Re: [Jmol-developers] ADFReader AtomType

Jmol.___JmolVersion="14.20.1" bug fix: ADF reader not accepting Xx.name atom ids This reads N.test as symbol="N" and name="N.text" On Mon, Jul 3, 2017 at 7:20 AM, Georg Eickerling < georg.eickerl...@physik.uni-augsburg.de> wrote: > Dear all, > > this is some kind of feature addon for the

Re: [Jmol-developers] set antialiasdisplay needs a click to aply changes

good catch. Found and fixed. Behavior changed in 14.6.1 Aug 2016. On Mon, Jun 19, 2017 at 2:34 PM, Angel Herráez wrote: > Dear Bob, > > We are finding a strange behaviour in JSmol-html5 within Proteopedia: > changing antialiasDisplay does not display any effect until you

Re: [Jmol-developers] scripts persisting after quit or exit

On Mon, Apr 17, 2017 at 3:01 PM, Angel Herráez wrote: > Hi Jeff > > Glad you are finding a solution. The lack of working of "!exit" straight > away is > disturbing. > exit to work the way you want must be the first command in a script. Otherwise it just acts on the

Re: [Jmol-developers] [Jmol-users] Jmol on Maven Central

Jmol.___JmolVersion="14.8.0" Release Note: switching to semantic versioning (http://semver.org/) Release Note: When releasing beta versions, add "-beta--MM-DD" This change replaces the former nonstandard Jmol.major.minor.patch_.mm.dd syntax where there were two running SVN directories,

Re: [Jmol-developers] Fwd: [sage-cell] Re: Encoding problems for jsmol context menu

On Wed, Nov 9, 2016 at 3:13 AM, Angel Herráez wrote: > Hi Jonathan > > while https://sagecell.sagemath.org/embedded_sagecell.js seems to be > encoded as "windows-1252" > > that would do it. --

Re: [Jmol-developers] Is it possible to create a .dll?

No, it's not a Windows program. It's a Java program. Unity probably does not work with Java. On Tue, Oct 25, 2016 at 9:37 AM, Anastasya Karchevskaya wrote: > Good day, everyone! > > I am trying to make an app with Unity (not UnityMol, different, but I need > to visualise

Re: [Jmol-developers] export to IDTF is brokwn

%204th%20Edition.pdf *8.3 There is no default model node, default light node, nor default view node.* On Wed, Oct 19, 2016 at 3:18 AM, Angel Herráez <angel.herr...@uah.es> wrote: > El 18 Oct 2016 a las 23:06, Robert Hanson escribió: > > IDTF does work correctly now, but you have to use

Re: [Jmol-developers] export to IDTF is brokwn

IDTF does work correctly now, but you have to use the additional LaTex file generated by Jmol to orient it, because that is where the orientation information is. (IDTF was designed specifically to *not* allow specifying of orientation. Go figure!) Bob On Tue, Oct 18, 2016 at 3:43 AM, Angel

Re: [Jmol-developers] export to IDTF is brokwn

thank you. fixed. Are people still using IDTF? On Mon, Oct 17, 2016 at 2:44 PM, Angel Herráez wrote: > Dear Bob, > > load $aspartate; > write IDTF Asp.idtf > > does nothing, reports nothing > > Jmol 14.6.4, 2016-10-02 application > > > --- > El software de antivirus Avast

Re: [Jmol-developers] (bug) set measurement in angstroms

I have added the fix for this to the version I hope to release tomorrow. Jmol.___JmolVersion="14.7.4_2016.10.08" bug fix: SET MEASUREMENTS x.x is 10x too wide bug fix: MO command does not allow SQUARED with PLANE bug fix: MO command SQUARED does not reset cutoff to its square bug fix: MO

Re: [Jmol-developers] cannot write menu to file in 14.6.2

---------- > > On 17 Sep 2016 at 15:51, Robert Hanson wrote: > > write menu ? > > worked fine for me at *https://chemapps.stolaf.edu/jmol/jsmol/jsmol/htm* > <https://chemapps.stolaf.edu/jmol/jsmol/jsmol/htm> > > > > On Sat, Sep 17, 2016 at 10:29 AM, Angel

Re: [Jmol-developers] cannot write menu to file in 14.6.2

let - so it may be that > > -- > > On 17 Sep 2016 at 9:53, Robert Hanson wrote: > > I don't think write menu was implemented in JSmol. Will take a look. > > > > > -- > > ___

Re: [Jmol-developers] cannot write menu to file in 14.6.2

I don't think write menu was implemented in JSmol. Will take a look. On Sat, Sep 17, 2016 at 5:37 AM, Angel Herráez wrote: > Is this a bug? > > On https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm > > in the console: " write menu ? " > gives this error after requesting

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

something like: $("ul.jmolPopupMenu ul:not(:has(ul))").css({"maxHeight":"25em", "overflowY":"auto"}) But I don't think that is quite it. On Fri, Sep 16, 2016 at 1:16 PM, Angel Herráez wrote: > I like CSS solutions; they are very clean and you do not mess up with the > js

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

something like "menus that do not contain any menus" --- li with no containing ul --- I think that can be done in jQuery. Can it be done in CSS? On Fri, Sep 16, 2016 at 12:40 PM, Robert Hanson <hans...@stolaf.edu> wrote: > We might be able to implement that only for terminal m

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

We might be able to implement that only for terminal menus. Have to think about how to do that. On Fri, Sep 16, 2016 at 12:39 PM, Robert Hanson <hans...@stolaf.edu> wrote: > I registered 2700 MSIE uses in April; 1.4% of 189,000. > > On Fri, Sep 16, 2016 at 12:41 PM, Angel Herr

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

I registered 2700 MSIE uses in April; 1.4% of 189,000. On Fri, Sep 16, 2016 at 12:41 PM, Angel Herráez wrote: > > The way too long problem is generally solved by dragging the menu higher > on the screen. > > I know. But still sometimes it's higher than the screen. > In

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

That's right, because the menu is based on an array in Language.js, not from a po file, like the word "Russian" is. Language is one of the classes that is included in corejmol.z.js. (If it were any other way, it would require loading all the language files initially.) Anyway, that is fixed. On

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

The way too long problem is generally solved by dragging the menu higher on the screen. I'm not sure there is any other solution than that. It's a standard jQuery menu. So if you can figure out how to solve this with that, we could implement your solution in JSmol. On Thu, Sep 15, 2016 at 3:29

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

Better -- I was missing the --charset UTF-8 flag on the Google Closure Compiler command line. On Fri, Sep 16, 2016 at 10:00 AM, Robert Hanson <hans...@stolaf.edu> wrote: > Hmm. This will be a good challenge. > > 1) The .java files are OK -- For example, Catal[`a] is correctly C3A

Re: [Jmol-developers] rendeirng problems with JSmol popup menu

Hmm. This will be a good challenge. 1) The .java files are OK -- For example, Catal[`a] is correctly C3A0. 2) The .js files are fine. 3) In the developer console, everything is OK: x = "Català" "Català" x "Català" 4) The JavaScript is messed up: x =

Re: [Jmol-developers] "color darkgrey" is rejected

of course, we could just not use "darkgrey" On Fri, Sep 2, 2016 at 2:08 PM, Angel Herráez wrote: > Bob, > I know you worked on this recently. > I am testing this on "14.6.2_2016.08.28 2016-08-28 07:48" > > color gray > color grey > color lightgray > color lightgrey >

Re: [Jmol-developers] Tag Jmol releases

steps to the release procedure. I'll look into additional options for > automating that with ant. > > On Tue, Aug 30, 2016 at 8:56 PM, Robert Hanson <hans...@stolaf.edu> wrote: > >> The date stamp on the file name is important and effectively constitutes >> the minor ve

Re: [Jmol-developers] Tag Jmol releases

s/v14_6 > http://svn.code.sf.net/p/jmol/code/tags/v14_6_2_2016_08_28 > > BTW, I'll be at the Web-based molecular graphics conference next week, so > we can discuss details then if you want. > > -Spencer > > On Mon, Aug 29, 2016 at 7:45 PM, Robert Hanson <hans...@stolaf.edu> wr

Re: [Jmol-developers] load models {0 0 1} is broken in 14.6.0 seires

s.setShapeVisibility(a,b)', 'this.setShapeVisibility' is undefined) > > Maybe not all files from the new version loaded properly? > > On 22 Jun 2016, at 7:14 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > Fixed. Will update at SVN later today or tonight. > > On Wed, Jun 22,

Re: [Jmol-developers] load models {0 0 1} is broken in 14.6.0 seires

Fixed. Will update at SVN later today or tonight. On Wed, Jun 22, 2016 at 10:52 AM, Angel Herráez wrote: > > load models {0 0 1} filename > > is broken in all 14.6.0 releases; it complains the closing brace was not > expected > > We are trying to fix a problem in

Re: [Jmol-developers] Reloading current structure fails

Does seem odd. Here is a way to do it, though: data "example" 2 testing C 1 1 1 O 2 2 2 end "example"; load inline @{data("example")} {1 1 1} spacegroup 22 unitcell [3 4 5 90 90 90] then you can use load "" or load inline @{data("example")} any time. Or you could define x =

Re: [Jmol-developers] application errors

gt; those files, which is why I was so surprised that it didn't do it. I guess > it has something to do with what is in the build.xml file, but I have never > understood the ant build files well enough to mess with those > > On May 27, 2016, at 10:30 AM, Robert Hanson <hans...@sto

Re: [Jmol-developers] application errors

and only needs it when I am running the > Jmol.jar (using java -jar Jmol.jar) but not when I am running it from > within eclipse? > > René > > On May 27, 2016, at 1:44 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > JmolBioResolver was decommissioned. Perhaps you have

Re: [Jmol-developers] myJmol as variable in Jmol.script

yes, if you check show orientation you will see a parameter "rotation radius" You can set that to a new number, then disable zoom. It sets the magnification for "100%". ​ -- Mobile security can be enabling, not

Re: [Jmol-developers] commit with localization files

great -- that's all now in the release branch as well. On Thu, May 19, 2016 at 6:00 PM, Angel Herráez wrote: > Forget that last one -- I found where the language must be added, > src\org\jmol\i18n\Language.java > > I am adding Russian since it is over 95% translated > > >

Re: [Jmol-developers] myJmol as variable in Jmol.script

Klaus, When you create an applet, it automatically creates a top-level object with the name of your applet. However, you can't do anything with that object until it is at least started to be created. Have you tried any of the html files in the jsmol/ directory? There are plenty of examples of

Re: [Jmol-developers] myJmol as variable in Jmol.script

I would put a line alert(name) in that function to see what that variable is. Perhaps it is not defined at the time you are making the call. Also, I don't recommend giving an applet a name like "A" or "B" -- to easy to use a variable that is used by something else. I would suggest "jmolA"

[Jmol-developers] build problems in Eclipse Mars

Continuing this discussion from a bug fix. Rene, I have to ask: Are you running build.xml, not build-eclipse.xml? Build-eclipse.xml is just for running within Eclipse, I think. No Jar file created. Could it be as simple as that? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry

Re: [Jmol-developers] Java 9 issue

OK. No rush, I think. On Thu, Feb 18, 2016 at 4:29 PM, Nicolas Vervelle <nverve...@gmail.com> wrote: > > > On Thu, Feb 18, 2016 at 8:52 PM, Robert Hanson <hans...@stolaf.edu> wrote: > >> Angel, it's just that the gtext processor is set up for "_&quo

Re: [Jmol-developers] Java 9 issue

Angel, it's just that the gtext processor is set up for "_" -- I guess, though, that must just be a setting. We liked "_" because it was so short, and actually that does help in keeping file sizes as low as possible. So, Nico, I guess it is this, right? On Thu, Feb 18, 2016 at 4:28

Re: [Jmol-developers] problem parsing DNA from assembly mmCIF (PDBe)

What is the difference between loading an "assembly" and FILTER "biomolecule 1" ? Is there some advantage to loading the assembly? I have never looked at those files. On Thu, Jan 28, 2016 at 5:33 AM, Angel Herráez wrote: > We are starting to work on reading mmCIF files

Re: [Jmol-developers] problem parsing DNA from assembly mmCIF (PDBe)

The DNA strands are there, but they are coming in as individual models. So we have 60 models (protein + 2 DNA strands) instead of 20 in that assembly file. It seems to be because the models are not in order. The sequence in the file goes protein models 1-20 dna strand models 1-20 dna strand

Re: [Jmol-developers] Escape.e function misidentifying P4 types as T3...

It's an ordering issue. Yes, P4 subclasses T4, which subclasses T3. I'll fix it. On Tue, Dec 29, 2015 at 7:59 PM, Jonathan Gutow wrote: > It appears that at line 117 in Escape.java, type P4 objects are being > misidentified as type T3. This means that the value of the "w"

Re: [Jmol-developers] Escape.e function misidentifying P4 types as T3...

I checked in a new Escape.java, which I guess fixes the problem. Do an update on that, Jonathan. I guess we could leave the SurfaceTool the way it is then. On Wed, Dec 30, 2015 at 10:46 AM, Robert Hanson <hans...@stolaf.edu> wrote: > In SurfaceTool.java, this: > > cmd

Re: [Jmol-developers] Escape.e function misidentifying P4 types as T3...

Go ahead the change that Escape.e to Escape.eP4 anyway, and check that in if you want. On Wed, Dec 30, 2015 at 3:02 PM, Jonathan Gutow <gu...@uwosh.edu> wrote: > I can verify that the reordering fixed the problem. > > Jonathan > > On Wed, Dec 30, 2015 at 10:50 AM

Re: [Jmol-developers] Interfacing Jmol with Oculus Rift VR

First thing you should think about is using set navigationMode This gives an "immersion" perspective that may be closest to your needs. See http://chemapps.stolaf.edu/jmol/docs/misc/navigation.pdf for ideas. ​ -- Go

Re: [Jmol-developers] Interfacing Jmol with Oculus Rift VR

ormManager.navZ but it didn't work. So I doubt if it's right to just > use functions like TranformManager.setNavigationXYZ. > > Any other ways to navigate? > > On Tue, Dec 8, 2015 at 8:04 PM, Robert Hanson <hans...@stolaf.edu> wrote: > >> First thing you should think about is us

Re: [Jmol-developers] SVN access problem

I support this idea in principle; I just started using Git on another project (Jalview), and I certainly see the advantages. No system is immune to failure, but it is true that the local repository aspect of Git does mean there cannot be a catastrophic failure that impacts us for weeks the way we

Re: [Jmol-developers] Changing Console Location and Adding a New Menu

Actually, it is div id=jmolApplet0_console style=background-color:blue;width:700px;height:400px;overflow:auto/div On Mon, Jun 29, 2015 at 11:01 AM, Robert Hanson hans...@stolaf.edu wrote: Note that I assumed you meant the Jmol console that comes up with the console command. If you

Re: [Jmol-developers] CrystalReader and external pressure

found it. Fixed. See http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.07.07b.zip (uploading shortly) On Tue, Jul 7, 2015 at 8:49 AM, Georg Eickerling georg.eickerl...@physik.uni-augsburg.de wrote: Dear all, this is a feature request for the CrystalReader of jmol. When doing

Re: [Jmol-developers] xml files?

Sam, I see this thread now. Those ANT tasks are only for the release version of Jmol. You are welcome to do this. Ideally we would incorporate your modifications into a future release of Jmol. It is highly modular for this very purpose. You need the corresponding _11, _12, and _13 tasks, not

Re: [Jmol-developers] Changing Console Location and Adding a New Menu

Good idea. I have modified JmolCore.js and JmolConsole.js such that you can now add a div: // BH 6/29/2015 9:50:21 AM adds option for user to set console as a div on a page. //as jmolApplet0_console where jmolApplet0 is the id of the applet. // for example: div id=jmolApplet0_console

Re: [Jmol-developers] Right click menu

you can drag it anywhere on the screen just by clicking on a separator and dragging; it will always come up at the point you clicked, though. On Fri, Jun 26, 2015 at 1:31 PM, Sam Blackman sa.blackma...@gmail.com wrote: Hello all, Would it be possible to make the right click menu in it's own

Re: [Jmol-developers] DOCUMENTATION AnimFrameCallback

Actually, it was a bug in JSmol in not delivering all the parameters. In fact, there are eleven parameters, including data = new Object[] { htmlName, Integer.valueOf(Math.max(frameNo, -2 - frameNo)), Integer.valueOf(fileNo), Integer.valueOf(modelNo),

Re: [Jmol-developers] Script debugging problem

On Fri, Apr 17, 2015 at 6:44 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi all, I have some problems debugging a complex script in Jmol. First of all, the command 'set scriptReportingLevel' doesn't seem to work in Jmol 14.3.13_2015.04.08. It is always setting the value to zero. Q: What

Re: [Jmol-developers] User-defined atom property type restriction

On Tue, Apr 14, 2015 at 3:43 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 04/13/2015 10:08 PM, Robert Hanson wrote: just the way it was implemented. But you can set atomName, atomType, and format in order to add string data to atoms. I'm sure that's not at all clear from

Re: [Jmol-developers] User-defined atom property type restriction

just the way it was implemented. But you can set atomName, atomType, and format in order to add string data to atoms. I'm sure that's not at all clear from the documentation. Bob On Mon, Apr 13, 2015 at 11:07 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi Bob and others, the documentation

[Jmol-developers] 20,000 commits

Just noticed that we are at revision # 20,448. -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get.

Re: [Jmol-developers] Loop speed optimization potential

On Wed, Apr 8, 2015 at 4:48 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Q: Does 'i' contain the hash key (as in Perl) or the value? the key -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop

Re: [Jmol-developers] Loop speed optimization potential

Rolf, I think you could have a lot of fun with the JavaScript functions Jmol provides. Jmol never does loops like that. Instead it initializes a three-dimensional binary tree -- we call it a binary forest :) -- and you specify a point and a radius, then iterate until done. It is far far faster.

Re: [Jmol-developers] accessing atom info

That's right. So that call is telling Jmol that there is a callback listener. So now look for implementations of JmolCallbakListener. You will find: public class AppConsole extends JmolConsole ... public abstract class JmolConsole extends GenericConsole ... public abstract class GenericConsole

Re: [Jmol-developers] Loop speed optimization potential

Rolf, you are definitely pushing the limit there, I think. What exactly happens inside the loop you are really interested in using? If it is anything much, then the looping itself is going to be insignificant compared to the other processing. I probably will regret suggesting this, but something

Re: [Jmol-developers] accessing atom info

What have you been able to learn from Integration.java? How does it work? ​ -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is

Re: [Jmol-developers] Alternative nested array element access syntax

Interesting idea. Rolf. Are you aware of Jmol's recently added .. notation? x = {a: {1: [x, y, z], 2: [I, II]}} print x print x..a print x..a..1 print x..a..1..2 Does that satisfy your needs? It is only for regular arrays or associative arrays with simple keys. You can't do this: print

Re: [Jmol-developers] Alternative nested array element access syntax

see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.03.27.zip ​ :) -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your

[Jmol-developers] Fwd: JSmol php vulnerability

FYI -- Forwarded message -- From: Robert Hanson hans...@stolaf.edu Date: Mon, Mar 23, 2015 at 8:19 AM Subject: JSmol php vulnerability To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net All developers are advised to replace on any server implementing JSmol

Re: [Jmol-developers] JSmol php vulnerability

The modified php file is part of Jmol 14.2 and 14.3 releases: https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.13/ https://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.13/ On Mon, Mar 23, 2015 at 8:19 AM, Robert Hanson hans...@stolaf.edu

Re: [Jmol-developers] JSmol php vulnerability

However, SourceForge has not updated the default download yet nor made the files available -- sorry, don't know why. On Mon, Mar 23, 2015 at 10:03 AM, Robert Hanson hans...@stolaf.edu wrote: The modified php file is part of Jmol 14.2 and 14.3 releases: https://sourceforge.net/projects/jmol

Re: [Jmol-developers] Slow print command

-leibniz.de wrote: On 03/10/2015 05:32 PM, Robert Hanson wrote: I could make print clear the console. That would be a very bad idea! Printing is done with a purpose. And for development and debugging it is really important to be able to see previous output and also the mixture

Re: [Jmol-developers] Slow print command

Try turning off the system console. Doesn't sound like you need it, and that is probably what is slowing things down, not the Jmol console. Info = { ... console: none, ... } On Wed, Mar 11, 2015 at 1:08 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 03/10/2015 10:07 PM, Robert Hanson

Re: [Jmol-developers] Slow print command

Rolf, I have not seen that issue -- I suppose this is going to the console, and maybe your machine has memory issues with that -- too much printing? I did recently set it to scroll to the end after each print, and that requires calculating the number of characters, which I think Jmol perhaps was

[Jmol-developers] list bounces

Who is handling these? Anyone? jmol-users-boun...@lists.sourceforge.net -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to

Re: [Jmol-developers] JSmol dipole bug?

schreef Robert Hanson hans...@stolaf.edu : Sorry about that! Jmol.___JmolVersion=14.3.11_2015.01.19 bug fix: DIPOLE command broken in Jmol 14.3.10_2014.11.27 (OK in 14.2) releasing later today On Mon, Jan 19, 2015 at 1:32 PM, Herman Bergwerf hermanbergw...@gmail.com wrote: select

Re: [Jmol-developers] JSmol dipole bug?

See http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.11_2015.01.20.zip ​This will read 2015.01.19 but its date should be today. Jmol.___JmolVersion=14.3.11_2015.01.19 bug fix: Languages lost in Jmol Application -- New

Re: [Jmol-developers] JSmol dipole bug?

of the time, especially after a bugfix) So I fetched the latest Jmol/JSmol version from SourgeFourge (14.2.9_2014.11.23) I think I will stick to sourgefourge for molview.org Op Tue Jan 20 2015 at 6:31:48 PM schreef Robert Hanson hans...@stolaf.edu : Understood. Jmol.zip at that site

Re: [Jmol-developers] JSmol dipole bug?

Sorry about that! Jmol.___JmolVersion=14.3.11_2015.01.19 bug fix: DIPOLE command broken in Jmol 14.3.10_2014.11.27 (OK in 14.2) releasing later today On Mon, Jan 19, 2015 at 1:32 PM, Herman Bergwerf hermanbergw...@gmail.com wrote: select *; calculate partialcharge; dipole bonds on;

Re: [Jmol-developers] Mysterious behaviour of JavaScript 'for' loops after initializing JSmol

I guess JSmol is incompatible with certain uses of String. In particular, when JSmol is initialized, x.toString() becomes a String Object, not just a simple string, as it must. There is no way around that. jqGrid in one place then uses the strictly equals === to compare the desired row id to

Re: [Jmol-developers] Mysterious behaviour of JavaScript 'for' loops after initializing JSmol

(so go into jqGrid and change that === to == ) ​ -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high

Re: [Jmol-developers] Mysterious behaviour of JavaScript 'for' loops after initializing JSmol

, Robert Hanson hans...@stolaf.edu wrote: (so go into jqGrid and change that === to == ) ​ -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we

Re: [Jmol-developers] setAppletCss

thanks -- found it. On Sat, Dec 6, 2014 at 6:37 AM, Angel Herráez angel.herr...@uah.es wrote: It seems that setAppletCss() is not working, tested in JSmol 14.3.10 Case example: the button has red border, but the JSmol object has not: head style type=text/css .grayBox { border:1px solid

Re: [Jmol-developers] Customized application menu

[I prefer to refer to the Java application as Jmol still, not JSmol, please. That's too twisted for me!] On Wed, Dec 3, 2014 at 6:48 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi developers, I would like to know if it would be possible to make the JSmol application main menu

Re: [Jmol-developers] Customized application menu

On Wed, Dec 3, 2014 at 9:19 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 12/03/2014 02:00 PM, Robert Hanson wrote: [I prefer to refer to the Java application as Jmol still, not JSmol, please. That's too twisted for me!] Bob, but wasn't it you who turned away from the separation

Re: [Jmol-developers] Bug in JSmol-JSme integration

this is fixed http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.10.12.zip On Tue, Sep 9, 2014 at 7:07 AM, Robert Hanson hans...@stolaf.edu wrote: I noticed that. Thanks for pointing it out. Let me know if you figure out what is happening there. On Tue, Sep 9, 2014 at 12:49 AM, Johannes

Re: [Jmol-developers] JSmol as network viewer

On Mon, Oct 6, 2014 at 6:32 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi developers, Q: I was wondering if it might be possible to achieve this by tuning the 'minimize' command with some extra parameters or maybe by enabling to define a custom 'minimize' function? I think if

Re: [Jmol-developers] JSmol as network viewer

. On Mon, Oct 6, 2014 at 9:55 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 10/06/2014 02:22 PM, Robert Hanson wrote: On Mon, Oct 6, 2014 at 6:32 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi developers, Q: I was wondering if it might be possible to achieve

Re: [Jmol-developers] java to javascript conversion

Kent, this is not an easy thing at all to describe. Basically a lot of customization was done. I have now converted two other programs (JSpecView and AztexViewer) The first took *me* a month, and the second took 10 days. So I am getting better at it, but it is no simple task to describe how it is

Re: [Jmol-developers] chainCaseSensitive is forced true in 14.3.7

I would appreciate thoughts on this: There was a bug in the chain case sensitivity that forced select :a to not match A in a PDB file chain designation, and that is fixed, but besides that there is an issue for which all should be aware and for which I would like your thoughts. Nine years ago

Re: [Jmol-developers] cartoon for Calpha-only is broken

Right - I forgot to do a full clean before creating the JAR file. Oh, I hate that bug in Eclipse Will update again now. On Mon, Sep 15, 2014 at 8:52 AM, Angel Herráez angel.herr...@uah.es wrote: 9 Sep 2014, 2:58, Robert Hanson wrote: In addition to that, the chain read from then HELIX

Re: [Jmol-developers] cartoon for Calpha-only is broken

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.15b.zip On Mon, Sep 15, 2014 at 9:58 AM, Robert Hanson hans...@stolaf.edu wrote: Right - I forgot to do a full clean before creating the JAR file. Oh, I hate that bug in Eclipse Will update again now. On Mon, Sep 15, 2014 at 8

Re: [Jmol-developers] Measurement bug?

is reported there) On Sep 9, 2014 10:19 PM, Robert Hanson hans...@stolaf.edu wrote: The normal, designed response is that any dragging of the model during a measurement terminates the pending measurement. You must start again. If that is all the problem is, then that's by design

Re: [Jmol-developers] Bug in JSmol-JSme integration

to contain version 14.3.6 ( http://edumol.fi/dev/jsmol-14.3.7_2014.09.07c/jsmol/jsmetest.htm) and the link where it is working has a number 14.3.7. Thank you. Johannes Robert Hanson kirjoitti 08.09.2014 15:34: I see still a different problem at http://chemapps.stolaf.edu/jmol/jsmol

Re: [Jmol-developers] cartoon for Calpha-only is broken

This relates to the chain case issue as well. Jmol is set to force case sensitivity if it finds (a) chain designations of more than one character or (b) ones with lower case. Unfortunately, it was considering 1 to be lower case. In addition to that, the chain read from then HELIX record was not

Re: [Jmol-developers] Measurement bug?

the issue? 2014-09-09 1:17 GMT+02:00 Robert Hanson hans...@stolaf.edu: Nope, I thought I had it, but I can't do it now. What's the trick? On Mon, Sep 8, 2014 at 6:03 PM, Robert Hanson hans...@stolaf.edu wrote: sure, I see. I can fix that... On Mon, Sep 8, 2014 at 2:36 PM, Herman Bergwerf

Re: [Jmol-developers] Measurement bug?

-09-09 20:00 GMT+02:00 Robert Hanson hans...@stolaf.edu: I can't reproduce the issue. Thought I could, but now I can't. Possibly had something to do with whether I was holding keys down after clicking (press+release) or just pressing. On Tue, Sep 9, 2014 at 9:24 AM, Herman Bergwerf hermanbergw

Re: [Jmol-developers] Bug in JSmol-JSme integration

I see still a different problem at http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm Am I correct that it is working correctly at http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm ? ​ -- Want excitement? Manually

Re: [Jmol-developers] Measurement bug?

This is news to me. See if you can describe a reproducible way of generating the problem. On Mon, Sep 8, 2014 at 1:57 PM, Herman Bergwerf hermanbergw...@gmail.com wrote: This is actually an old bug but I was wondering if it is possible to fix it. When I perform a measurement, sometimes the

Re: [Jmol-developers] Measurement bug?

atom AND HOLD + DRAG try to finish your measurement (works sometimes but pre-dotted line is gone) I'm not sure if there is something else causing this issue too or I'm dragging the pointer ~1px every time this happens. I let you know if I find a better method. 2014-09-08 21:25 GMT+02:00 Robert

Re: [Jmol-developers] Measurement bug?

Nope, I thought I had it, but I can't do it now. What's the trick? On Mon, Sep 8, 2014 at 6:03 PM, Robert Hanson hans...@stolaf.edu wrote: sure, I see. I can fix that... On Mon, Sep 8, 2014 at 2:36 PM, Herman Bergwerf hermanbergw...@gmail.com wrote: I can't find a way to reproduce

Re: [Jmol-developers] Jmol.resizeApplet

only the latter [w,h], I think. On Sat, Sep 6, 2014 at 6:27 PM, Angel Herráez angel.herr...@uah.es wrote: Bob, are both syntaxes supported? Jmol.resizeApplet(appletid, w, h) Jmol.resizeApplet(appletid, [w,h]) I only had the 2nd documented

Re: [Jmol-developers] Jmol.resizeApplet

If you have two applets, you need to be sure they have different names. That could cause this sort of thing. On Sun, Sep 7, 2014 at 9:04 PM, Robert Hanson hans...@stolaf.edu wrote: only the latter [w,h], I think. On Sat, Sep 6, 2014 at 6:27 PM, Angel Herráez angel.herr...@uah.es wrote: Bob

Re: [Jmol-developers] Bug in JSmol-JSme integration

I believe I have that fixed. Check the latest zip file: http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.07b.zip (uploading now) ​ -- Want excitement? Manually upgrade your production database. When you want

Re: [Jmol-developers] Jmol.resizeApplet

I think I found it. It will be part of 14.3.7 and 14.2.7, probably later this weekend. On Sat, Sep 6, 2014 at 5:14 PM, Herman Bergwerf hermanbergw...@gmail.com wrote: On my tablet, Jmol.resizeApplet(JSmol, [w,h]) creates a new canvas insead of resizing the existing canvas causing JSmol to

Re: [Jmol-developers] Jmol.resizeApplet

Sorry - that was in response to your other message, about multitouch. I am not seeing any issue with Jmol.resizeApplet(appletid, width, height) Looks to me like you do not have an applet with id JSmol. These are two unrelated issues, right? On Sat, Sep 6, 2014 at 5:51 PM, Robert Hanson hans

Re: [Jmol-developers] how to modify circle color of element node

Hanson hans...@stolaf.edu: ps -- make sure you are checking out svn.code.sf.net/p/jmol/code/trunk/Jmol On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote: It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian

  1   2   3   4   5   6   7   8   9   10   >