[Jmol-users] Apology, and request for help
Hi people *I'd like to apologise for how much of a prick I can be when all you's are doing is trying to help me*. *Thank you for your great patience*, which I do not deserve. I am currently writing a blog post and I would love to be able to include a few JSmol applets in it, if possible. I know to do this I need to use *HTML markup language* but I'm a bit of a noob in this area, so could you please show me a code I can use, that I can customise (by changing the PDB file being used) to suite my needs? I have check this http://wiki.jmol.org/index.php/Jmol_JavaScript_Object and, the noob that I am, I can't seem to do anything with it, so could you please either help me or direct me to a page that explains how to code this up in a simple way (if you want to know my knowledge base, basically think, Would a two-year-old under this? as that's the sort of level I'm at. Thanks again, for your time, Brenton -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Apology, and request for help
understand this^, )^ On Fri, May 16, 2014 at 10:42 PM, Brenton Horne brentonhorn...@gmail.comwrote: Hi people *I'd like to apologise for how much of a prick I can be when all you's are doing is trying to help me*. *Thank you for your great patience*, which I do not deserve. I am currently writing a blog post and I would love to be able to include a few JSmol applets in it, if possible. I know to do this I need to use *HTML markup language* but I'm a bit of a noob in this area, so could you please show me a code I can use, that I can customise (by changing the PDB file being used) to suite my needs? I have check this http://wiki.jmol.org/index.php/Jmol_JavaScript_Object and, the noob that I am, I can't seem to do anything with it, so could you please either help me or direct me to a page that explains how to code this up in a simple way (if you want to know my knowledge base, basically think, Would a two-year-old under this? as that's the sort of level I'm at. Thanks again, for your time, Brenton -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Apology, and request for help
Brenton, That's not easy. Not just a question of how to edit html code, but blogs have their underlying engines designed to easy editing TEXT, which make doing advanced under-the-hood things actually more complex. Have a look at http://wiki.jmol.org/index.php/Blogs_Using_Jmol http://wiki.jmol.org/index.php/CMS_Using_Jmol On the other hand, the HTM files included in J(S)mol download are templates that you could use as code to use and customize, but that's probably not going to work in a blog. Another choice is using Jmol Export to Web, an utility included in the Jmol application. It will build fpr you web pages with embedded JSmol into them, but probably not working inside a blog. I'd rather not discourage you, but you may need to abandon your plan. Doing sophisticated things requires time to learn, by practice, trial and error. No quick simple recipe! Good luck! -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] JavaScript benchmarks
Always hopeful that Javascript performance might become “adequate” for even intensive JSmol tasks (such as surface renderings), I benchmarked Safari using http://krakenbenchmark.mozilla.org/kraken-1.1/driver.html The value was ~3000 ms. Reading http://arstechnica.com/information-technology/2014/05/apple-integrates-llvm-compiler-to-boost-webkit-javascript-performance/ I re-ran it using Webkt which is supposed to use compiler technology. About ~2700 ms. Chrome (does 32 vs 64-bit impact upon JavaScript?) is ~1800 ms. I wonder how much more can be squeezed out of Javascript? Not an order of magnitude? Nor even a factor of say 4? I estimate a factor of ~20 is needed to remove the frustrations associated with surface renderings in JSmol? signature.asc Description: Message signed with OpenPGP using GPGMail -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JavaScript benchmarks
On 05/16/2014 04:40 PM, Rzepa, Henry S wrote: Always hopeful that Javascript performance might become “adequate” for even intensive JSmol tasks (such as surface renderings), I benchmarked Safari using http://krakenbenchmark.mozilla.org/kraken-1.1/driver.html The value was ~3000 ms. Reading http://arstechnica.com/information-technology/2014/05/apple-integrates-llvm-compiler-to-boost-webkit-javascript-performance/ I re-ran it using Webkt which is supposed to use compiler technology. About ~2700 ms. Chrome (does 32 vs 64-bit impact upon JavaScript?) is ~1800 ms. I wonder how much more can be squeezed out of Javascript? Not an order of magnitude? Nor even a factor of say 4? I estimate a factor of ~20 is needed to remove the frustrations associated with surface renderings in JSmol? Another problem with Javascript performance in JSmol is that it can vary by about a factor of ten even on the same system. I observed this for example with Firefox 26 on OpenSuse 12.2 (QuadCore i5-2500 CPU @ 3.30GHz, 24 GB RAM). 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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Apology, and request for help
Sorry for some unwanted english mistakes, but I am writing from iPad and the automated corrector changed something here and there Inviato da iPad Il giorno 16/mag/2014, alle ore 21:34, Pierluigi Quagliotto pierluigi.quaglio...@unito.it ha scritto: Dear Brenton, and Dear Angel, The task could not be easy, but also, an answer could be done. At least for the two most important and used Content Managing Systems, also known as CMS, the thing is possible. For the easiest CMS to be managed, Wordpress, the most used to host blog sites, please refer to this address: http://pinostriccoli.altervista.org The author, Pino Striccoli, used this to give a lot of info and examples to his students. Several pages are a good way to shed light on the way JMol or JSMol can be used into it. I am ready to publish a site made with Joomla, the other CMS. This site should have to be ready about two months ago, but unfortunately, the hosting service of my University was rebuilt in those last months, so I am waiting that all the system can work well before activating the site. So, it is possibile and the real problem is how to solve some problems. As Angel anticipated, in CMS site or blogs, the author and users can normally introduce plain text. Sometimes it is possibile to format the text with some HTML commands, but this is related to a choice of the site Administrator that can activate this option. If the blog is your personal blog you should have access to the administrative panel of the blog. In this case you should be able to solve our problems even it could seem a bit tricky at a first sight. The page of an article or post is built by the CMS that drive all the process. The text of the post is inserted in a large part of HTML code that the CMS build to let your browser to give the typical graphical aspect of the site. You have to face 2 main problems. To prepare a HTML page that uses JSMol, you should introduce the declaration of the jsmol file, with javascript. The second one is to make able the CMS to read the post as an HTML code so that it can be introduced by the CMS into the page to be delivered. Those two problems can be solved since those CMS can be extended in their basic fucntins by using extension that can be modules, components and plugins. Both Joomla and Wordpress have plugins that can help the admiistrator to insert code into the HEAD section, to solve the Javascript declaration and also plugins that can let you inserting HTML code into the post. Depending the complexity of the JSMol use into the blog post, you should become familiar also with javascript and PHP, two programming languages. you can start to replicate some very basic example pages of JMol eamples by looking into their code and trying to put all things in the right place into the CMS. Only when things will become a bit more complicated, you should acquire javascript and PHP knowledge. I started in the last days of December and a version of my site was working and to be published by the end of February, but the problems in the hosting service caused me to delay. Do not give up... We were all noob at our beginning... The great problem is to have time. Just a final note: all what I described is possible if you are the administrator of rhe blog. if you only want to show some JSMol application into a post of an existing blog of which you are not the owner and administrator, it is nearly impossible, because to avoid hacking, the blogs and sites do not permit to introduce code to simpel users. Good luck! Pierluigi Quagliotto Inviato da iPad Il giorno 16/mag/2014, alle ore 15:36, Angel Herráez angel.herr...@uah.es ha scritto: Brenton, That's not easy. Not just a question of how to edit html code, but blogs have their underlying engines designed to easy editing TEXT, which make doing advanced under-the-hood things actually more complex. Have a look at http://wiki.jmol.org/index.php/Blogs_Using_Jmol http://wiki.jmol.org/index.php/CMS_Using_Jmol On the other hand, the HTM files included in J(S)mol download are templates that you could use as code to use and customize, but that's probably not going to work in a blog. Another choice is using Jmol Export to Web, an utility included in the Jmol application. It will build fpr you web pages with embedded JSmol into them, but probably not working inside a blog. I'd rather not discourage you, but you may need to abandon your plan. Doing sophisticated things requires time to learn, by practice, trial and error. No quick simple recipe! Good luck! -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium
[Jmol-users] an animation loop with pauses
Hi all, I am using a series of models as an animation using anim mode loop. Is it possible to add a pause at a given frame? I know we can add pauses at the first and last model using animation MODE LOOP [time-delay1] [time-delay2] But I would like to add a pause every time the animation repeats (loops) at one or two different specific frames. I can think of some workarounds to make this happen, but I am wondering if there is a more direct ‘animi’ command that would work here. Thanks, Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] tying echoes to sets of frames
Hi Bob et al., I would like an echo to appear at the top of the frame during frames 1-10 of an animation, then a different echo to appear in the same spot for frames 15-25, and a third for frames 30-35. I’ve been looking at 'set echo' in the script doc, where I see: Echo text can be associated with a specific model, with visibility controlled by the frame command. See below. and then below (as advertised) set echo id MODEL (model number) By default, when multiple models are present, all echo text is visible regardless of the model currently displayable using the frame command. The set echo ... MODEL command associates an echo with a specific model, allowing the text or image to appear and disappear when different models are displayed using the frame command. I have tried many different permutations of this without success. I am clearly misunderstanding something, possibly several things… Can someone point me in the right direction? What would a simple example command look like? Frieda-- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] tying echoes to sets of frames
Frieda,
If I responded with the idea before, forgive my aging memory.
A while back we wanted to do some animations where we had complete frame by
frame control of the flow (echos, timing, atom display, etc). We settled on
wrapping our multi frame file in a script loop of our own. The basic concept is
very simple, and best illustrated with an example. I'll append a Diels/Alder
animation loop script to this email.
You really have great control - echos anywhere, atoms leave and return to the
stage, delays, frame interval changes, you name it...
Otis
The script:
var filePath = ../animations/diels_alderF.TXT;
var frameInterval = .1;
load @filePath;hide *;background black;set echo top center;font echo 36
serif;color echo yellow;echo VMK Molecular Movies|Presents|A Diels-Alder
Reaction;delay 3;
animation off;hover off;color label pink;select formalCharge 0;label %C;set
echo top left;font echo 16 sansserif;
color echo yellow;select *;var j = getProperty(modelInfo,modelCount);
for (var i = 1; i = j; i++){
frame @i;
if (i ==1) {var k = {model=i}.atomIndex.max + 1;var t =
{model=i}.atomIndex.min;select within(branch, {atomIndex = k}, {atomIndex=t});
color cpk;hide selected;echo 2-methoxy-1,3-butadiene, an electron rich
diene;delay 4;echo;}
if (i ==3) {var k = {model=i}.atomIndex.max + 1;var t =
{model=i}.atomIndex.min;select within(branch, {atomIndex = k}, {atomIndex=t});
color cpk;hide selected;echo Rotation around the C2-C3 bond;delay 4;echo;}
if (i 58) {var k = {model=i}.atomIndex.max + 1;var t =
{model=i}.atomIndex.min;select within(branch, {atomIndex = k}, {atomIndex=t});
color cpk;hide selected;}
if (i == 57){echo generates this reactive conformation,;delay 4;echo;}
if (i == 58){display *;echo ready to react with MVK, an electron poor
dienophile;delay 4;echo;}
if (i == 58){display *;echo once the two reactants are properly
oriented.;delay 4;echo;}
if (i == 167){display *;echo The pi systems align.;delay 3;echo;}
if (i == 190){display *;echo They approach in parallel planes.;delay 4;echo;}
if (i == 233){display *;echo partial bonds all around;delay 4;echo;}
delay @{frameInterval};
}
echo The final product is this substituted cyclohexene. ;delay 3;boundbox
{*};centerat boundbox;zoom 0;
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 16, 2014, at 10:13 PM, Frieda Reichsman frieda...@mac.com wrote:
Hi Bob et al.,
I would like an echo to appear at the top of the frame during frames 1-10 of
an animation, then a different echo to appear in the same spot for frames
15-25, and a third for frames 30-35. I’ve been looking at 'set echo' in the
script doc, where I see:
Echo text can be associated with a specific model, with visibility
controlled by the frame command. See below.
and then below (as advertised)
set echo id MODEL (model number)
By default, when multiple models are present, all echo text is visible
regardless of the model currently displayable using the frame command. The
set echo ... MODEL command associates an echo with a specific model,
allowing the text or image to appear and disappear when different models are
displayed using the frame command.
I have tried many different permutations of this without success. I am
clearly misunderstanding something, possibly several things… Can someone
point me in the right direction? What would a simple example command look
like?
Frieda
--
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