Re: [Jmol-users] JSModel demo control problem

…all solved now I hope. Angel explained how to apply the css vw and vh to a div containing a Jmol canvas to resize it dynamically. It took me a little time to apply to my own page because of the constraints of pre-existing css, but I fixed it and also applied it to the width of the control “

Re: [Jmol-users] JSModel demo control problem

Angel wrote: > I think this has been discussed before in this list. That syntax for > selecting > chains was supported, but it is not very precise and some versions stopped > supporting it. > You should be safe adding a colon before the chain, > select *:A > Which confirms my conservatism i

Re: [Jmol-users] JSModel demo control problem

So it turns out that the source of my problems with developing with JSmol for mobile is the horrendously vicious caching of Safari on the iPhone. This was because I was switching between an old and new version of JSmol and Safari was looking for old files. 1. One has to go into settings> safari

Re: [Jmol-users] JSModel demo control problem

Angel and list, Sorry to keep posting. The error on my phone is from my server saying: mol/j2s/core/corejmol.z.js could not be loaded. Script error: Unexpected token ‘<‘ But only on the phone. (Web still gives same origin error on Safari). I’ll go to bed and wind everything back tomorrow. Da

Re: [Jmol-users] JSModel demo control problem

Angel and list, Spoke too soon. Rendering ok on browser, but giving me errors on phone, and when I look at the error console on Safari I’m getting errors of this type, even after reverting to the old version of JSmol which certainly did run on the iPhone because I was punching it about last nig

Re: [Jmol-users] JSModel demo control problem

Angel and list, Have modified the code as suggested and it seems to be working fine. Thanks. As to why my code was convoluted (did you really want to know?). One sets these things up years back, then it becomes obvious that the Java web plugin is doomed and one is overjoyed to find JSmol. And

Re: [Jmol-users] JSModel demo control problem

Thanks Angel, I’m on reflected so I didn’t get your attachment and have only just seen the emails. I’ll play with your suggestions this evening and post back to the list. David ___ Dr. David P. Leader, Boyd Orr Building, University of Glasgo

Re: [Jmol-users] JSModel demo control problem

Hi Angel, No it’s not specific to the latest version. I was running a 2014 version and then just before posting thought I’d better check the latest version just in case. Fortget to say I’d only tested on Mac Safari and iPhone 5, but it’s not likely to be broswer-specific. David On 19 Jul 201

[Jmol-users] JSModel demo control problem

I have just been revamping some teaching material I wrote for (former) colleagues — I am now “retired”. Most of this is numerical, but there is one JSMol demo of the DNA double-helix. In the course of putting this in a “responsive” web page I noticed a slight bug that I can’t figure out. The de

Re: [Jmol-users] SVG

In reply to my query about SVG and preparing Jmol images for publication, Angel wrote: As I understand it, Jmol renders by generating a bitmap on screen and updates it continuously. So I don't thik it is possible to convert to a vector image. Ok. Apologies for my naivety. I guess I wasn’t think

[Jmol-users] SVG

I was recently implementing SVG for some simple graphics generated by a Java Servlet of mine and adding the ability to download as an svg file for editing in Adobe Illustrator. It struck me that the option to download an image as vector graphics from JSmol would be most valuable. The average bit

[Jmol-users] Loading Aesthetics

Apologies for sending the whole digest back to the list. Never done that before and not quite sure how it happened. Posted last night from my personal address at home, mail bounced, and all I thought I had done was to change the address and resend. Anyway I don’t expect Bob will be able to answe

[Jmol-users] Jmol-users Digest, Vol 105, Issue 7

Send Jmol-users mailing list submissions to jmol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/jmol-users or, via email, send a message with subject or body 'help' to jmol-users-requ...@lis

Re: [Jmol-users] Selecting specific hydrogen atoms

Angel, On 28 May 2015, at 19:52, Angel Herráez mailto:angel.herr...@uah.es>> wrote: Hi David So, NH hydrogens may be selected by select *.H and backbone oxygens by select *.O You could do e.g. calculate hbonds; hbonds on; select 118-123 and (*.H, *.O); hbonds 0.3; color hBonds cyan; Thanks. Di

[Jmol-users] Selecting specific hydrogen atoms

I’m trying to prepare some figures for publication and I want to show hydrogen bonds between NH and O of backbone peptide bonds. If I use the command: restrict (118,119,120,121,122,123) AND NOT (*.H???, *.1H???, *.2H???, *.3H???) wireframe 0.3 This selects the residues I want and their side chai

Re: [Jmol-users] JSmol menu on iPad

Otis Wrote: I have also noted the lack of iPad touch response with the Jmol menu, which can also be accessed with the menu command. Since I'm primarily interested in "buttonizing" menu commands, this has not been a big problem for me, but I can understand that this capability would be a nice featu

Re: [Jmol-users] Label Font Problems

Apologies for leaving out the subject of my posting of 25th Jan. As nobody on this list ever seems to trim messages, I’ll repeat it here so it threads properly. (And, yes, I’ve finally changed my subscription address. That was the last straw as far as gmail is concerned.) Bob wrote: I must be

[Jmol-users] (no subject)

Bob wrote: I must be missing something in reading: *I have now done quite a bit of experimentation with html5/canvas pages of my own (documentation available on request, but a test page is viewable at http://motif.gla.ac.uk/JSmolTes

[Jmol-users] JSmol menu on iPad

I wrote on another thread > > However... > ...I have another question about JSmol since testing it on all sorts > of platforms. On the iPad (and other tablet platforms) there is no > such thing as hover or mouse-over. OK, one has to live with that for > mouse-over an atom in the structure, but it

Re: [Jmol-users] Label Font Problems

Bob wrote: = I have already released this as Helvetica Neue. OK? = OK, but not necessary as MacOS X is already using Helvetica Neue as Sans-Serif. and = http://www.identifont.

[Jmol-users] Label Font Problems

Bob replied to my description of the Safari 7 font-rendering problem on JSmol: == Certainly very curious. It must be considered a Safari bug that they are not picking up the sans-serif bold, which is required by HTML5 standards. But we can ge

Re: [Jmol-users] Label Font Problems

In response to my report of font problems with Safari, Bob wrote: === All JSmol is doing is setting the canvas.context.font using a simple string like "bold 12px Serif" So perhaps some experimentation on your part with a simple canvas could fix that. === I

Re: [Jmol-users] Label Font Problems

In reply to my posting on suboptimal font rendering on Safari, Bob wrote: David, thanks for the very thorough testing. All JSmol is doing is setting the canvas.context.font using a simple string like "bold 12px Serif" So perhaps some experimentation on your part with a simple canvas could fix th

[Jmol-users] Label Font Problems

button for individual motifs and then on Motif 1 - marked up as 12 plain - and Motif 2 - marked up as 12 bold. I wonder if the font (if any) that is being specified is the problem. Or is there some IE-only code somewhere? David Leader (University of Glasgow

Re: [Jmol-users] Transition from Jmol to JSmol: scripting problem

Angel supplied me with the following code to fix my spinning problem: - Jmol.jmolCheckbox(myJmol, "reset;", "reset; if (_spinning);rotate x 90;spin on;else;rotate x 90;endif;", " Toggle Base-stackin

[Jmol-users] Transition from Jmol to JSmol: scripting problem

First, congratulations to the developers who ported Jmol from Java to JavaScript / HTML5. It really satisfies the need for allowing Jmol to continue in the tablet environment and in a locked-down student desktop environment. It must have been a huge amount of work. Well done! It's a long time sinc

Re: [Jmol-users] Remove Jmol Watermark

Robert Hanson gave a long and obviously carefully thought-out reply to my message regarding the division between coders and interface designers. (I didn't mean to say I spoke *for* one of the camps - I speak for myself *as* a member of one the camps.) I will not quote all of Robert's messag

Re: [Jmol-users] Remove Jmol Watermark

Although I know that this is not likely to produce any improvement in the ambiguous Jmol interface (and those that donate their time to a project are free to decide in what areas they will direct their effort), I feel that William Reusch's posting should not go without comment. He wrote:

Re: [Jmol-users] Remove Jmol Watermark

I've mounted a mockup pic of the current Jmol frank and what I proposed some years ago at: http://www.q7design.demon.co.uk/temp/JmolMockup.html. On reflection, although the drop down nature is made clear, my proposal has a couple of defects: 1. It is more obtrusive than the current frank. 2.

Re: [Jmol-users] Remove Jmol Watermark

Graeme wrote: Sorry if this is another silly question but is it possible to remove the bottom right "Jmol" water mark? Usually these things can?t be removed but I haven't seen an open source application do this before. In which case what are you hoping to achieve by adding it there because a

Re: [Jmol-users] Use of Java in teaching?

hese reasons. I don't know if that is really the problem in this case, but it could be. That's a very odd message -- it isn't coming from Java. It's coming from whatever custom package "GMSIntegration" is. What is that, anyway? Bob On Mon, Mar 16, 2009 at

Re: [Jmol-users] Use of Java in teaching?

Rolf wrote: and although this might be easier, I did it my way. Don't see anything like this in Flash out on the web. http://doolittle.ibls.gla.ac.uk/leader/GMS/index.html When I tried to run the applets with Java 1.4.2_18 in Firefox 3.0.4 on Linux I got the following error messages and the

[Jmol-users] Use of Java in teaching?

Ewen McLaughlin wrote: Could I canvass your opinions of the following statements, which were given in response to a request to install Java, for chemistry teaching purposes, at a college I work with? "a) Java allows malicious activity that could damage the system" Well my Mac comes with

[Jmol-users] Hydrogen Bonds up on Motivated Proteins

Just a line to say that I've now traced the tortuous path from SQL, java servlet, Perl CGI, javascript, to Jmol scripting language and have my web application, Motivated Proteins ( http://motif.gla.ac.uk/ motif/index.html), showing the HBPlus Hydrogen Bonds from our dbase in the 3D -> Single

Re: [Jmol-users] Deleting connections

Bob wrote: hbonds off should work, provided you have selected all atoms involved in those hbonds. OK, I rearranged the order of my statements added an hbonds on and it seems to be working now. David, please define "switch to another motif" in terms of Jmol script commands. It's not r

[Jmol-users] Deleting connections

Am starting working on my defined hydrogen bonds and have run into a minor snag. I have radio buttons that on clicking run a jmolScript that displays a motif and creates defined hydrogen bonds, the latter with a command of the sort: select atomno=2362, atomno=2440; connect hbond; However if

Re: [Jmol-users] Protein Hydrogen Bonds again

Bob wrote: > ah -- ok, I see. Well, that sounds terrific. I'd be interested just in > peeking at the C code, then, in that case. Just to see what sort of > considerations you made. Who knows. It might be an almost trivial > addition > to Jmol. I'll send it you. David _

Re: [Jmol-users] Protein Hydrogen Bonds again

Bob wrote: It might be interesting to see how the HBplus program works. I see http://www.csb.yale.edu/userguides/datamanip/hbplus/algorithm.txt but that suggests there is no energy calculation here, just a set of angle/distance rules. HOWEVER -- NOTE!!! The HBPlus program itself is not public

Re: [Jmol-users] Protein Hydrogen Bonds again

Angel wrote: > David, have you measured the length of the Hbonds you want to show up? > You might nedd some longer spec. > I've just tested > connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE; > with > http://doolittle.ibls.gla.ac.uk/top500H/1osaH.pdb > and Jmol 11.6.3 and it creat

Re: [Jmol-users] Protein Hydrogen Bonds again

Just to report that: connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE; does NOT display the side-chain H-bonds that define the first motif I have tested (an Asp CO / peptide-bond NH Hbond). Clearly, you get what you pay for. If Jmol is going to display side- chain/main-chain

Re: [Jmol-users] Protein Hydrogen Bonds again

Angel wrote: David, connect 1.8 {H andetc. is not correct; you need "_H" or "hydrogen", not "H" So I do. It works now. Many thanks! I'm very curious to see whether it does the right thing with the relevant motifs. But it's been a hard day in the bioinformatics lab, so it will ha

Re: [Jmol-users] Protein Hydrogen Bonds again

Bob, Sorry but I can't get the script line you sent to work. To check it wasn't my version of Jmol I went to your tutorial site and got the example page for "connect". Then I: 1. Uploaded an example file with Hs: http://doolittle.ibls.gla.ac.uk/ top500H/1osaH.pdb 2. Pasted some script in

Re: [Jmol-users] Protein Hydrogen Bonds again

Bob wrote: Sure, but -- you said you had the H atoms Are you saying you might want to move them? On Thu, Nov 6, 2008 at 11:01 AM, David Leader <[EMAIL PROTECTED]>wrote: However I still might see if there is a student up to integrating the C code. My colleague tells m

Re: [Jmol-users] Protein Hydrogen Bonds again

Bob wrote: David -- none of the work I just did will be of help to you, since you have the H atoms already present. But I'm glad you started this discussion anyway, because that will certainly be of interest to others. I really think a simple command such as connect 1.8 {H and connected(_O o

Re: [Jmol-users] Protein Hydrogen Bonds again

Thanks for the response to my message. I've been tied up with something and now it's quite late in Europe so I'll just send a brief reply to a couple of points and any further info later. 1. My interest is only in proteins where the hydrogens have been added. The database of the proteins I w

[Jmol-users] Protein Hydrogen Bonds again

I wish to return to the question of Jmol and the display of H-bonds in proteins which I let lapse after raising it a year or so back. I would like Jmol to be able to display H-bonds between amino acid side chains and main-chain atoms and have some questions for the development team relevant

Re: [Jmol-users] javascript command fails in Safari?

Not sure that it has anything to do with Eric's problem, but remember when using Jmol and Safari to look at the Mac's own Console application (lives in utilities, but I keep it in my dock) for Jmol output. David ___ Dr. David P.Le

[Jmol-users] (no subject)

Green links work fine on Safari 3.1 and Firefox 2 on Mac OS X 10.4.11 and 10.5.2 for 1eve. David ___ Dr. David P.Leader, Biochemistry and Molecular Biology, FBLS, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-59

Re: [Jmol-users] How to avoid alert message on loading ?

Shameer Khadar wrote: > I am a Jmol newbie. Currently using Jmol as a part of a webserver am > developing. > Everything works fine, except when I load my Jmol window from my cgi > program. > Jmol is generating an alert message >"In general, an absolute URL is not recommended for > codebaseDi

Re: [Jmol-users] announcing Jmol handbook - in English

Angel posted the following last month, and on my digest it appear as follows: Message: 8 Date: Fri, 28 Dec 2007 17:39:36 +0100 From: "Angel Herraez" <[EMAIL PROTECTED]> Subject: [Jmol-users] announcing Jmol handbook - in English To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTE

Re: [Jmol-users] Spinning molecules

Ewen wrote: > I showed Jmol to a colleague and he tried to rotate the model like > this: > > > > He clicked onto the molecule, dragged it round and then let go; he was > disappointed when the molecule did not continue its rotation. I > think he > thought it would act like an globe which you ca

Re: [Jmol-users] new.htm updated

Dean wrote in reply to mine: I can't reproduce this problem on my system (also OS X 10.4.11). Jmol loads just fine and all the example scripts appear to work. Dean Johnston On 11/28/07 3:44 AM, "David Leader" <[EMAIL PROTECTED]> wrote: > Bob wrote: > &

Re: [Jmol-users] new.htm updated

Bob wrote: > I've updated > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > with the very latest for Jmol. Most notably: But on Mac 10.4.11 the applet on the page does not load using either Safari or Firefox (both latest versions) The Sun Java wait thingy just keeps going round

[Jmol-users] Safari, Windows, Jmol and Java

I notice from the Safari 3beta download page that in addition to "Latest security updates" - how very Windows - there is a list of "Coming Soons" which includes 'LiveConnect' support (already in Safari 3 beta Mac as it's in Safari 2). This means (a) No point my trying it at the moment, (b)

Re: [Jmol-users] Citing Jmol

ar viewer for three-dimensional > chemical structures" > plus the URL: http://www.jmol.org/ > > > El 4 Jun 2007 a las 13:34, David Leader escribi?: > >> Is there any prefered way of citing Jmol in publications? > Two points regarding this. 1. The url redirects automatic

[Jmol-users] Citing Jmol

Is there any prefered way of citing Jmol in publications? David -- ___ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.g

Re: [Jmol-users] Sidechain H-bonds?

Thanks, Bob, for specific suggestions for using the H-bond data in our database to display sidechain mainchain H-bonds in motifs. I'll have to consider the best way to proceed within the constraints of our setup. As a general comment, however, I would say that I appreciate that Jmol is in a di

Re: [Jmol-users] Sidechain H-bonds?

I asked about representing mainchain-sidechain H-bonds for short three-dimensional hydrogen bonded motifs. Bob replied: >If the motifs are well-described in the PDB file, this would be no >problem. If they are to be generated from scratch, that's more of a problem. No. The way the thing works is

[Jmol-users] Sidechain H-bonds?

Currently Jmol calculates mainchain-mainchain hydrogen bonds very nicely, but, like RasMol doesn't calculate sidechain hydrogen bonds. I imagine that this question has come up before, but I'd be interested to know whether the technical difficulty of calculating them is the problem. The hydrogen

Re: [Jmol-users] Motivated Proteins incorporates Jmol 11

Bob wrote: >Say, David, I really like this feature: > >Protein 1blu not found in the Protein Motif database. >This protein is catagorized as: ELECTRON TRANSPORT >Proteins in the database of type ?ELECTRON TRANSPORT? are listed below: We needed to do that because our db is representative, rather t

[Jmol-users] Motivated Proteins incorporates Jmol 11

Thought I'd post to say that I've finally updated our protein motif web facility with Jmol 11 (.1.36) using the new 'zoom (selected)' functionality and the perspective mode 11, and it seems to be working on all Mac browsers and Windows IE7. Anyone interested can see it at: http://doolittle.ibls

Re: [Jmol-users] zoomTo an atom

I wrote: >I've tested it on the residue groups that constitute our motifs. I >find that I have to use something like: > >zoom (selected) 0 *10 > >to get it the right size. > >'zoom (selected) 0' certainly zooms it, but I would estimate the >motif occupies perhaps 1/10 of the area in a particular

Re: [Jmol-users] zoomTo an atom

Bob wrote: >checked in for Jmol 11.1.36: > > >zoom (atom expression) 0 >zoomTo timeSec (atom expression) 0 > >zooms to the atom expression, filling the screen (roughly) with that set >of atoms. > >Additional options include any of the following after the zero: > >+ x >- x >* x >/ x Wow! Thanks Bo

Re: [Jmol-users] zoomTo an atom

Bob wrote: > > fyi -- All you need there is > > AND NOT (*.H???, *.?H???); > > not all the other possibilities. Blush, blush. Someone else wrote the original for me, honest. I hated it. >> >> PS Angel said that zooming automatically until the selected molecules >> fill the screen is not possib

Re: [Jmol-users] Configuration

I have finally resolved my problem with the 'memory effect' when using 'configuration'. The magic words were "wireframe off"! Putting these at the start of each script does the trick. So the final code for the radio buttons was of the type: jmolRadio("echo; wireframe off; restrict (80,81,82,83)

[Jmol-users] configuration (was Jmol 11 woes)

I wrote: >but "conformation A" does nothing for me. It seems to be 'taking' in >the script, because if I load the page that way, I no longer have >conformation options on the menu. Any idea what I'm doing wrong? (That was a typo, I had used 'configuration') and Bob replied >configuration 1 >di

Re: [Jmol-users] Jmol 11 woes

Angel wrote: >> As regards the bad display, select single motif display and then >> Catmat: 48,48,50 . Glu 50 is screwed up. >> > > That looks that an alternate position (Alt) problem; there are e.g. > [Glu]50:A.CD%A and [Glu]50:A.CD%B, and Jmol is drawing both. > I have not used Alt locations, bu

Re: [Jmol-users] Jmol 11 woes

I have now sorted things out and established that: 1. 'restrict (0)' supported in Jmol 10 has to be replaced by 'restrict none' I don't mind that. I knew it was a silly hack when I couldn't get things to work for some other reason and should have changed it. 2. The edited pdb files with Hydrogen

Re: [Jmol-users] Jmol 11 woes

A quick note to say that 11.1.32 fixes my short-HET line PDB file- load problem. Thanks Bob. I'll get back about the scripting problems later - I hope later today, but, if not, tomorrow. David - This SF.net email is spons

Re: [Jmol-users] Jmol 11 woes

Regarding my parsing problem with Jmol11, Bob wrote: > It is fixed at Sourceforge. But not in the compiled download -- > just in > the code. It will appear in 11.1.32. > Sorry about the confusion. That's fine - no hurry, you're doing a hundred and one things Bob. We appreciate it. and > The

Re: [Jmol-users] Jmol 11 woes

Regarding my problem with Jmol 11 using Richardson 500 files, Bob wrote: > Yes, it was because that format they use involves short lines -- no > filling to 80 characters. > I just had a statement in there that presumed full-width PDB files; > that's gone now, and I don't > see any other situations

Re: [Jmol-users] Jmol 11 woes

Regarding my problem with Jmol 11 using Richardson 500 files I wrote: > I can't see how it can be anything but the pdb files. Would that > fit with changes made in file reading between 10 and 11? Then I hit send. Then I reflected, and downloaded the straight pdb files and confirmed that I was

[Jmol-users] Jmol 11 woes

Following my zooming post, I downloaded 11.0.2 and tested it on a number of pre-server local tests I had working with 10. On one of these the molecule loaded and confirmed that a motif was more zoomable than on Jmol 10. (There were some bugs, but these were that are minor compared with the

Re: [Jmol-users] Zooming and labelling limitations

Bob wrote: >David, what version are you using? I was hoping you wouldn't ask. I'm still using version 10, in that it does what I want and if it's not bust... ...but if upgrading to the latest version fixes it, then I'll upgrade. David -- __

[Jmol-users] Zooming and labelling limitations

I'm working with Jmol again (after several months) in relation to my database-driven web app and have one question and what I fear may be a feature request. 1. There is a limit to the extent that I can zoom a motif of a few amino acids in a large protein, which is marginally insufficient for m

Re: [Jmol-users] update of documentation for Javascript Library and some Jmol.js fixes

it accurate, unlike the link on the present download page which states that the current official release is version 10.2, and then leads you to a page in which 10.2 is nowhere to be found, and all the versions available seem to developmental versions. David Leader -

Re: [Jmol-users] does this work?

Bob wrote: > I'm experimenting today with the serialization business. > > http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/ > snapshot.htm > > 1) Does the page open to show you a helical set of triangles? Yes > > If so, click "random moveTo" and then "live snapShot" > > 2) Do you n

Re: [Jmol-users] new documentation popup method

> > Please try the "atom expressions" example. > Tested on Safari under Mac OS X 10.4.7 > Q: Did the page load? Yes > Q: Did the page title change to reflect that particular example? Yes: 1blu.pdb > Q: Did the list and textbox areas load? Yest > Q: Did the model load? Yes > Q: Did the dat

Re: [Jmol-users] Pop-up documentation not working on Mac

Quoting Philip Bays <[EMAIL PROTECTED]>: > This works for me, with the exception of the hydrogen bonds button -- > or else my eyes are showing their age:-) It does work, but you have to zoom in and tilt to see it. It's adapted from a student demo I built and have been polishing for the coming t

Re: [Jmol-users] Pop-up documentation not working on Mac

I've already mailed Bob with the url of a demo I set up in response to his request: All we need is one simple example of someone on this machine successfully doing the following: 1) pop up a window having in it an applet, either or , hard-coded or using Jmol-js itself. 2) demonstrate successful

Re: [Jmol-users] Pop-up documentation not working on Mac Safari

Bob replied to one of my postings (sorry that this is not automatically marked up): An interesting difference between FF and Safari in this regard. If you choose "View Source" on FF you get the source, on Safari you get blank. Likewise if you try to save the page on Safari it says it can't. How a

Re: [Jmol-users] pop-up documentation not working on Mac 10.4

An interesting difference between FF and Safari in this regard. If you choose "View Source" on FF you get the source, on Safari you get blank. Likewise if you try to save the page on Safari it says it can't. How are you generating the pop-ups, Bob? Oh, and Opera refuses to show the source eithe

Re: [Jmol-users] pop-up documentation not working on Mac 10.4

I did the same tests as Frieda did on Safari with the same results, but also on FireFox. For interest I'm giving the FF replies as well > > > --- >> Test 2: Does my test work at all? >> --- >> > > js: 1+2 >I do ge

Re: [Jmol-users] pop-up documentation not working on Mac 10.4

I wrote a long message and Bob replied: I need to be clear whether we are talking about the "interactive" scripting documentation at a) http://www.stolaf.edu/people/hansonr/jmol/docs or the library examples at b) http://jmol.sourceforge.net/jslibrary/ Both have pop-up windows. Are both mal

Re: [Jmol-users] pop-up documentation not working on Mac 10.4

I have now mounted a replica of the pages relevant to the pop-up problem on my personal website, where they will be available until the weekend (I'm short of space). The url is . Mac users will see that, in contrast to the real pages on

Re: [Jmol-users] pop-up documentation not working on Mac 10.4

Bob wrote: > On Aug 6, 2006, at 9:33 AM, Frieda Reichsman wrote: > >> The pop-up windows of the Jmol interactive scripting documentation >> are appearing but remain totally blank.] > > > By now this has been fixed such that the content of the pop-up > windows appears, but the commands (links) to

[Jmol-users] Opera 9.01 Mac still broken for jmol.js

...at least in my hands and with my demos, that work under Safari and FireFox. Still getting wierd js errors. Wonder if someone else with a Mac could check an officially approved demo with checkboxes (or point me to one). David -- ___

[Jmol-users] Requirements for jmol.js

This was discussed a while back, but I forget what the score was, and the jmol.js page on sourceforge still refers to the 'upcoming realease Jmolv10'. I have just switched my site from using the Jmol applet with Chime buttons to the Jmol 10.0 applet with jmol.js. This seems to mean dropping al

Re: [Jmol-users] Jmol.js checkboxes and Opera 9

In response to my posting: > I have been playing with the Jmol.js checkboxes and have just found >that they don't appear to work on Opera 9 Mac - the javascript >console throws up errors on clicking the checkboxes. There was a request for details of the error message that Opera threw out. Thi

[Jmol-users] Jmol.js checkboxes and Opera 9

I have been playing with the Jmol.js checkboxes and have just found that they don't appear to work on Opera 9 Mac - the javascript console throws up errors on clicking the checkboxes. I have a test page at which works fine (ie th

[Jmol-users] Jmol.js modification for 'smart' checkboxes

At the end of last summer I posted to the list about my need for a modified checkbox which was aware of other checkboxes. I was generating a series of checkboxes to highlight motifs in a protein, and, because often there were quite a few of them, I had an 'all motifs' checkbox as well. The thin

[Jmol-users] Jmol success

I was visited by a rep from a book publisher the other day, who gave me a booklet with details of the forthcoming 6th edition of Stryer's Biochemistry (Berg et al.), the premier textbook for teaching undergraduate biochemistry. I quote from a booklet about the edition:

[Jmol-users] Re: Jmol Interface

I may have strayed across the boundaries of dispassionate criticism in my last message. Apologies. We all contribute what we can to Jmol. David --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? St

[Jmol-users] Re: Jmol Interface

JMOL INTERFACE: RANT 3 - COMMENTS ON OTHER INTERFACE FEATURES This is my third and final part of my analysis of the current interface of the Jmol application. TOOLBAR As I believe I said before, the items here are arbitrary and should be removed. They are neither a help to learners or acceler

[Jmol-users] Re: Jmol Interface

JMOL INTERFACE: RANT 2 - WHAT IS WRONG WITH THE MENUS I posted my initial general thoughts about the Jmol interface yesterday. These were concentrated mainly on the Application, which I hadn't previously given too much thought to as I only use the Applet, and that mainly on Mac OS9. Having rec

[Jmol-users] Jmol Interface (was: menu items and terms)

JMOL INTERFACE: RANT 1 Here are my first thoughts on the topic - general points on what should be in the different interface controls. WHAT IS STANDARD INTERFACE PRACTICE? Standard Human Computer Interface (HCI) practice differs somewhat between platforms, but in a *standard* software applica

[Jmol-users] menu items and terms

Angel Herraez wrote: Upon updating the translation of Jmol menus for the current 10.00.45 release, and after some former suggestions by Gonzalo Claros, I would like to raise some discussion in this mailing list regarding terms in Jmol top menu (application) and Jmol pop-up menu (both applicat

[Jmol-users] Re: Who is *not* using Jmol.js?

As you may recall, I'm not. This is because I am still using the chimetoggle thing with Jmol applet 10.0. The reason I'm doing this is because I'm still using Mac OS9, where there main browser (IE5) doesn't support live connect. From my standpoint, that is fine. As I mentioned over the summer

Re: [Jmol-users] html & xhtml

Egon wrote: At 8:20 pm -0800 9/11/05, [EMAIL PROTECTED] wrote: On Wednesday 09 November 2005 10:52 am, David Leader wrote: PS But there have been flame wars about this on the web-design list. Sam Marshall - webmaster for the Open University - is a persuasive advocate for the "leave

Re: [Jmol-users] html & xhtml

Bob wrote: yup, that's pretty much my conclusion. Long live HTML 4.0! It's long dead. Replaced soon after appearance by 4.01 to correct mistakes :-) David PS But there have been flame wars about this on the web-design list. Sam Marshall - webmaster for the Open University - is a persuasive

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