.edu -- This SF.net email is sponsored by Make an app they can't live without Enter the
Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?
Sweet! Wonder what's different about 4.0? On Mon, Aug 16, 2010 at 4:37 PM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, Am 16.08.2010 um 17:48 schrieb Philip Bays: This seems to be another example of Mac Firefox (and I suspect Camino and SeaMonkey) behaving differently. I would be interested in the results of the following three experiments: 1. What happens if you use the signed rather than the unsigned applet? still slow: http://weirdbyte.de/jmol-test/html/slow_callbacks_signed.html 2. What happens if you remove the javaembedding plugin files (FirefoxcontentsMacOSPlugins)? There are two: JavaEmbeddingPlugin and MRJplugin. Don't throw them away, since once removed manipulating the structure in the applet will be disabled. But does it affect the callback speed. both removed: fast, but callbacks seem to be ignored, no messages JavaEmbeddingPlugin removed: Error _jmolSetCodebase is not defined MRJplugin removed: 1st load opens a program called Java Applet Host, fast, but callbacks seem to be ignored, 2nd subsequent loads (with Java Applet Host program open), fast callbacks with messages 3. What happens if you use Firefox 4.0b3 to open the page? first, there is a warning the browser would not be fully compatible with jmol, but nevermind, because... ... the slow callbacks are gone :-) Alex Phil Bays On Aug 16, 2010, at 9:50 AM, Alexander Rose wrote: Hi, does someone else experience painfully slow callbacks in firefox on mac osx? http://weirdbyte.de/jmol-test/html/slow_callbacks.html I did some measurements. The numbers do very, but there is always a huge difference between callbacks registered and not. Best Alexander The numbers: * Firefox 2.6.8 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:10:09.660 END load pdb: 3:10:10.155 DURATION [495 ms]load pdb START load append pdb: 3:10:10.158 END load append pdb: 3:10:10.510 DURATION [352 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:10:10.652 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 null 3 1.1 jmol_load_struct_callback: 3:10:19.638 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:10:19.705 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:10:19.763 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:19.821 END load pdb: 3:10:19.857 DURATION [9205 ms]load pdb START load append pdb: 3:10:19.862 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:24.416 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) null 3 1.1 jmol_load_struct_callback: 3:10:24.420 END load append pdb: 3:10:24.423 DURATION [4561 ms]load append pdb * Safari 5.0.1 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:45:35.845 END load pdb: 3:45:36.496 DURATION [651 ms]load pdb START load append pdb: 3:45:36.497 END load append pdb: 3:45:36.734 DURATION [237 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:45:36.782 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:36.801 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:45:36.935 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:45:36.989 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 3 1.1 1.1 jmol_load_struct_callback: 3:45:37.000 END load pdb: 3:45:37.161 DURATION [379 ms]load pdb START load append pdb: 3:45:37.161 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) 3 1.1 2.1 jmol_load_struct_callback: 3:45:37.230 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.360 END load append pdb: 3:45:37.408 DURATION [247 ms]load append pdb jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.430 jmol_anim_frame_callback: jmolApplet0 -1 0 0 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.437 -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users J. Philip Bays Professor of Chemistry Department of Chemistry and Physics Saint Mary's College Notre Dame, IN 46556 (574)
Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?
OK. The issue is with the embedding plugins and OS 10.6, as my issue was. There is no workaround that I know of. The author of the plugin is working on a revision, but it is not clear when that will be available and if it will be useful for current versions of firefox. The beta versions of Firefox 4 have a place marker where the plugin directory ought to be, and no plugins. I do not know if they plan to implement plugins and what effect that will have down the road. I am about to edit my index page to tell Mac users to avoid firefox for my tutorials for the time being. I believe the browser warning for Firefox 4 is from Jmol. Phil Bays On Aug 16, 2010, at 5:37 PM, Alexander Rose wrote: Hi, Am 16.08.2010 um 17:48 schrieb Philip Bays: This seems to be another example of Mac Firefox (and I suspect Camino and SeaMonkey) behaving differently. I would be interested in the results of the following three experiments: 1. What happens if you use the signed rather than the unsigned applet? still slow: http://weirdbyte.de/jmol-test/html/slow_callbacks_signed.html 2. What happens if you remove the javaembedding plugin files (FirefoxcontentsMacOSPlugins)? There are two: JavaEmbeddingPlugin and MRJplugin. Don't throw them away, since once removed manipulating the structure in the applet will be disabled. But does it affect the callback speed. both removed: fast, but callbacks seem to be ignored, no messages JavaEmbeddingPlugin removed: Error _jmolSetCodebase is not defined MRJplugin removed: 1st load opens a program called Java Applet Host, fast, but callbacks seem to be ignored, 2nd subsequent loads (with Java Applet Host program open), fast callbacks with messages 3. What happens if you use Firefox 4.0b3 to open the page? first, there is a warning the browser would not be fully compatible with jmol, but nevermind, because... ... the slow callbacks are gone :-) Alex Phil Bays On Aug 16, 2010, at 9:50 AM, Alexander Rose wrote: Hi, does someone else experience painfully slow callbacks in firefox on mac osx? http://weirdbyte.de/jmol-test/html/slow_callbacks.html I did some measurements. The numbers do very, but there is always a huge difference between callbacks registered and not. Best Alexander The numbers: * Firefox 2.6.8 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:10:09.660 END load pdb: 3:10:10.155 DURATION [495 ms]load pdb START load append pdb: 3:10:10.158 END load append pdb: 3:10:10.510 DURATION [352 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:10:10.652 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 null 3 1.1 jmol_load_struct_callback: 3:10:19.638 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:10:19.705 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:10:19.763 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:19.821 END load pdb: 3:10:19.857 DURATION [9205 ms]load pdb START load append pdb: 3:10:19.862 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:24.416 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) null 3 1.1 jmol_load_struct_callback: 3:10:24.420 END load append pdb: 3:10:24.423 DURATION [4561 ms]load append pdb * Safari 5.0.1 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:45:35.845 END load pdb: 3:45:36.496 DURATION [651 ms]load pdb START load append pdb: 3:45:36.497 END load append pdb: 3:45:36.734 DURATION [237 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:45:36.782 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:36.801 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:45:36.935 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:45:36.989 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 3 1.1 1.1 jmol_load_struct_callback: 3:45:37.000 END load pdb: 3:45:37.161 DURATION [379 ms]load pdb START load append pdb: 3:45:37.161 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) 3 1.1 2.1 jmol_load_struct_callback: 3:45:37.230 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.360 END load append pdb: 3:45:37.408 DURATION [247 ms]load append pdb jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:37.430 jmol_anim_frame_callback: jmolApplet0 -1 0 0 101 201 0 1 1 jmol_anim_frame_callback:
Re: [Jmol-users] does someone else experience painfully slow callbacks in firefox on mac osx?
From the early days of Jmol, I remember having to install the embeddingPlugins into firefox because it did not play well with Jmol and apparently other applets. I thought the issue was taken care of, but instead Mozilla moved to embedding the embeddingPlugins in the firefox distribution. OS 10.6 broke the plugin. Firefox 4.0b works for things that previously did not work, even though it does not have the embedding plugin installed. I am not sure if Mozilla decided to address the issue, after all these years, or if they have not got around yet to doing whatever they did in the past to break the compatibility with the Mac OS. It may be down the road that they will incorporate the plugins and break it all over. I am keeping track of each beta release to see what happens. Phil On Aug 16, 2010, at 5:47 PM, Michael Evans wrote: Sweet! Wonder what's different about 4.0? On Mon, Aug 16, 2010 at 4:37 PM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, Am 16.08.2010 um 17:48 schrieb Philip Bays: This seems to be another example of Mac Firefox (and I suspect Camino and SeaMonkey) behaving differently. I would be interested in the results of the following three experiments: 1. What happens if you use the signed rather than the unsigned applet? still slow: http://weirdbyte.de/jmol-test/html/slow_callbacks_signed.html 2. What happens if you remove the javaembedding plugin files (FirefoxcontentsMacOSPlugins)? There are two: JavaEmbeddingPlugin and MRJplugin. Don't throw them away, since once removed manipulating the structure in the applet will be disabled. But does it affect the callback speed. both removed: fast, but callbacks seem to be ignored, no messages JavaEmbeddingPlugin removed: Error _jmolSetCodebase is not defined MRJplugin removed: 1st load opens a program called Java Applet Host, fast, but callbacks seem to be ignored, 2nd subsequent loads (with Java Applet Host program open), fast callbacks with messages 3. What happens if you use Firefox 4.0b3 to open the page? first, there is a warning the browser would not be fully compatible with jmol, but nevermind, because... ... the slow callbacks are gone :-) Alex Phil Bays On Aug 16, 2010, at 9:50 AM, Alexander Rose wrote: Hi, does someone else experience painfully slow callbacks in firefox on mac osx? http://weirdbyte.de/jmol-test/html/slow_callbacks.html I did some measurements. The numbers do very, but there is always a huge difference between callbacks registered and not. Best Alexander The numbers: * Firefox 2.6.8 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:10:09.660 END load pdb: 3:10:10.155 DURATION [495 ms]load pdb START load append pdb: 3:10:10.158 END load append pdb: 3:10:10.510 DURATION [352 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:10:10.652 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 null 3 1.1 jmol_load_struct_callback: 3:10:19.638 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:10:19.705 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:10:19.763 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:19.821 END load pdb: 3:10:19.857 DURATION [9205 ms]load pdb START load append pdb: 3:10:19.862 jmol_anim_frame_callback: jmolApplet0 1 2 1 101 201 0 1 1 jmol_anim_frame_callback: 3:10:24.416 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) null 3 1.1 jmol_load_struct_callback: 3:10:24.420 END load append pdb: 3:10:24.423 DURATION [4561 ms]load append pdb * Safari 5.0.1 on Mac OSX 10.6.4: === NO CALLBACKS REGISTERED === START load pdb: 3:45:35.845 END load pdb: 3:45:36.496 DURATION [651 ms]load pdb START load append pdb: 3:45:36.497 END load append pdb: 3:45:36.734 DURATION [237 ms]load append pdb === CALLBACKS REGISTERED === START load pdb: 3:45:36.782 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 201 0 1 1 jmol_anim_frame_callback: 3:45:36.801 jmol_anim_frame_callback: jmolApplet0 0 0 0 0 0 0 1 1 jmol_anim_frame_callback: 3:45:36.935 jmol_anim_frame_callback: jmolApplet0 0 1 1 101 101 0 1 1 jmol_anim_frame_callback: 3:45:36.989 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 3 1.1 1.1 jmol_load_struct_callback: 3:45:37.000 END load pdb: 3:45:37.161 DURATION [379 ms]load pdb START load append pdb: 3:45:37.161 jmol_anim_frame_callback: jmolApplet0 http://weirdbyte.de/jmol-test/data/1u19.pdb 1u19.pdb 1U19 (modified) 3 1.1 2.1 jmol_load_struct_callback: 3:45:37.230 jmol_anim_frame_callback: jmolApplet0 1
