Re: [Jmol-users] color chain and color blindness
Sorry, Andreas, I don't get it How should we used this color table? What color is chain A, etc? -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] color chain and color blindness
Chain A is 104BA9 B ... AA00A2 C ... C9F600 D ... FFA200 E ... 284A7E etc does that make sense? Ok, let me try -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] questions
El 18 Nov 2010 a las 8:31, pieremanuele canepa escribió: 2) can you expalin me again how you would add a new atom, into a pre- existing structure, knowing its Cartesian coordinates. I lost the e- mail you sent me 1 or 2 weeks ago. Piero, the email list is archived at the Jmol web site and at other mirror sites. You can easily search for past messages -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] color chain and color blindness
That sounds terrific, Rolf! Good work! -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] color chain and color blindness
Andreas, first save the script to a file (or implement it inside your web page) then load the script file script colorchain.spt or drag and drop onto the Jmol app load a file and then, type at the console color_by_chain() It has worked for me -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] assigning boundbox volume to a variable
Hello Martin Getting the right syntax is a bit tricky, bust most likely you can do it in javascript using jmolGetPropertyAsArray, jmolGetPropertyAsString or jmolGetPropertyAsJSON http://jmol.sourceforge.net/jslibrary/#jmolGetPropertyAsArray and in JmolScript using the equivalent http://chemapps.stolaf.edu/jmol/docs/#getproperty Good luck! -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Simple popup window with Jmol in JavaScript
Nico, please check out http://wiki.jmol.org/index.php/Jmol_in_Pop-up that should be enough, don't you think so? -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Simple popup window with Jmol in JavaScript
Maybe, but it's not working for me with the current Jmol wiki. With Chrome, I get an empty popup about:blank... That reminds me about something I found previously. Let me see... the HTML code of the main window as Javascript (so it's quite complex). I am looking for a function with simple parameters (mainly, just the URL of the file to be loaded by the Jmol applet) that would then entirely create the popup window. Well, the HTML code must come from some place :-) I guess that code could be generated in the Javascript. Does it make any difference to have it there rather than in the php? -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Simple popup window with Jmol in JavaScript
Maybe, but it's not working for me with the current Jmol wiki. With Chrome, I get an empty popup about:blank... It's something specific to Chrome. Other browsers work, including Safari (Windows) I'm trying to find out what it is... -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Simple popup window with Jmol in JavaScript
Hello Nico I have no strong opinion on this new way for the extension you are proposing, but I will share some thoughts. Anything that can put Jmol in Wikipedia will be a great achievement. 1. The Chrome problem with jmolWikiPopupWindow(). As far as I can test (Windows only), this is something specific to Chrome. Even Safari works, despite being Webkit-based too. My testing suggests that the applet tag is somehow not rendering when built on-the-fly into a new window in Chrome. The source code gets there fine, the square is there, but the applet does not render. I can only fix it by a combination of a) instead of opening an empty window document, open an existing html page and then feed the new content into it (overwriting in fact whatever the html page has). b) avoid the use of w.document.close() I can put these changes into the current Extension in SVN. I don't feel very happy about (b) not using document.close() --sometimes the browsers remain loading the page forever--, but it seems not to be giving much trouble in this case in all my test browsers. As for (a), it's one more file but no big fuss. I've tried to avoid using document.write in favour of DOM methods, but cannot manage to do that from one window for the other. Still, I find no way to have the window title set in Safari and Chrome (text showing in the window top bar should be matching what has been given in the jmolWikiPopupWindow call). 2. In view of #1, I've been doing some testing for an alternative: rather than opening a popup window, create a div floating over the page content. This solution may also be preferred by the WP people.One requisite, in my opinion, is that it can be resized to get a larger Jmol. For this, one has to resort to additional external code, like jQuery + jQueryUI I have something working, but I'm not sure about the overload that jQuery means (both in terms of downloaded files, not much, and also of dependency on external code). People may or not like the solution more than the popup. With the reactions from Wikipedia people, I havedecided to make the Jmol extension much simpler to use by editors of Wikipedia contents. 3. Are you sure that the WP people will not object to popups? We must be sure of that before proceeding. For example, I am currently designing basic tags instead of the jmol tag :jmolFile to open a popup window with a Jmol applet for a molecular file already uploaded into Wikipedia, ... With this simpler tags, I think the PHP / Javascript / HTML can also be simpler. 4. Using a single tag will certainly help. I've been testing on several occasions the possibility of including a Jmol popup in the ChemBox and a major problem are the nested tags needed with the current Jmol Extension. They are impossible to fit in a wiki template (or at least I've been unable to find the way). A single tag will probably overcome this problem. My idea for the moment : * Having a HTML template for the popup window, that is an HTML file with a few variable parts. If we need to havedifferent kinds of popup window (one for crystallography, one for proteins, ...), we can have several templates and even let other people create their own templates. 5. So your idea is to depend on premade html templates that will contain the popup content. That can be a solution, although in principle seems to complicate things, since the template files will go in the Extension set of files you are right. I can help with that part. * The JavaScript file has a function with only a few parameters (url of the molecular file, title, template to use, ...) for creating a popup window : it reads the HTML template, replaces the variables parts anddisplays it in a popup window. There may be a bit of trouble passing the parameters to the opened window, but it should be possible using template documents. -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Simple popup window with Jmol in JavaScript
Some follow-up on these topics: 1. The Chrome problem with jmolWikiPopupWindow(). This is now fixed in the latest Extension in SVN. It was something specific to Chrome --not displaying applet that is part of a pop-up window wholly generated from javascript-- and has been now circumvented (hopefully a later Chrome update will remove this quirk behaviour and hence the need for this trick). Still, I find no way to have the window title set in Safari and Chrome (text showing in the window top bar should be matching what has been given in the jmolWikiPopupWindow call). It's ok for Safari, but Chrome still inisits on displaying the default empty page title. Using div can be good, but I am not sure having too muchdependencies will be much appreciated. I also resist the idea. Still, this system for free resizing of the applet based on jQuery is what is currently used in the PDB site. And it's really cool! I am not sure if resizing is really required (if we let each user choose the size of the applet in its preferences) To me, resizing is really important. Firts a general view of the model is enough, but then either one needs to see details, or to display in the classroom. Being able to grow or even maximize the window --and have Jmol applet follow the size automatically-- is very useful. Can really the user (not the wiki admin) choose that preference? I agree that the new simple tags offer great potential for WP. I will be able to put some time into desgining templates (html or mabe php), later in January I hope. -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Simple popup window with Jmol in JavaScript
Good news for jQuery : it's already used by MediaWiki ! Ha! How surprising. We would also need jQuery UI, but maybe we culd add it or duplicate the needed functionality. For MediaWiki 1.16.0, you have jquery.js version 1.3.2 in skins/commons There's also a jquery.min.js : Idon't know if it's the same, but minized (not comments, not carriage return, ...) Yes, it usually is that. I didn't get the point of your suggestion to have a look at the map in fr.Wikipedia. I could only see images. -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JmolButton click counter?
Hi Yingjie Mike's solution seems the best thing you can do. It basically means that instead of using jmolButton() you use your own input type=button with jmolScript(). That way you have more control --or easier at least. You could probably still use jmolButton() giving it the ID parameter and then take care of your clicks by getElementById or associating events to it. But I don't think it's worth the effort. I have something similar to what you want. It's an old page, so I don't remember exactly how I implemented it, but you may get an idea looking at the source code (not particularly simple) http://biomodel.uah.es/en/model4/dna/dnapairs.htm The code is in http://biomodel.uah.es/en/model4/dna/utils.js look for function writeZoomBtns() and function zoomer(z) -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Connecting atoms of different models
Dear Jmolers, Has any of you tried to use connect between atoms that belong to different models (1.1 and 1.2)? Is there an option to do that? (This was prompted by a post by Gian Garduque on the MolVis-list, to whom I am copying this) The 2nd question was: can we have monitor lines without the measure label? I will answer it here, since I've just found it in the online doc: To turn off just the labels, use set measurement OFF Hey, it doesn't seem to work. The label is still there. (Jmol 12.1.15) -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Connecting atoms of different models
OK, so I'll reply to myself: To turn off just the labels, use set measurement OFF It's set measurementLabels OFF Bob, so there's a typo in the online doc http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#k477 -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] hbonds calculate broken on old PDB file
I have two files with DNA, obtained time ago by trimming the protein out of 1d66.pdb (Jmol version of Eric's DNA Tutorial, now in 6 langauges). I am trying to upgrade to 12.0 On both 12.0.24 and 12.1.25, hbonds calculate reports 0 hydrogen bonds Previous versions of Jmol (11.4) produce the correct H bonds in base pairs If I do load =1d66 it works well So it seems like a problem with old PDB formatting maybe? Any hints about the change in behaviour? -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] hbonds calculate broken on old PDB file
Ah, here are the files: http://biomodel.uah.es/model4/dna/dna.pdb http://biomodel.uah.es/model4/dna/1d66-pwz.pdb -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] hbonds calculate broken on old PDB file
After looking at the online doc I have found, quite by chance, a hint for the change in behaviour. The file in question has 2 hydrogen atoms (added manually since that is a non-H pdb file). Other 2 files that I use (single nucleotide pairs) have a full set of hydrogens. On any on them, hbonds calculate calculate hbonds both fail to produce any bonds in Jmol 12. If I do select not _H before, then the bonds are generated. That's the way it's written in the doc, but I find no sense in it. I gather this is something new in relation to new and better ways of calculating H bonds in Jmol 12, but still don't see the convenience of this behaviour -- and in fact I think it will break many existing scripts. What is the expected behaviour for a H-containing model when one uses calculate hbonds? Would it do anything under any circumstances? -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] hbonds calculate broken on old PDB file
Thanks, Bob. That's sort of what I was imagining. I'm still uneasy about such a change in defaults. I've already added a description to the Wiki, http://wiki.jmol.org/index.php/Backward_compatibility Can you confirm if this only affects pdb files? -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] hbonds calculate broken on old PDB file
By the way, I have no idea where that H3O atom comes from in that file you are using. It's certainly not in the original 1d66. It's a terminal H, I guess, but it isn't HO3 or HO3'. Maybe Eric inserted that. Yes, it was inserted manualy (either Eric or me), and it's meant to be the 3'-end hydroxyl. One of the pages is aimed at showing the ends in detail. I think we made it from a neighbouring phosphorus. The name may be nonstandard, as you suggest. I'll have a look at that. But it was working fine, and should keep working now too. Then I had the individual files for AT and GC pairs, which have hydrogens but are hidden using set hydrogens off, so the Hbonds do not display when they are now being calculated to reach the hydrogens. We were using the N to N Hbonds even when the Hs are displayed optionally later on. The select not _H makes it work without change. I am concluding this change will not affect any normal pdb files (either with or w/o hydrogens) That's why I fear any upgrade in Jmol for existing pages, smooth as it may seem ;-) I'd like to have a single set of applet files for my whole website, but I don't dare do it without exhaustive etsting of all sections... so I cannot do it :-) -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] picking atoms
Hello Jan First, make sure what version of Jmol you will be using --this has changed historically across versions. I do not remember details right now, but I have some (old) example page from where you can likely get the key: http://biomodel.uah.es/Jmol/inicio.htm and then Reading information and properties from the molecule I see that's using Jmol 10.x :-( I should have something more recent, but don't remember where now. See what you can do meanwhile. If you need more help, say so -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Language about Jmol Web Page Maker
Dear Anbang Li, Thanks for bringing this to attention. It's great that you are interested on localization of the Export to Web module. First of all, no matter what language I choosed, the text below the label of Introduction is always in English. I want to ask, how can I translate them? The interface is translated with the same system as the Jmol application and applet, except for some items (big portions of text); those are probably the ones you are seeing in English. You are welcome to contribute translations and they will automatically be available in the next prelease (12.1.x) I am checking now the status of zh_CN translation http://wiki.jmol.org/index.php/Internationalisation/Current_Status and surprisingly it seems that the 12.1 series has not started to being translated, while the 12.0 series is mostly translated (357 of 374 strings). That's strange, since 12.1 has inherited from 12.0. Maybe the translation was done later. It would be important to copy all translations to the latest prerelease, I will check that with Nico. So, first question: Are you using 12.0 ior 12.1? Second: Do you see all the E2W interface in English, or only some words? (when you use Jmol 12.0.x) For a better definition of the problem, it would help if you send some screenshots where the problems are displayed. You can send them to me directly at aherraez(AT)users.sourceforge.net Anyway, you can go ahead and translate 12.0 or 12.1 using either the PO system or the Launchpad online system (which is easier for nonexperienced translators). Instructions are provided at http://wiki.jmol.org/index.php/Internationalisation#Translating_the_ap plication.2Fapplet Feel free to ask for more help if you need it. Second, when I view the created webpage, I found the encoding of the normal text in the webpage is right, but the encoding of the widgets is NOT right, I have to change the encoding of the widgets ( GB2312 for zh_cn) by hand. Maybe this need to be checked. This we need to check. Probably we have not had any previous experience with double-bit character sets in the E2W module. Are you seeing GB2312 literally? I think that it should be set by default to iso-8859-1. Either me or Jonathan Gutow will let you know when whe check this. -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Language about Jmol Web Page Maker
Sorry, my mistake. The Chinese translation is complete in Jmol 12.1.26 So your problem, Li, must be in the part of the interface that needs separate translation. I will come back to you this evening with details. -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] picking atoms
I have updated my page to use Jmol 12.0 http://biomodel.uah.es/Jmol/getProperty/ The same code is still valid to get the atom info. -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Language about Jmol Web Page Maker
Jonathan Gutow wrote: http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/openscience /jmol/app/webexport/html/ That's right. I don't think there is another way to do this. All is explained at http://wiki.jmol.org/index.php/Internationalisation/Offline/Export_to_Web Regarding the proper coding of Chinese, I think we have two ways: 1. The Chinese pages have inserted the proper charset declaration in HTML 2. We decide to change all localizations of these pages to use UTF8 charset. #1 is easy to do. #2 is the best for the future, I think. I'm sill not sure whether UTF8 covers the characters needed by Chinese (I think that's 2-byte characters) We currently have English and Spanish, that use ISO basically because support for accented characters was needed for Spanish, that's the codepage I normally use and I just copied it in English pages too (where it really doesn't matter). But UTF8 seems a more general and future-proof solution. As for the widgets, the problem may lie in the same codepage issue. We need to see examples to be sure. -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] getting the display type of an object
Hello, Yingjie There is some limitation in your approach: a part of the model ca have several styles simultaneously, like ballstick, trace, ribbon. They are not exclusive of one another. Then, there is a numeric parameter indicating their size or thickness, and a color. I'm not sure if there is a way to read those properties, but you would need to check all of them, not a single value. -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applet within pages in wiki.jmol.org?
Eric, apart from what Nico has pointed out, there is a category in the wiki that collects pages that use the applet: http://wiki.jmol.org/index.php/Category:Pages_Using_Jmol_MW_Extension (pages must be added to that category manually; see any of them for the source wikicode needed) -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] DOCUMENTATION COLOR chains
Eric, thanks for the detailed report and suggestions. I will take care of those changes in the jscolors webpage (next week) -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Every third or fourth alpha carbon?
Is there some way I can delete every other alpha carbon? Or filter to get only the alternate ones, or every third or fourth? Would it be a solution to pick them by residue number? I think it should be possible to check that in JmolScript / JmolMath and whether it divdes by 2 or 3 without remainder. But of course you would need to iterate over every chain. I could come up with a way to connect them using connect I'm not sure a connect would give an easy solution. If t's just for display, I would try draw instead. I think we have polylines now in draw. But any user manipulation from popup menu will destroy that. Or maybe not, since drawn objects are not available from menu. -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] DOCUMENTATION COLOR chains
Eric, you description was -of course- precise and correct. I have checked that the source code was designed to do what you were seeing in assigning colors to chains. The erroneous description must have been either a misconception in the doc or an obsolete description. The documentation has now been corrected and updated in the SVN system following your suggestions and will be available on the website the next time that Nico updates it. -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.app default dir in OS X?
On 17 Jan 2011 at 14:48, Jonathan Gutow wrote: 2) I am not aware of a way to pass the path to use to Jmol on launch except as a script. At least in Windows, a batch file should be able do that. Not sure now what exactly you are needing. (I haven't followed the thread fully) -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] PubChem SDF
Just my 2 cents: Evidently, a fair number of PubChem's sdf's have partial charge data. I see aproblem here. The format shown in your example is not according to SDF spec (I think it does not suppor partial charge, only formal charge). They shouldbe using a different format, like MOL2. So if Jmol is made to support reading that, it is not really SDF import. That should be made clear. What other software reads those PubChem SDF files? -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol Without Applets Using Websockets
Something to check out: http://depth-first.com/articles/2011/01/19/jmol-without-applets-using-websockets/ -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] extract min and max resNo to javascript
Hello all
This must be trivial, but I'm stuck
I need to extract the minimum and maximum residue nurmber from a one-chain pdb
file into
a Javascript variable.
The Jmol commands are
m1 = {*}.resno.min
m2 = {*}.resno.max
but I don't know how to pass those to a javascript variable (I need to check
user input against
them)
Thanks,
Angel
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Re: [Jmol-users] extract min and max resNo to javascript
Great, Alex, thanks
I had forgotten about jmolEvaluate()
This does the trick:
alert( jmolEvaluate( {*}.resno.min; ) );
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Re: [Jmol-users] extract min and max resNo to javascript
Mmmm... I see that jmolEvaluate() is not in the doc for Jmol.js Maybe we should add it there (under Advanced) -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] extract min and max resNo to javascript
On 26 Jan 2011 at 9:53, Robert Hanson wrote: oh, yes! It's very valuable. 2011/1/26 Angel Herráez angel.herr...@uah.es Mmmm... I see that jmolEvaluate() is not in the doc for Jmol.js Maybe we should add it there (under Advanced) Done. Will be online in the next update of the website, http://jmol.sourceforge.net/jslibrary/ Also added jmolScriptEcho() and jmolScriptMessage() which were undocumented so far. -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] changes in Jmol.js
Dear Jmolers, A failure has been detected to display Jmol when using the Chrome browser under MacOS. The reason has been tracked down to a change of behavior in Chrome (and future versions of Safari or other WebKit-based browsers) together with an old browser detection routine in the Jmol.js library. A new revision of Jmol.js has been made to avoid this problem, and will be included in the next releases of Jmol, probably 12.0.30 and 12.1.33 Please stay alert for: 1. your existing pages stop working under Mac/Chrome 2. any unexpected misbehavior in your pages when you upgrade Jmol (If you need to fix #1 but don't want to upgrade Jmol now, be welcome to contact me through the jmol-developers list so we can forge a cure into your copy of Jmol.js) I'm rather confident that nothing will be broken by applying the new version of Jmol.js to existing pages, but one never knows. Particularly for singular combinnations of browsers and OSs which I am unable to test. The browser-checking page at the Jmol website will also be updated accordingly and should now provide a more specific report of browser detection and what Jmol.js will do for inserting JmolApplets for that browser. If you see problems in your pages, please visit http://jmol.sourceforge.net/browsercheck/ and report a copy of that page so the problem can be recognized and fixed. (The website might take some longer time to be updated, particularly so since the SourceForge servers are experiencing problems these last days) -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] changes in Jmol.js
I realize that my previous message may sound too alarming, so I will be more specific. The changes introduced into Jmol.js affect only the way the JmolApplets are inserted into the page depending on the browser. So you just have to see if the applet shows up or not and if the javascript interaction with it works. Changes only affect Chrome, Safari and related, particularly under MacOS but also in part in other OSs. There may be some change too for Firefox in MacOS -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Unable to make new releases on sourceforge
New downloads are available, but I still cannot browse the SVN Guess I'm not the only one -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] loading Amber files
I am experimenting with an Amber set of files (topology + coordinates from a molecular dynamics calculation). The files load fine into Jmol (load trajectory) but I cannot get any cartoons or trace renderings. Is this a limitation with the TRAJECTORY option, or a problem with the Amber format? I can send the files if needed, but they are 9MB gzipped Thanks -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading Amber files
Possibly related to this: I cannot select atoms based on atom name e.g. select Lys # 88 atoms selected select Lys and *.CA # 0 atoms selected select Lys and alpha # 0 atoms selected Hover displays them correct label %a # works fine -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Noob question
Hi David It could be done, but I don't think Jmol is the right tool for what you intend, and it wuld hardly worth the effort needed. Jmol is just the graphical end for whatever data you give to it. Although you can do basic calculation and move the atoms, for your idea you should rely on some more powerful calculation engine that can take some kind of equations for force fields and movement. -- The modern datacenter depends on network connectivity to access resources and provide services. The best practices for maximizing a physical server's connectivity to a physical network are well understood - see how these rules translate into the virtual world? http://p.sf.net/sfu/oracle-sfdevnlfb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bug: nitrogen unrecognized as protein
Part of the problem there may be that, as far as I understand, Jmol algorithm for protein is more complex than identifying amino acid residues by name (that's what amino does). I think I read about the algorithm inside the source of JmolConstants.java I do not mean to defend that every atom must be a member of one of those three groups should not be true. But it's tricky. -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bug: nitrogen unrecognized as protein
Maybe this: select amino and not protein # will pick those anomalous atoms select protein,amino # will pick all protein atoms -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] molecular orbital linear combinations
Probably the jQuery solution is better, but in case it's of use I have a couple of simple slider demos at http://biomodel.uah.es/Jmol/sliders/ -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bug: nitrogen unrecognized as protein
Thanks everyone. Angel I like your solution. I thought so. It's more logical and general. Why do we need both protein or amino? amino is rasmol-compatible. protein is Jmol chemical intelligence, particularly to account for funny cases like yours. Also, I think, it includes nonstandard-name residues (hetero) that are normal enough to be aa residues --or maybe I'm wrong. In the code for FirstGlance, I enumerate all 20 amino acid names in order to select protein atoms that lack alpha carbons. amino is much easier! If I am interpreting it rigth, this is what Jmol source code says: (from http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/vi ewer/JmolConstants.java?view=markup) @amino _g0 _g=23 that is, ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, UNK carbohydrate is [AFL],[AGC],[AHR],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA],[FCA],[FCB], [FRU],[FUC],[FUL],[GAL],[GLA],[GLB],[GLC],[GUP],[LXC],[MAN],[RAA], [RAM],[RIB],[RIP],[XYP],[XYS],[CBI],[CT3],[CTR],[CTT],[LAT],[MAB], [MAL],[MLR],[MTT],[SUC],[TRE],[ASF],[GCU],[MTL],[NAG],[NAM],[RHA], [SOR],[XYL] protein and nucleic are based on atom names AFAIK Is a similar situation possible for nucleic? I don't think so. is, is there one atom that is required in order for other atoms in the same group to be deemed nucleic (like alpha carbon for protein)? Probably P, I'm guessing. Deeper exploration of the source is needed to be sure. No, see the wiki link below what would be the safe syntax to select ALL atoms in standard nucleotides, regardless of atoms that may lack coordinates? Maybe use select A, G, C, T, U, DA, DG, DC, DT of course that misses unusual nucleotides (like inosine?) See also http://wiki.jmol.org/index.php/AtomSets (that's what I cold collate-infer some time ago) -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading pdb files in a looping statement
Hello Vineet I'm not sure what you mean. If you want to load several files, you can do load files molec1.pdb molec2.pdb molec3.pdb You could also set them in a loop, like for (var i = 1; i = 4; i = i + 1) var x = molec + i + .pdb; load append @x; end for -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bond picking woes
Hello Adam There is no reason why the bond should be deleted. This must be a bug. Please provide details of the exact version of Jmol you are using -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bond picking woes
Oh, I didn't know this feature existed. To me, changing bonds 1. is not suggested by the word picking 2. makes sense only in the context of ModelKit mode 3. could be implemented, if intended out of ModelKit mode, in the callback function, e.g. using connect Having bonds dissapear in normal Veiwer mode (which seems to make them unpickable, of course) is rather worrying. So I'd rather vote for a picking just reporting the atom IDs, not acting on the bond. -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problems with Chrome/Mac OS/Jmol
Hello Nick Thanks for reporting. I think this is a known issue with newest Chrome versions that I tried to fix recently. The fix is in Jmol.js, and it seems that the pages you have tested are using different versions of that. For examplehttp://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm That uses Jmol 12.1.31 with Jmol.js 12.0 4/5/2010 as ishttp://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm And that uses Jmol 12.1.36_dev with Jmol.js 12.0 1/31/2011 The latter includes the key text: // ah 1/2011 -- wider detection of browsers; more browsers now use the object tag instead of the applet tag; // fix of object tag (removed classid) accounts for change of behavior in Chrome So I think that's it: latest Mac-Chrome needs the new Jmol.js It only affects MacOS (a limitation of the way the browser detection was implemented in old Jmol.js, together with a change in behaviour of WebKit in recent versions; should also affect Safari soon) -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Grouping of arbitrary elements
Evgeny, Yes, you can add dummy atoms using a script. See http://www.mail-archive.com/jmol- us...@lists.sourceforge.net/msg16573.html for some more info and an example. You should best use the existing Xx notation for an undefined element. Then you can select Xx to act on it, set its size, color, etc. Points and lines can be drawn giving their position with atom IDs, but I'm afraid when you rotate the atoms the drawn objects will not follow them, you would have to redraw. So you will have to resort to using the dummy atom itself as a sphere and the bonds you define (using connect command) as lines. Those will rotate (rotateselected command). Not too straightforward, but possible. Good luck -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Set Picking Eror
Otis, from the top of my head, it used to be set picking none But maybe the others are/were also valid -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how to start writing scripts
Hello Sam Welcome to Jmol I'd advise that you browse the website and then the Jmol Wiki. There is the Jmol Scripting Documentation, but that's better suited for a more special use, when you have doubts about how to use a command. First, you need to know that such a command exists. The wiki has links to pages that use Jmol and, specially, to tutorials on its use and a book (that I wrote). Those are the best way to start learning. Good luck. When you have specific doubts, the jmol-users list is here to give a hand. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Calculate structure results
OK, bad assumption on my part. I was assuming it was identifying beta turns. The Colors document on the Jmol site does indicate blue for beta turn. My fault. So we should say just turns, right? Will do that Aha, that's why I put beta in parentheses last time! strand [255,200,0] FFC800 () turn [96,128,255]6080FF :-) -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] moveto question
On 5 Mar 2011 at 13:50, Robert Hanson wrote: instantaneously. Is that different compared to moveto 0 (etc.)? -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] detecting base pairs in RNA
Hi all I am tryng to write a script that will detect paired bases (A-U, G-C) in a RNA molecule. Before I start trying, any ideas about how to address it would be welcome. For now, I am thinking of using WITHIN with distance. (I am assuming that in large pdb files maybe the hbonds detection is not reliable, so I would not depend on that) Thanks for any ideas Angel -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] detecting base pairs in RNA
Thanks, Bob, that's what I needed It seems that your 2 solutions work the same. I'm finding out which one is the best solution for me. Of course, working with RNA is mroe tricky, but that's why I need the algorithm. -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] viewing structures contained in jar archives with the Jmol applet
Jim, since a JAR is a zipfile, I'd say that you just need the same syntax as for loading a JMOL or ZIP file. Maybe it's LOAD ... FILTER. Check the scripting doc -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Command line communication with the Jmol application?
Alex, I think I am not getting the whole picture. Can't you use the Jmol script console for that? Maybe together with a few script files. -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] select *y, select *x; select *z
Hi Paul select *:y is the notation I use regularly Not sure about why *y gets you all atoms; looks like it has something to do with coordinates (xyz) -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] magic value error
Hello On a colleague's site, I am getting this error in the Java console when he pages tryes to load the applet: java.lang.ClassFormatError: Incompatible magic value 1008813135 in class file JmolApplet What is this about? (It's an old Jmol version, maybe 11.6) Thanks for any tips -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] magic value error
you have a mix of versions or a bad file. Thanks, Bob. We'll check that -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] one label per residue
Hello Yingjie
You can probably use the atoms array, and either use their geometric
center (not for a label, but an echo) or the first atom in the array.
The result will probably not look very nice.
I cannot give you the exact syntax, but check the doc under atom
expressions. It will be something like
select {resno=3}[0]; label %r
Good luck!
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Re: [Jmol-users] jmolEvaluate problem
Hello Yingjie 1. Are you sure that when your jmoEvaluate() call is executed the applet has finished loading? That could be a reason. 2. I doubt that boxSize is predefined. Or do you mean YOU have defined it? Jmol predefined variables start with an underscore, like _version Hope this helps, Angel -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmolEvaluate problem
Hello Yingjie Below is an example of usage I found on http://jmol.sourceforge.net/jslibrary/#jmolEvaluate alert( jmolEvaluate(a) ); // Displays the value of the 'a' variable if set in Jmol script. I think the example might be a bit confusing for newbies like me :) Why do you think so? It says clearly that a must be a Jmol variable. I don't see where your myvariable comes from. Javascript? -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmolSetTarget() for 2 out of 3 applets
Hi all I'd like to use jmolSetTarget() to target two applets but not a third one. I started using all as the parameter when I only had 2 applets in the page, but after adding the 3rd one I'm stuck. Any solutions? Thanks -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] passing a variable from JavaScript to JmolScript
Yingjie, I think it's easier I have a variable X in JavaScript, and I am looking for a way to pass it back to Jmol. How about jmolScript(var myJmolVar = + myJSvar) that would pass the value to the 'myJmolVar' variable in JmolScript. Or do you need something more complicated that just getting the variable? Also, in the documentation, the webpage parameter _jmol.noEval should be set to true. Unfortunately, I am not sure where this parameter is set. I think that is true by default. Anyway, you can set it from anywhere in your page javascript. Just do _jmol.noEval = true; -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmolSetCallback usage
Hi Yingjie Both #2 and #3 are calling a script befire the applet has had time to load. That's what you must avoid. Maybe this would work: jmolInitialize(../jmol/); jmolApplet(600, ..; set pickCallback 'moveBox'; ) because the 2nd parameter in jmolApplet() is not run until the applet has finished loading. Version #1 I think is ok. What are the symptoms? Java errors? Check the Java console to see. -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Continuing Saga of Jmol Talking to Public Databases
Michael, I have no experience with VB, but regarding Javascript calls to Jmol, all support is in the Jmol.js library, and it supports html IDs for both applets and controls. Maybe that's what you need. That immediately leads to the question of how to obtain a list of available functions and their parameters/formats, etc. Any Jmol command can be passed through jmolScript() I see that the tagName may be a group of elements (such as INPUT) rather than a unique name. So the ID or index is needed to refer to a unique element. For example I can send a Jmol command via elements 11 (the text) 12 (the button to click), but there is no guarantee that 11 and 12 are stable indices for future versions. Then it would help provide an ID for the button (12). maybe like jmolButton(script, label, id, title) ?? -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Firefox 4.0 on Macs: Detachable Jmol problems
Hi Eric I'm no Mac person, as you know, but one of your descriptions ticked a neuron. Long time ago, I read that one of the new Java updates was bringing the possibility of detachable applets. At that time, I tried it and it worked for Jmol (tweaking the Jmol.js, I guess). Then I lost interest. The description of your top title bar and dragging Jmol out of the browser sounds exactly the same I saw then. So it's a JVM feature that somehow MacFf4 has unearthed. My message is: if you like the feature, I think I may be possible to impose it for other OSs and browsers. I'm afraid I don't have a sample page located now, and it's time for bed and I have urgent work to do these weeks, but I can give you a hint if you need it along the next days. Have fun, Angel -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] disable translation by mouse
El 28 Mar 2011 a las 23:54, Yingjie Lin escribió: Is there a way to disable translation with double clicking and hold? As far as I know, you can redefine mouse gestures by attaching behaviours. Search the online doc or the email list archive -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Firefox 4.0 on Macs: Detachable Jmol problems
On 30 Mar 2011 at 14:46, Eric Martz wrote: Chrome: PROTEOPEDIA fails: It thinks java is disabled but it is not. I suspect this may be a problem with the java detection routine in Proteopedia. Eric, this may be a known problem I detected some time ago with browser detection in Jmol.js, together with a recent change in Chrome handling of applets. It affects Chrome/Mac (and reportedly should affect Safari/Mac also whenever it is updated to the same engine version). The problem was fixed by me in an update of Jmol.js somewhere in the 12.x series, but I see that Proteopedia is still using 11.8 I haven't got the time to recollect details now, but basically it is that Chrome and Safari will be using the applet tag rather than the object tag, and Chrome behaviour for applets has changed. It should be documented inside Jmol.js, if I remember correctly. There was also some discussion about it on the email list. So the fix is either upgrade Proetopedia to use Jmol 12 (I guess you don't want to do that lightly) or to patch the Jmol.js it is using with the fix. If you need help, pelase let me know -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmolResizeApplet() behaves strangely in Firefox
Hello Yingjie
I don't understand what is exactly the problem you are seeing. Your
page works well in my Windows Firefox 3.6
There is an alternative: you can put jmolApplet inside a DIV and then
resize that div rather than the applet
div id=jmolContainer
script
jmolApplet(100%)
/script
/div
INPUT TYPE=RADIO NAME=resizeAppletRadioGroup
onclick=document.getElementById('jmolContainer').width = '300px';
document.getElementById('jmolContainer').height =
'300px');(300*300)
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Re: [Jmol-users] super-easy method to insert a Jmol applet into a web page or email message
Very promising. Congratulations! the popup example link opens a window with this content: could not be loaded. (This is Firefox 3.6 WinXP) -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] show labels on startup
Hi Lamar Sounds like a timing issue maybe. I'm not sure why it fails, but try using label %a; instead of set label '%a'; just in case -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] show labels on startup
Some further ideas: 1. try loading the menu before the model 2. select ALL; is not necessary right after loading set autobond OFF; load menu http://130.18.154.148/~lamar/jmol.mnu;; load http://130.18.154.148/~lamar/JmolInput.txt.xml;; label %a; -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol and Android
Dear Bob, I don't remember any discussion about Android. The question, of course, is how are Java apps run in Android, what's the JVM and compatibility. Should we open a page in the Wiki for this? -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and Android
There it goes! Two primers. Please fell free to add your comments, experiences, links... http://wiki.jmol.org/index.php/Support/Android http://wiki.jmol.org/index.php/Support/iOS -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] show labels on startup
This is the original message http://sourceforge.net/mailarchive/forum.php?thread_name=BANLkTi%3DR%2BnAP_yaq9g Ph-if_BQd6%2B8xy8A%40mail.gmail.comforum_name=jmol-users Currently I have Jmol loading a script at startup that loads a file and custom menu. However, I would also like it to show the labels by default. My script is as follows. set autobond OFF; load http://130.18.154.148/~lamar/JmolInput.txt.xml;; load menu http://130.18.154.148/~lamar/jmol.mnu;; select ALL; set label '%a'; The script correctly loads the file and the menu but does not display the labels. But whenever I type the select all, set label '%a' in the console it does display the labels. Obviously I am not doing something correctly even though it works in the console. Thank you, Lamar B -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Select ssbonds and hbonds
Hello, Jaime
I'd say you cannot use labels, but you can use echos with 3D
coordinates. Also, you can draw an arrow pointing to the bond
midpoint.
Regarding selecting bonds, I'm not sure. You really select atoms
always I think. But it makes no difference.
More difficult will be to aim at all ssbonds at a time.
For a single bond, if you know the atom IDs there is no problem. For
all bonds, you probably have to find out how to extract them one by
one, maybe from the array of atom pairs.
I would suggest something like
select _S and connected(_S)
# this works is there is only one SSbond
set echo myBondOne {selected}
echo -- This is a disulphide bond
select connected(hbond)
# here you will need to work by pairs
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Re: [Jmol-users] Select ssbonds and hbonds
Bob, it seems that connected and connect do not accept ssbond as a parameter. Would that be too dificult to implement? e.g. I can do select all; hbond calculate; select connected(hbond,cys); but cannot do select connected(ssbond,cys); Hey! I forgot we have select cystine Jaime, maybe that's useful for you -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please evaluate: Jmol and 3D-alignment
Jmol, not JMol, please! I support that, and it is stressed in the website, but -for the record- actually Will York's JMol vanished into thin air time ago. There is no way to find it on the web. -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Error message: File reader was not found:Pdb
Laurent, are you sure youhave the whole set of jar files in the server? If it works with jmolAppletSigned.jar and not with jmolAppletSigned0.jar, it sounds like that may be the key. As Bob said, you better use Jmol.js. That will invoke *0.jar, so the comment still aplies -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with IE9
My copy of IE9 (both 32 and 64 bit versions, under 64bit-Win7) says there is a problem with the page and that IE has had to close and reopen the tab whatever that means. In fact, the page is displayed briefly (black Jmol) and then dissapears. Same happens with my page :( May be something with Java or IE updates? I have 1.6.0_20 In Firefox 3.6 , your page, the applet does not end loading. OK; after reloading the page 3 times it worked. -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with IE9
I have added some description based on this thread at http://wiki.jmol.org/index.php/Support/Windows for future reference -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
Hello Reinhold You are right, rotation, zoom etc. affects all frames/models. The only way is to use the rotateSelected command. But that doesn't work by mouse, only does defined angles. I think there is no way to do interactive rotation of a single model. -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] copy text from Jmol console
I can no longer copy text output to the Jmol script console (like show orientation) This seems to be related to the update of Java. I have just installed 1.6.0_25, under WinXP I think there was recent discussion about this in MacOS. Any ideas will be welcome -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
I don't know if this was there in 1.6.0_24 (but I have used this way of getting orientation moveto many times before). I have now found a workaround: I'm using the unsigned applet script console. I select (mouse drag) what is in the upper panel, output area; press Ctrl-C, but it cannot be pasted in any other program. But it can be pasted into the lower panel, input area. Then clicking on Run executes it. Then I open the Java console, the recently executed command is there and from there I can copy it (with some extra garbage) and paste to my text editor. Ugly! -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
Thanks, Wayne I was quite sure I had read similar issues here, thoughtit was with the Mac. I cannot confirm if 1.6.0_24 was working or not for me. 25 is not, and it's the first time I've noticed but there may have been several updates in between. Bob, thanks, now I see that the output of show orientation is also displayed in the Java console. Before I didn't see it there, that why I executed it -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] google chrome under jre 1.6.24
Jay, Otis knows better abaout this, but there is a chnce that your problem may not be his. There have been changes in Chrome support of the APPLET tag, and that has been fixed recently in Jmol.js. So, it's important that you check and tell us 1- what is your OS 2- do you see the applets using other browser? 3- what is the Jmol version you are using (newer Jmol.js includes the fix) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] google chrome under jre 1.6.24
Thanks for the details, Otis. I just tested my Chrome WinXP: 2) Chrome supplies some command line line switches to turn off features, including the the Java version police (editorial sarcasm). In my hands the Java related command line switches do not work: --always-authorize-plugins works for me regarding Jmol applet: without it, Chrome requests permission; with it, it does not. Java is 1.6.0_25 Chrome is 12.0.742.30 dev-m 5) There is now a button (latest Chrome) that says Always run on this site. That seems to work, For me too. -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] announcment - update of my Jmol book
Dear Jmol users, You may remember that I published an introductory manual for Jmol. Unfortunately I haven't yet found the way and time to write the promised volume 2 with more advanced content. However, I have just released an update to Vol.1 in the form of a 30- page supplement. It updates a few things that have changed in Jmol and adds an extra chapter devoted to using the Export to Web module. The supplement is available only from lulu.com, both in print and downloadable pdf (just over 2 US$). See http://stores.lulu.com/angel_herraez -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Modifying partial bond (dashed stick by dotted sticks)
Hello Néstor I'm afraid that dashed bonds cannot be changed. You can change thickness and color, but not the dashes. -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] two models in same scale but zoomable
Dear users, I have two models that I want to display at the same scale. I know I can use set scale3d = set scaleAngstromsPerInch, bot that disables zoom. What I would like is display the two models at the same scale, then let the user zoom (I'm adding sync so the 2 models change at a time) I've been trying to figure out what zoom command I should give at model loading so that they get the same intiial scale, but haven't been successful in finding out the right zoom difference. 1. Will set rotationRadius be useful for this maybe? 2. Can set scaleAngstromsPerInch be disabled later? i.e. zoom reactivated? Any clues will be appreciated -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] restore state
Hi all I am using for the first time save state and restore state. Sounds great! But restore takes quite a time, seemingly it loads the model again. Is that so? Would there be a way to restore the state without reloading the file? I am seeing that re-running the initial script (which I have in a variable) is much faster. Of course, that's not so safe since many things may have been done by the user in between. This is with a short DNA molecule in my hard disk, unsigned applet 12.0.42. -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Modifying partial bond (dashed stick by dotted sticks)
Hi again Néstor Rather different, but may useful for you: you could use solid translucent sticks for those bonds It would be something like select connected(partial); connect (selected) (selected) single yellow translucent; -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] undo ramachandran?
Dear Eric, Not sure where I got that trick, but look at the source of http://biomodel.uah.es/quimica/get_structures.htm The model command removes the Ramachandran plot and goes back to the structure. The current doc says that ramachandran is an obsolete command superseeded by plot ramachandran but does not mention model. Maybe plot model? -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] two models in same scale but zoomable
Thanks, Bob. set rotationRadius is my best choice. I have also applied it now to other pages that were hardcoded by hand. Great! For anyone interested, please note that any moveto command contains rotationRadius as one of the parameters, so it will effectively alter the initial setting. -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MSIE 9
Otis, I have not IE9 now at hand, but in part this sounds like the last problem reported in Jmol-users list: IE was closing down the page. I'm not sure what the fix was then (some saw it, some not), but yesterday in a colleague's PC we had the problem again (she had just upgraded to IE9) and it was fixed with a Java update. Sorry I cannot be more helpful. I'm on XP and that does not allow IE9 -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
