Re: [Jmol-users] Ketcher

Yes, many Javascript libraries involvedin Ketcher -- things may get complicated. @Philip: The design of Ketcher interface is not very flexible -- I don't like much these systems whose functionality relies on modern html (javascript, html5 canvas, SVG) and yet rely on a fixed-size interface

[Jmol-users] scaling an image echo

Hi all I have an image echo. It's working at its full size, but now I need to (conditionally) reduce its size. The doc says this is possible using a scaling factor option in font size. However, I am unable to male it work: set echo formula 0 0; font echo 22 sans plain 0.75; set echo image

Re: [Jmol-users] scaling an image echo

Ok, solved it using set echo scale 0.75 I found that using Google, at http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm number 10 However, the doc should then be fixed since it says otherwise http://chemapps.stolaf.edu/jmol/docs/?ver=13.0#font

[Jmol-users] pausinf and resuming a script from the webpage

Hi I have some long scripts running (from spt files) in a JmolApplet within a webpage. I would like to include buttons in the page that pause and resume the running script. Pause works, but resume seems to be impossible to achieve from the page (it works from the applet's console). I have

Re: [Jmol-users] Cartoon only erases labels - feature or bug?

Hi Rolf Since labels are attached to atoms, I think this is the way it works. When atoms are not visible, labels go off. Still, I think I have some trace-only models with labels. I will need to find out. An alternative could be to use 3D-attached echos.

Re: [Jmol-users] !quit question

My feeling is that !quit is a radical end everything. I vote for it stopping all efects: animation, vibration, minimization... How about spinning? I am seeing that at least quit does not stop spinning. Permanent spinning is irritating to me, so I'd be happy that it is also stopped by one or

Re: [Jmol-users] !quit question

in Jmol app !quit does stop spinning. Also in HTML5 and Java applet. Maybe you have an older version? No. I've being typing quit, no !quit Now I see, !quit does stop spinning. Good! -- LogMeIn Rescue: Anywhere,

Re: [Jmol-users] Hello to jmol

Hello I think that using Jmol for just displaying several 2D structures is overkill. From your MOLfiles many pieces of software can offer a display. For example, JME is much ligther than Jmol. Or you probably should try some of the html+javascript based viewers that do not rely on Java.

Re: [Jmol-users] Hello to jmol

There are a few 2D viewer applications that could be used to display the MOLfiles as flat structure images. For example, ChemDoodle WebComponents may well do it: http://web.chemdoodle.com/installation/download http://web.chemdoodle.com/tutorial/2d-structure-canvases/viewer-canvas

Re: [Jmol-users] Hello to jmol

@LMH, see for example a simple demo of table with images of structures generated on the fly from MOLdata: http://biomodel.uah.es/en/DIY/ChemDoodle/2d-viewer_4.7.0/test1.htm That should be easy to connect to whatever you use to generate the html page and table, right?

Re: [Jmol-users] Hello to jmol

Bob: It's ChemDoodle Viewer -- simple enough, and small js files. Not interactive at all. It reads the MOLfile data which seems to be what is available for LMH. LMH: You will have to read the documentation available at the ChemDoodle WebElements website. There are a lot of choices for

Re: [Jmol-users] JSmol initiatlizing messages

Hello Wayne I've done something of the sort in one of my tests. Don't recall the exact details now, but it was along this line: The output console that rolls many text lines during initialization is defined in the Info object, by default it is located in the same position where the JSmol goes

Re: [Jmol-users] gzip pdb file in JSmol

glad I asked because I would have been somewhat stymied by the link on that page at the wiki that does not let one download a functional version. Wayne, can you explain that? Which is that link? I can fix it --

[Jmol-users] spurious alerts in JSmol

Hello, I am running several scripts in pages using JSmol (downloaded on 21st Dec.). Those involving draw commands are raising a series of alerts. I guess it is some debug commands left over in one of the JS files. For example, draw pep45 scale 1.2 color yellowTint (4:B.CA) (4:B.O) (5:B.CA)

[Jmol-users] image fallback alternative in Jmol-JSO

Hi all While working on an updated version of export an image from Jmol applet that will be compatible with the new Jmol-JSO method and applet surrogates, I see that the image fallback alternative is not working at http://chemapps.stolaf.edu/jmol/jsmol/test2.htm On the other hand I cannot find

Re: [Jmol-users] image fallback alternative in Jmol-JSO

OK. I was trying to cover all known variations. Interestingly, I found that by loading a PNG+Jmol file (saved from the app) instead of the PDB file, when I specify image as the only option in Info, the png image is indeed displayed. Nice!

Re: [Jmol-users] Future of the Jmol applet == JSmol

Dear Bob, Thanks for the comprehensive summary on the state of Jmol applet and JSmol. First of all, a huge thanks for the tremendous effort you have put in such a short time and the extraordinary product you have achieved to make. We all owe you much. A few notes of my own to share with

[Jmol-users] JSmol-compatible new version to export an image from either Jmol applet, Jmo-JSO, JSmol

OK, so I have an update of my former Exporting from Jmol applet an image of the current view method, http://biomodel.uah.es/Jmol/export-image/ that is now compatible with Jmol-JSO-HTML5 (JSmol), Jmol-JSO-Java and Jmol-JSO-WebGL it is temporarily located at

Re: [Jmol-users] Future of the Jmol applet == JSmol

I have not had any problems with this, at least with Firefox. I think what you say is true for MSIE. It's also possible that I set some sort of flag to allow that. No, seriously. I'm using Firefox and the JS libraries do not finish loading from local files. I gave up trying to understand

Re: [Jmol-users] R: JSmol-compatible new version to export an image from either Jmol applet, Jmo-JSO, JSmol

Thank you, Pino I thought that was updated to the last version, but maybe not. I will check the files again. I did have some problems loading some pdb files that gave format-not-recognised errors. I played a bit with file extensions and gzipped or not, so I may have it broken. Right now, both

[Jmol-users] disable pop-up menu in JSmol?

Quick question: Can the (recently implemented) pop-up menu in JSmol be disabled/enabled? It would be good to have that feature and, if possible, to use something similar to the applet method, i.e. set disablePopupMenu TRUE in script Another choice would be some tag in the Info variable

Re: [Jmol-users] Java

I'll share my experience in Windows on this issue: Today my Firefox also started blocking the Java plugin I had. After an update from java.com, the plugin is not fully blocked but Firefox is asking for permission to run each instance of Jmol applet (unsigned) -- at least on first use of that

Re: [Jmol-users] Is there a fix that allows cut and paste from Jmol console to txt editor

Hello, Henry Yes, that is becoming a nuisance. For me (Windows), although copy does not work, selecting the text and dragging it to a text editor works, depending on the precise text editor (cannot give a rule for them, even Word may accept the drag). A colleague using Mac reported this

Re: [Jmol-users] JSmol speed varies widely with browser

Dear Eric, glad to hear from you In Windows 7, I find huge speed differences between browsers for JSmol. Sorry if this has already been reported. I am also seeing this, although I haven't done a systematic analysis. I understand all comes down to the Javascript engine or implementation of

Re: [Jmol-users] No select segid command ?

not comparing Jmol to this or that software, but it seems that Jmol would adopt canonical selection rules that coincide with the PDB formatting style. Is the segid in the PDB specification? I never saw it · Dr. Angel Herráez Biochemistry and Molecular Biology, University of Alcalá E-28871

Re: [Jmol-users] No select segid command ?

Hello again I suspect this is an issue of different terminology, but the functionality you ask for is likely there. Some pointers: http://chemapps.stolaf.edu/jmol/docs/#atomexpressionsfunctions see WITHIN SEQUENCE e.g. select within(PGATG,*) //would select all atoms in that peptide sequence

Re: [Jmol-users] No select segid command ?

Hi So this is a question of file format. PDB file format specification has not any hint of columns 72-75 or the segID field, either in the current Version 3.3: July, 2011 / Nov. 21, 2012 http://www.wwpdb.org/documentation/format33/sect9.html#ATOM or in the oldest referenced in wwPDB, Version

Re: [Jmol-users] How to float Jmol right in IE9?

I'm pretty sure I can help you out, Eric, but not right now. You'll need to give me some time. First shot: have to tried to wrap the jmolApplet() call in a div that has style float? -- Master Java SE, Java EE,

Re: [Jmol-users] How to float Jmol right in IE9?

I'm pretty sure I can help you out, Eric, but not right now. You'll need to give me some time. First shot: have to tried to wrap the jmolApplet() call in a div that has style float? -- Master Java SE, Java EE,

Re: [Jmol-users] Jmol on the Android: rotation axes wrong way around

Egon, does that depend on whether your tablet is in landscape or portrait orientation? I'm just curious... -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now

Re: [Jmol-users] Jmol on the Android: rotation axes wrong way around

An what about JSmol? Will it run in the Nexus web browser? I am reading it's got Chrome -- it should run! -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now

[Jmol-users] faster Javascript in Firefox

The release notice for Firefox 18.0.1 includes this line: - Faster JavaScript performance via IonMonkey compiler good for JSmol ! and - better image quality with our new HTML scaling algorithm -- Master HTML5,

Re: [Jmol-users] R: JSmol-compatible new version to export an image from either Jmol applet, Jmo-JSO, JSmol

Hi Pino Nothing to do with my site or with Jmol/JSmol. It's an issue of Java version and browser version and policies. Nasty indeed. Anyway, for me once I accept the alert the applet loads fine in Firefox 13, IE 9, and Chrome (Java 1.7.0_11) And the JSmol boxes should be working fine, right?

Re: [Jmol-users] JSmol update

Mike, I downloaded it like 2 hours ago and it unzipped well (Windows, WinZip) -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills

Re: [Jmol-users] help - Question about JSmol

Hi Jonathan I don't think that download or ftp will be your problem. It is a zipfile, so the contents will not be altered during file retrieval. Make sure you are downloading the correct file, http://chemapps.stolaf.edu/jmol/jsmol.zip Then it might be a question of how it is unzipped, but I

Re: [Jmol-users] help - Question about JSmol

http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm I am not sure, but it is possible that this line within Info in your page j2sPath: j2s, is read as find the files in subfolder j2s of the current (i.e. this page) folder So it's no surprise that it does not load I think you

Re: [Jmol-users] can you visualize more than one molecular orbital at a time?

Hi Jonathan I have no experience with MO, but some with surfaces. Although you can include color and translucency in the same surface command, I' ve found it tricky and the safest is to do it separately. You must give a name to each surface first. Try this: isosurface surf1 mo 6; isosurface

Re: [Jmol-users] Windows: Java 7 very sluggish

I find that Java 7 (1.7.0_11) on Windows is very sluggish. So slow that it could well drive away most users of complex Jmol pages (e.g. Proteopedia, FirstGlance in Jmol). That's strange, Eric. I've been using Java 7 for a long time in one of my PCs and have not noticed this problem. It

Re: [Jmol-users] Apple blocks java 6 applets on Snow Leopard

In Windows, since a week or so when this Java danger started, Firefox blocks all applets but allows you to activate them by one click -- until next time a page is loaded, then you must do it again. -- Everyone hates

Re: [Jmol-users] Location of j2s directory

Thanks. It seems to be working now for me. Great! And the solution was...? -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today:

Re: [Jmol-users] Two embedded JmolPanels: FileNotFoundException #NOC#

Hi David I'm afraid I have no experience in building apps, but as a first line of attack I'd ask: is this problem restricted to the use of 2 JmolPanels? To me it seems indeed that the path is not being properly parsed and you get a mixture of the base path + the chosen path. Another thng to

Re: [Jmol-users] Up-to-date Javadoc API Reference available online?

There's probably no updated API documentation written anywere Bob may tell you for sure what's the state, or towhat extent you can keep using the old one. -- Everyone hates slow websites. So do we. Make your web apps

Re: [Jmol-users] Adding bonds explicitly for xyz format

Hi David I don't know about doing this at the development level, but with scripting he regular app or applet: xyz format does not provide connectivity (bonds) mol format is also quite simple and does include bond information

Re: [Jmol-users] JMol applet stopped working on Opera...?

Simone, do you have a url we can test? -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb

Re: [Jmol-users] JSmol and JSpecView

Hi Jennifer http://sourceforge.net/mailarchive/forum.php?forum_name=jmol-users is the official archive, but I agree there is no apparent way of searching through it There are several mirrors, e.g. I regularly use http://www.mail-archive.com/jmol-users@lists.sourceforge.net/maillist. html that

[Jmol-users] paper on Jmol and orbitals

Dear Jmolers, You may be interested on reading this -- it is offered for free by ACS Interactive Web-Based Pointillist Visualization of Hydrogenic Orbitals Using Jmol Shane P. Tully, Thomas M. Stitt, Robert D. Caldwell, Brian J. Hardock, Robert M. Hanson, and Przemyslaw Maslak J. Chemical

Re: [Jmol-users] Jmol Java problem

Hi Tony As the test report says, Safari should be compatible. The most likely cause for your problem is recent policies of blocking Java applets due to the vulnerabilities reported. In particular, Apple remotely forces applet disabling in Safari. I'm not a Mac user, so I cannot offer specific

Re: [Jmol-users] JSmol size reductions

Hi Bob We had some problems with MSIE 9, but that should be fixed. If someone would try this with Safari 5.1, I would appreciate it. Particularly the link down on the middle column, load k04041.cif {1 1 1} http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm Works in Safari 5.1.7 (Windows

Re: [Jmol-users] Distances/angles with mouse broken in applet?

Dear Eric, I cannot reproduce your problem. Fixing the monitor line with the mouse also fails at http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm (Jmol 13.1.11 signed applet). That works correctly for me. I can set monitors for distance and angle using the mouse. Firefox 18,

Re: [Jmol-users] ellipsoid that envelops a model

This feature sounds interesting. Simplistic protein rendering! :-) I think you are suggesting: ellipsoid {atom set} Should we give that a try? Oliver, would it be useful to allow an option that includes atomic masses? I had a request (off-list) recently as to how to find the center of

Re: [Jmol-users] FirstGlance now works in IE9

El 13 Feb 2013 a las 18:00, Eric Martz escribió: This restructuring of FirstGlance HTML was greatly facilitated by the resizable Jmol template B generously provided by Angel Herráez http://biomodel.uah.es/Jmol/resizable/inicio.htm I am deeply thankful to Angel! So glad to pay you back

Re: [Jmol-users] Web kit browsers and JSmol--partial answer to my own question...

Jonathan, I'd say that has nothing to do with JSmol but with server configuration. I saw that for JSmol pages, being all js loaded into the browser, gets a different behaviour than with Java. For example, from my server the extension also raised different behaviours when loading (I don't

Re: [Jmol-users] Web kit browsers and JSmol--partial answer to my own question...

I agree with Otis regarding the use of txt. I still try to avoid using txt systematically (beacuse I quite prefer to know what's in a file) but it may be a sensible mesure. Served file suffixes have to be registered. I don't understand why this would be browser dependent, however. Well,

Re: [Jmol-users] I can't get chrome and safari to load JSmol pages where all files are ASCII...

If a file is a binary type, some browsers simply won't be able to read it ever from your hard drive. But they will from a server, provided you have the jsmol.php file installed there, which will convert the binary file to BASE64 and pass it back to those binary-incapable browsers in that

Re: [Jmol-users] Problem with switching to JSMol

Hello Simone #1 I believe (but am not sure) that with the latest versions you only need to call JSmol.min.js The call to j2sjmol.js will be done internally based on the path specufied in the Info variable. #2 Information in the Wiki is not up-to-date (must find time to do it, and the WIki was

Re: [Jmol-users] Problem with switching to JSMol

Ah, OK JSmol distribution is still not well roganized, I'm afraid. There's also a bit of confusion between Jmol-JSO and JSmol (which I'm planning to sort out and explain in the wiki) I suggest that you download from StOlaf. The link is in the wiki http://wiki.jmol.org/index.php/JSmol (there

Re: [Jmol-users] Drawing Options

Robert Hanson wrote: draw scale 500 arc ... 5-Angstrom diameter 500 == not 5 angstrom, I'd say ? * What's the best way to draw a line without an arrow head? Use 'draw cylinder'? Yes, I think so. There is draw line (polyline) and draw curve, which is useful e.g. for arbitrary curves

Re: [Jmol-users] JSmol 13.1.13 released

On 23 Feb 2013 at 15:36, Robert Hanson wrote: with unreleased updates going to http://chemapps.stolaf.edu/jmol/jsmol/jsmol.zip That should be http://chemapps.stolaf.edu/jmol/jsmol.zip -- Everyone hates slow

Re: [Jmol-users] Drawing Options

, these behaviors are still present in 13.0. Thanks for updating, Andreas. Thanks, -Spencer On Sat, Feb 23, 2013 at 3:38 AM, Angel Herráez angel.herr...@uah.es wrote: Robert Hanson wrote: draw scale 500 arc ... 5-Angstrom diameter 500 == not 5 angstrom, I'd say

Re: [Jmol-users] JSmol

El 24 Feb 2013 a las 20:29, Robert Hanson escribió: Anybody know if that's the case? -- That if you access your local machine via localhost and an apache server, you can access files that are not downstream of the path of the HTML page? I'm not sure right now if in my case the paths resemble

Re: [Jmol-users] R: Re: JSmol

right -- let's get that clarified on the wiki. OK, I will do it. Still I cannot grasp what is the exact limitation, all being javascript any folder should be possible. We are not talking about getting files from other server.

Re: [Jmol-users] Directories

On 25 Feb 2013 at 13:27, Fred Ziegler wrote: All: Uploaded to the serverFEZtest5.html (subdirectory), and JSmol and cyclohex.mol to the directory, one level up). Does not work. Used ../ annotation in three locations. What am I doing wrong. Fred Fred, I tried your source code locally,

Re: [Jmol-users] Error Question

When is a bug not a bug? I guess it depends on the number of legs it has :-D -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today:

Re: [Jmol-users] JSMol not working with JSmol.min.js

http://biology.kenyon.edu/BMB/biomolecules_jsmol.htm Working for me , too (Firefox on WIn7) Clear your cache, maybe -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download

[Jmol-users] documentation on JSmol in the Wiki

Dear Jmolers, Information about JSmol and Jmol JavaScript Object is more or less complete and up-to-date now in the Wiki, http://wiki.jmol.org/index.php/Jmol_JavaScript_Object More details will be need to be added later, but I believe this now agrees with the current state and, even if not

Re: [Jmol-users] JSMol not working with JSmol.min.js

http://biology.kenyon.edu/BMB/jsmol/simple2.htm Yes! Same result as Mike: first it loads the Java applet, but the HTML5 links loads the JSmol version OK -- Everyone hates slow websites. So do we. Make your web apps

[Jmol-users] problem running scripts in JSO

I am hitting my head against the wall. Cannot trace what's going on. Can this error be due to location of files and folders? Error: TypeError: b._script is not a function Archivo de origen: http://localhost/jsmol_28feb/JSmol.min.js Línea: 289 It's happening with both Jmol.Java and JSmol.HTML5

Re: [Jmol-users] Definition of atom property - substructure

Rolf, you can check out http://wiki.jmol.org/index.php/Protein_Community Hope it is correct -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today:

Re: [Jmol-users] JmolApplet.class problem

Hi Richard That error usually displays when the applet JAR files are not found, either because of a wrong path or because you specify signed applet and have only the unsigned files (or vice versa). I don't think it has anything to do with Java policies. Maybe because of the blocking dialog the

Re: [Jmol-users] hmm. css question

I would say: 1. you need an envelope div#1 or other element that has position:relative (absolute will do too) 2. inside that div#1, you set div#2 with position:absolute; left:0;top:0; 3. inside div#1 and next (sibling) to div#2, you set div#3 also with position:absolute; left:0;top:0; div#3

Re: [Jmol-users] hmm. css question

Based on current (generated) source code in http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm this could be enough (portions in red added over the existing code): div id=jmolApplet0_appletinfotablediv style=width:300px;height:300px;position:relative; div id=jmolApplet0_appletdiv etc canvas

Re: [Jmol-users] cover image

I can see how we might want two different images, one first and then one during loading. A nice animated GIF would be handy for the loading part. My previous tests (but not with current JSmol) showed that the browser cannot cope with animated GIFs while loading JSmol libraries. They just

Re: [Jmol-users] JSmol in ePub3

Greg, this sounds very interesting. I hope you can succeed. I have successfully included JSmol in our VLE pages It would be interesting to the Jmol community if you could share some guidance abbout that implementation. There is a section in the Jmol Wiki,

Re: [Jmol-users] Console Question

Otis, have you tried show PDBHEADER ? -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For

Re: [Jmol-users] accented characters

Olá Sérgio This problem comes back from time to time, I thought we could be forgetting it. All depends on whether the browser knows the encoding of the JavaScript and JmolScript files. You are using the Java applet, not JSmol, right? First choice I would suggest is to make sure that all

Re: [Jmol-users] accented characters

El 11 Mar 2013 a las 9:04, Sérgio Ceroni da Silva escribió: Already tried that using Notepad++, encoding in UTF-8 with and without BOM. No success. m... Weird Do you have a link url I can see? -- Symantec

Re: [Jmol-users] old Jmol, new JSmol

Richard, my experience is that IE behaviour changes dramatically depending on the (compatibility) mode it adopts --particularly for CSS-related things. For that, including a proper DOCTYPE in the page header is crucial. But I'd expect IE8 to work correctly for most things also in JSmol.

Re: [Jmol-users] WRITE working

That's great, Bob Users: you may be also interested on my tests along this issue: http://biomodel.uah.es/en/noJava/export-image/index.htm Maybe it's the same technique Bob has implemented. Note that page is not using the latest JSmol files. Server-side processing is only needed for IE clients.

Re: [Jmol-users] old Jmol, new JSmol

How do you tell? Is there a version number somewhere? There is a number inside the files, and in the popup menu. Bob was explaning this recently in another thread, maybe just yesterday. I know it's a big download, but I cannot find an explanation to your problem, so it might be a bug that

Re: [Jmol-users] old Jmol, new JSmol

This is not an answer. It's a parallel question. Is this link the source for the latest JSmol development update? http://chemapps.stolaf.edu/jmol/jsmol.zip Yes, it is that, Otis Explained at http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Installation

Re: [Jmol-users] About adjustment of jmol applet window size by mouse

But the cartoons structure of my test applet looks not very smooth and has jagged edges. I am wondering if there are any other features to get smoother structure. It may depend on your particular molecule, but yes you can control smoothing of the cartoons. See the documentation:

Re: [Jmol-users] language localization for JSmol

Console: The content text is in Spanish. The close link in the top yellow bar is in English (probably rightly so), as well as the buttons at the bottom. The popup menu shows in Spanish allright Firefox 19.0.2 navigator.userAgent = Mozilla/5.0 (Windows NT 6.1; WOW64; rv:19.0) Gecko/20100101

Re: [Jmol-users] super light-weight JSmol?

TwirlyMol maybe? 14 kb! -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar

Re: [Jmol-users] language localization for JSmol

What is the language flag checked for enabling localization ? I think Bob is using the language reported by the browser navigator.language (Mozilla at least) navigator.userLanguage (MSIE) This is different to Jmol-Java which relies on Java, which reads the operating system language,

Re: [Jmol-users] old Jmol, new JSmol

I am seeing the same problem as Richard in my IE8, using StOlaf page http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm during loading, this error is presented and the page stalls Object does not accept this property or method core.z.js, Line 2789 Character 430 saying

Re: [Jmol-users] language localization for JSmol

More testing: Firefox: - all OK Chrome: - console and menu display in English - J.i18n.GT.getLanguage() reports es - popup menu reports Spanish option selected - switching languages via menu does not work Opera - all OK: - console and menu display in Spanish - switching languages via

Re: [Jmol-users] old Jmol, new JSmol

Correct. We do not support MSIE 8. Oh, my bad I understand why (the lack of canvas support), but at some stage I became convinced that I had seen JSmol running on IE8 here. Sorry for all the pointless discussion.

Re: [Jmol-users] Visualization of a sphere packing

Hi Andrea Since PQR format is so similar to PDB format, you must instruct Jmol to read it as such. That could be the reason for your problem (or maybe not, but it is worth a first try) load pqr::myfile.pqr (I wrote pqr, but the file extension is irrelevant; it's the prefix before the ::

Re: [Jmol-users] Visualization of a sphere packing

Hi Andrea Yes, I went quite mad to arrange the columns in the correct format. Well, column positions in your example do NOT match what I take for the correct format, as exemplified in http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/pqr/1 FAS.pqr I had to shift your Q and R

Re: [Jmol-users] Visualization of a sphere packing

Further clarification: I am not sure how strict the Jmol reader for PQR will be for column positions, but it is safer to stick to the standard. This is what I have from PDB format specs: 1 2 3 4 5 6 7 8

Re: [Jmol-users] Visualization of a sphere packing

This mean that the maximum radii ratio that can be visualized correctly is about 18 (if the lengths are conveniently scaled). Is there a solution if I would like to visualize packings of spheres with very different radii, say for example 1:100 or more? If this limitation is confirmed, you

Re: [Jmol-users] Center of mass of visible atoms

Note: what is used is not the center of mass, but the geometric center See http://wiki.jmol.org/index.php/Recycling_Corner#Center_of_mass if you want center of mass -- Everyone hates slow websites. So do we. Make your

Re: [Jmol-users] Visualization of a sphere packing

Andrea, this script seems to do what you want: n1 = {*}.atomno.min; n2 = {*}.atomno.max; for (i=n1; i=n2; i++) { m = s + i; d = 2 * {atomno=i}.vanderwaals; // print d; draw id @m diameter @d {atomno=i}; } spacefill off; Tested with file: REMARK 1 PQR HETATM1 X-403.3

[Jmol-users] proposal for filename change in non-jQuery alternatives

For consistency, I propose that JSmol.lite.js should be called JSmol.lite.nojq.js while JSmol.lite.jq.js should be renamed JSmol.lite.js The reason is that by default, both standard JSmol and lightweight JSmol need jQuery. Since the standard has JSmol.min.nojq.js as an exceptional alternative,

[Jmol-users] inverted stereochemistry in JSmol Lite ?

It seems that stereochemistry gets inverted in JSmol Lite. I am loading a few amino acids (in MOL format) and they display as D forms, not L. Check for example getting alanine from NCI on http://chemapps.stolaf.edu/jmol/jsmol/lite2.htm versus http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm

Re: [Jmol-users] inverted stereochemistry in JSmol Lite ?

Yes, stereochemistry is OK now Thanks (Our April's fool is on Dec. 28, so I was not expecting this ;-D ) -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn

Re: [Jmol-users] posterity link -- Jmol-7

But files in that SF folder cannot be downloaded -- they do not exist. I found a download for 0.6.1 in a Yahoo site. Thinking about a museum of Jmol! El 3 Apr 2013 a las 22:47, Egon Willighagen escribió: Nice, but it does not beat Jmol 0.6 from March 2001: jmol-0.6.1.tar.gz 2001-03-26 2.9 MB

Re: [Jmol-users] Problem running commands immediately after a 'compare' alignment

Hello Shane Should I do something to wait until the animation stops before calling Jmol.script again? If so, is there any state function that lets me know that it is okay to start executing commands? There is probably a way to do both of those, but it is not trivial. Is there a reason

Re: [Jmol-users] Problem running commands immediately after a 'compare' alignment

El 4 Apr 2013 a las 19:38, Shane Ó Conchúir escribió: However, the alignment of the LG1 residue [...] does not seem to work as well [...] I did notice that the order of the atoms in LG1 is different between 1.1 and 2.1. As a last resort, you can add a 1-to-1 matching list to the command.

Re: [Jmol-users] Draw a box without DRAW boundbox

Ciao Paolo if after your commands you type show draw you will see this: draw ID grid_box POLYGON 8 {18.908 -15.639 7.5060005} {34.658 -15.639 7.5060005} {34.658 -15.639 25.506} {18.908 -15.639 25.506} {18.908 0.1116 7.5060005} {34.658 0.1116 7.5060005} {34.658 0.1116 25.506}

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