Re: [Jmol-developers] de.po 404 error

2017-07-25 Thread Angel Herráez
On the other hand, Why http:/_ ? That is not correct You need either two slashes (and then it must be an absolute server url) or no http (relative url) > is a complete unreasonable path.  It should be: > http:/_INCLUDE/JSMOL/idioma/de.po that is not correct. You need /_INCLUDE/JSMOL

Re: [Jmol-developers] de.po 404 error

2017-07-25 Thread Angel Herráez
Hello Klaus 1. Yes, the location of the language files cannot be specified. As far as I remember, it always looks for them in a 'idioma' folder which is a sibling of the 'java' folder. I'm not sure what happens when you don't specify the java folder 2. Some javascript error loading the languag

[Jmol-developers] some wrong characters in localization of popup menu

2017-06-28 Thread Angel Herráez
Dear Bob, I have noticed that some characters do not display properly in the pop-up menu, Languages submenu in JSmol-HTML5 Checked in JSmol 14.6.4 and 14.9.1 in two different pages, see snapshot https://ibb.co/hpdWck Many foreign characters display well, but not those few in Russian, Chinese a

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

2017-06-19 Thread Angel Herráez
Dear Bob, We are finding a strange behaviour in JSmol-html5 within Proteopedia: changing antialiasDisplay does not display any effect until you click on the JSmol canvas. Test case: go to http://proteopedia.org/wiki/index.php/1a2m open the JSmol console and type zoom 300 set antialiasDisplay t

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

2017-04-17 Thread Angel Herráez
Hi Jeff Glad you are finding a solution. The lack of working of "!exit" straight away is disturbing. "move" is considered an obsolete command and that may be the reason there is no method to interrupt it, but I agree that some things are not easy to reproduce with other commands, as you are

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

2017-04-15 Thread Angel Herráez
Hi Jeff I've done a little testing. It seems that the problem is in the "move" commands, that cannot be interrupted. I found about "set waitForMoveTo" and "moveTo stop", so this seems to work: 1. Edit you spt files to change the move commands to equivalent moveTo commands. // move 0 0 0 80 0

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

2017-04-11 Thread Angel Herráez
Hi Jeff That's a little strange. "exit" should do what you wish, at least according to the documentation (I have no direct experience) I suggest that you try this: add !exit as the first line of your script files or the first command of your inline scripts that are callled from buttons. Follo

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

2016-11-09 Thread Angel Herráez
Hi Jonathan I've seen this kind of a problem occasionally (my system is configured for Spanish so the JSmol popup menu opens in Spanish, and has accented characters), but have not been able to track it down. I think it may be a bad combination of charsets in the several files involved. I cannot

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

2016-10-19 Thread Angel Herráez
El 18 Oct 2016 a las 23:06, Robert Hanson escribió: > IDTF does work correctly now, but you have to use the additional LaTex file > generated by Jmol to Yes, I had seen that part. However, I was expecting for a way to make a complex PDF (with text, flow, etc) without learning Latex. The PDF ge

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

2016-10-18 Thread Angel Herráez
> thank you. fixed. Are people still using IDTF? Yes, hardly anyone, given the amount of information that can be found online. Still, there is some life -- see [1] But I am picking again the idea of producing PDFs with 3D models, and IDTF -> U3D is the only route. I just found that Power PDF f

[Jmol-developers] export to IDTF is brokwn

2016-10-17 Thread Angel Herráez
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 ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus --

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

2016-10-08 Thread Angel Herráez
set measurements 0.25 (any width in angstroms) is failing in versions below -- it used to work as expected, giving a not s thick cylinder 14.6.4_2016.10.02 14.6.2_2016.08.28 14.7.0_2016.06.27 14.6.0_2016.06.22 used at Proteopedia --- El software de antivirus Avast ha analizado este correo

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

2016-09-17 Thread Angel Herráez
/jmol/jsmol/jsmol/htm On Sat, Sep 17, 2016 at 10:29 AM, Angel Herráez wrote: Ok, thanks I have later been able to do it from Java applet - 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

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

2016-09-17 Thread Angel Herráez
Ok, thanks I have later been able to do it from Java applet - 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. -- __

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

2016-09-17 Thread Angel Herráez
Is this a bug? On https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm in the console: " write menu ? " gives this error after requesting the file name: ERROR en guión: TypeError: er.printStackTrace is not a function --

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

2016-09-16 Thread Angel Herráez
I like CSS solutions; they are very clean and you do not mess up with the js code. > 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? Not actually straightforward, since you cannot apply css to pa

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

2016-09-16 Thread Angel Herráez
> 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 many pages of mine the JSmol panel is 100% height, locked and cannot be scrolled down (overflow:none), so it's actually impossible to reach the l

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

2016-09-16 Thread Angel Herráez
Fine, Bob The funny thing was that the first string (language name translated to current name) was correct, the second was wrong (language name in the original language). If you siwtch to Russian, you can see in the same line one correct, one wrong. So I understand this is fixed for next rele

[Jmol-developers] rendeirng problems with JSmol popup menu

2016-09-15 Thread Angel Herráez
Dear Bob, I have noticed two issues with the rendering of the pop-up menu in JSmol-html5 1. The language submenu is way too long, and may become taller than the screen, so in some page designs the lower half of the languages may be unreachable. 2. The names of some languages display wro

[Jmol-developers] "color darkgrey" is rejected

2016-09-02 Thread Angel Herráez
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 color darkgray // all ok up to here color darkgrey // script ERROR: a color or palette name (Jmol, Rasmol) is required

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

2016-06-22 Thread Angel Herráez
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 Proteopedia (Jmol 14.4.1) with rendering of beta strands when the file does not contain SHEET records(note*). I realized that bug is fixed i

Re: [Jmol-developers] Reloading current structure fails

2016-06-03 Thread Angel Herráez
The documentation under "data" says http://chemapps.stolaf.edu/jmol/docs/#data Using load data instead of just data you can load model data with all of the loading options of the standard LOAD command. Also, it says that you should probably use model as part of your data label; this may be the

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

2016-06-03 Thread Angel Herráez
Hi Klaus Go to http://chemapps.stolaf.edu/jmol/docs/ and search for "rotationRadius" You will see there is "set rotationRadius" therefore you can try show rotationRadius and it works! Examples of use: show rotationRadius // rotationRadius = 20.94923 rr = rotationRadius; print rr; // 20.94923

Re: [Jmol-developers] Reloading current structure fails

2016-06-03 Thread Angel Herráez
Ok, Abel So you are not loading a mol2 file, you are loading data. Reloading of data might not be possible, or may need a different syntax. More investigation is needed on this, I cannoy say right now. What happens if you copy that data into a text file and load it into Jmol? Bob will know, b

Re: [Jmol-developers] Reloading current structure fails

2016-06-03 Thread Angel Herráez
Hello Abel We need to narrow the problem I've just tested with Jmol 14.6.0_2016.05.24, with a pdb file, a mol file and a mol2 file, and "load" works fine. e.g. load =1crn; load ""; load $caffeine; load ""; load "https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/mol2/csc

Re: [Jmol-developers] commit with localization files

2016-05-19 Thread Angel Herráez
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 -- Mobile security can be enabling, not merely restricting. Employees

Re: [Jmol-developers] commit with localization files

2016-05-19 Thread Angel Herráez
I just noticed in my local build that Russian (the latest added language) is not available in the pop-up menu. It appears there, though, after I enter this in the console: set language ru and it stays in the menu upon more language changes So I guess there is something that must be changed so

[Jmol-developers] commit with localization files

2016-05-19 Thread Angel Herráez
Bob, I am committing changes in the localization. All the files were old due to lack of a recent rebuild of the POT files. I followed instructions for Nico and rebuilt those files in my Eclipse. That includes some updates of terms in Export to Web ad maybe some string that was not internationali

Re: [Jmol-developers] update on Export To Web

2016-05-19 Thread Angel Herráez
(Just for the record and to finish this thread) Those changes in the Export to Web interface and the templates it uses for produced pages were finally committed to the trunk a few days ago. They are now used in Jmol 14.6.0 > > As a consequence, I am starting some revision of the page code gener

[Jmol-developers] commits r21103-05

2016-05-15 Thread Angel Herráez
Ok, those were my first commits from within Eclipse, so it took me a few trials and errors. I believe all is well. That was an update to the Export to Web interface, to better match descriptions for JSmol. -- Mobile se

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

2016-05-09 Thread Angel Herráez
Hello Klaus I think that it should be possible to do what you want without using eval(), which is usually not recommended by javascript gurus. The variable is indeed an object and not a string, but that is what Jmol expects. There may be a problem when the variable has not been defined befor

Re: [Jmol-developers] JAVA applet in WebPages

2016-05-05 Thread Angel Herráez
two JSmol-HTML5 panles that report a different version, Jmol 14.4.1 So in order to get the same behaviour you should use the same JSmol files and just change the Info.use parameter in the source code · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University

Re: [Jmol-developers] JAVA applet in WebPages

2016-05-04 Thread Angel Herráez
Hello Klaus Yes, the files are now different since JSmol. It is recommended that you change to the new JSmol Object syntax (see the Wiki for guidance) Otherwise, you could possibly still run it the old way. The Java applet files are inside the "java" folder which is inside the "jsmol.zip" fil

Re: [Jmol-developers] "nihResolverFormat" cannot be set

2016-04-12 Thread Angel Herráez
It seems this previous post (4th April) went unnoticed > Bob, > > This parameter can be shown but not set: > > $ print _versionDate > 14.4.4_2016.03.29 2016-03-29 22:33 > $ show nihResolverFormat > nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE"; > $ set nihResolverFor

[Jmol-developers] "nihResolverFormat" cannot be set

2016-04-04 Thread Angel Herráez
Bob, This parameter can be shown but not set: $ print _versionDate 14.4.4_2016.03.29 2016-03-29 22:33 $ show nihResolverFormat nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE"; $ set nihResolverFormat = "https://cactus.nci.nih.gov/chemical/structure/%FILE"; ERROR en gui

Re: [Jmol-developers] Java 9 issue

2016-02-18 Thread Angel Herráez
if I may throw a suggestion, "L10N" is a term commonly associated to localization It could also be used for the current "idioma" folder in the jsmol package (I am happy with idioma, but others may not understand what it is for) -

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

2016-01-28 Thread Angel Herráez
Thanks, Bob As far as I've seen, for whatever reason the EBI PDBe people are doing changes in the CIF format of those files; in several respects they do not match their regular CIF files. They remove some fields and others change names. I talked to them and basically they say that's how it's go

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

2016-01-28 Thread Angel Herráez
We are starting to work on reading mmCIF files from PDBe, for "assemblies". This means the actual biological unit of the molecule, be it monomer, dimer, tetramer, etc -- manually checked since there are often several automatically prepared biological units in PDB Apparently EBI has been applyin

[Jmol-developers] update on Export To Web

2015-12-20 Thread Angel Herráez
Dear developers, in particular Bob and Jonathan, Over the last weeks I was teaching a course where whe learned to produce webpages from Jmol Export to Web. As a consequence, I am starting some revision of the page code generated, to be more HTML5-compliant and cleaner in terms of tags (e.g. less

Re: [Jmol-developers] partially selected state in checkbox groups

2015-11-13 Thread Angel Herráez
Yes, it's working through all levels (tested with 3, see http://biomodel.uah.es/JSmol/test_cbGroup.htm On 13 Nov 2015 at 16:25, Robert Hanson wrote: > > Did you get the sub-group business working? > > On Fri, Nov 13, 2015 at 1:46 PM, Angel Herráez < angel.herr...@uah.es>

[Jmol-developers] partially selected state in checkbox groups

2015-11-13 Thread Angel Herráez
Dear Bob I've being working on checkbox groups, to implement the display of partially selected state --which is a supported feature in html5. https://sourceforge.net/p/jmol/feature-requests/228/ Can you consider this for inclusion in next release? I don't know where that should be located in t

Re: [Jmol-developers] How to display smoothly varying XYZ geometries in Jmol?

2015-07-11 Thread Angel Herráez
Hello Krishna, and welcome to Jmol community There are probably several ways you can try for your purposes (although I am not sure to closely understand your setup). Here are some tips: 1. Do not use "zap", as it clears one model before starting to load the next. Maybe just load file1.xyz; lo

Re: [Jmol-developers] xml files?

2015-07-01 Thread Angel Herráez
> I am trying to convert the Jmol source code to JSmol using Java2Script. > I've made some changes to it and I want to know how they affect JSmol. I > got the code from here: http://jmol.sourceforge.net/#Obtain%20Jmol Ah, ok That's a purely developer-programmer issue, then. It's clear now. I ca

Re: [Jmol-developers] xml files?

2015-07-01 Thread Angel Herráez
ad that you guys had to heavily augment > Java2Script for it to work, what's the scoop on that? This is confusing. Do you want to convert Jmol source code? Or Jmol commands / scripts? These need no conversion, as they work equally in JSmol. Please, clarify what "your" Jmol cod

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

2015-06-23 Thread Angel Herráez
> Wow, that's very helpful, thank you! So I assume if you can create a > permanent console in Jsmol, > it's possible in Jmol as well. Java is a different business, the console IS a java window so you cannot fix it in the page. Example test: http://biomodel.uah.es/JSmol/test_console.htm?_USE=JA

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

2015-06-23 Thread Angel Herráez
Sam, Nearly there, just with CSS as I envisaged: http://biomodel.uah.es/JSmol/test_console.htm -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that m

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

2015-06-23 Thread Angel Herráez
It seems that the console div is created when either the "console" command is executed or the popup menu option is picked. It is appended after the BODY tag, with this content: etc So you need to fing where is that code generated. Maybe search for class="jmolConsole" in the source

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

2015-06-23 Thread Angel Herráez
Hello Sam Note there are no windows, it's all html in the single page, so my bet is you can do it (maybe) just using CSS, rather than modifying the source. I am not sure though whether the console panel is created every time or is always present and hidden. Case 2 will suit CSS, while case 1 wil

Re: [Jmol-developers] Bug Found

2015-06-19 Thread Angel Herráez
Hi Sam What you describe is very uncommon. Please, describe the procedure you have used to load the files. example: load files "=4KKS" "=1PD6" Hey! I see now! The particular 1PD6.pdb is a structure resolved by NMR as so it contains 28 different structures (conformations) -- taht's the reason

Re: [Jmol-developers] Displaying Multiple Structures and Manipulating Coordinates

2015-06-18 Thread Angel Herráez
Hello Sam, and welcome (This rather belongs into jmol-users list) > I'm emailing to ask a few questions about JMol. From what I've > found on your emailing archives, it seems like it is possible to load > multiple structures at once, but how exactly would one do that using the > frame co

[Jmol-developers] ligand contacts are broken in PDB

2015-06-17 Thread Angel Herráez
Dear Bob, I thought you'd like to know that the ligand contacts view, "View Pocket in Jmol" in the PDB website seem to be broken. When I click on the link, nothing happens. Maybe a consequence of their updates in viewers. (I've tried to reproduce that nice display manually via the console, and

[Jmol-developers] DOCUMENTATION AnimFrameCallback

2015-06-17 Thread Angel Herráez
Dear Bob, http://chemapps.stolaf.edu/jmol/docs/#setcallback set AnimFrameCallback says 9 parameters are returned. I only see 8; I think that maybe "isAnimationRunning" and "animationDirection" are merged into one? 14.2.14_2015.06.11 Regards, Angel -

Re: [Jmol-developers] Loop speed optimization potential

2015-04-03 Thread Angel Herráez
Hi Rolf I was about to suggest what Bob is putting forward: if Javascript is faster, you might take part of the code out from JmolScript into JavaScript. I believe he has demo'ed how. Another idea: I found that in Javascript there is much improvement in loops when they are decrementing instea

[Jmol-developers] rotate selected @variable fails in recent versions

2015-02-13 Thread Angel Herráez
I am seeing a problem in using COMPARE() and ROTATE SELECTED with only recent versions: My script is of the type load a.pdb // 10 frames load append b.pdb // single frame select protein; trace only; color trace gray; rotMx = compare({2.1 & alpha}, {1.10 & alpha}); show rotMx; select 2.1; color

[Jmol-developers] problem loading multimodel pdb file in jmol-14.3.12_2015.02.11b

2015-02-13 Thread Angel Herráez
Bob, A 10-model pdb file that loads fine in previous versions (up to jmol-14.3.12_2015.02.07.zip) breaks jmol-14.3.12_2015.02.11b.zip from St.Olaf load 3o80_3o8m_altB_17-485_508362-32078.pdb ERROR en guión: ERROR creating model: java.lang.NoSuchMethodError: org.jmol.modelsetbio.AminoMonomer.

Re: [Jmol-developers] list bounces

2015-01-23 Thread Angel Herráez
El 23 Jan 2015 a las 7:02, Robert Hanson escribió: > Who is handling these? Anyone? > jmol-users-boun...@lists.sourceforge.net I've done it a couple of times, but in others when I logged in, the problem had already been taken care of (Nico, maybe?) On the other hand, I suspect I have admin acces

[Jmol-developers] setAppletCss

2014-12-06 Thread Angel Herráez
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: .grayBox { border:1px solid red; } Jmol.setAppletCss('grayBox'); Jmol.setButtonCss('grayBox'); Jmol.getApplet('myJmol', Info); Jmol.jmolButton(myJmol,

Re: [Jmol-developers] JSmol as network viewer

2014-10-07 Thread Angel Herráez
Hi Rolf This is interesting but not what I can really discuss about, but I'd contribute one or two hints: One really nice thing (I've seen it in other tree viewers) would be the ability for the user to pull a node and have the whole thing rearrange dynamically. That's a force field and Jmol a

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

2014-09-17 Thread Angel Herráez
Bob, that sounds fully reasonable to me. The way I see it, old PDB files used to have just uppercase chain IDs and in many old scripts we just got used to use lowercase. When some Upper+Lowercase PDB files started, set chainCaseSensitive appeared so the user could cater for those and still the

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

2014-09-15 Thread Angel Herráez
9 Sep 2014, 2:58, Robert Hanson wrote: > In addition to that, the chain read from then HELIX record was not > stored the same way, so helixes and sheets were not read for any > chain that was outside the range "A" - "Z". Partly solved, but with another glitch now present: > in 14.3.7_2014.09.0

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

2014-09-09 Thread Angel Herráez
sorry, that's not Calpha-only But the problem is present --now I don't know the reason -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control

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

2014-09-09 Thread Angel Herráez
in 14.3.7_2014.09.08b cartoon is broken for Calpha-only files It used to render cartoons, now it just renders trace load =1LMB cartoon only // ok for dna, not for protein -- Want excitement? Manually upgrade your pr

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

2014-09-09 Thread Angel Herráez
There is also a problem with numeric chain IDs: load =1LMB; select *:1; //selects chains 1 and 2 select *:2; // same atoms select *:3; //selects chains 3 and 4 select *:4; // same atoms I notice that hover display quotes around the ID, like [DG]37:"2".O3' so I tried select *:"1" wi

[Jmol-developers] chainCaseSensitive is forced true in 14.3.7

2014-09-09 Thread Angel Herráez
in 14.3.7_2014.09.08b "chainCaseSensitive" is being ignored and acts as true That is, load =1crn select *:a //0 atoms selected select *:A // 327 atoms selected irrespective of the setting of chainCaseSensitive -- W

Re: [Jmol-developers] Jmol.resizeApplet

2014-09-06 Thread Angel Herráez
Bob, are both syntaxes supported? Jmol.resizeApplet(appletid, w, h) Jmol.resizeApplet(appletid, [w,h]) I only had the 2nd documented http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#resizeApple t -- Sla

[Jmol-developers] still problmes with MOVETO after MOVE

2014-07-31 Thread Angel Herráez
Dear Bob, After the last update of Jmol, 29th July, I am still having trouble when my page runs a script with "move" command and later a "moveto" or "zoomto". I've prepared a simplified test-demo page at http://biomodel.uah.es/en/model4/dna/_test_.htm That's using an older version of Jmol, but

[Jmol-developers] Script error: missing ] after element list

2014-07-25 Thread Angel Herráez
Dear Bob, I am getting this error when running a page in Firefox 30 from local disk (file:// protocol), in an alert box wehn loading the page: [Java2Script] Script error: missing ] after element list ../../JSmol/j2s/core/corescript.z.js [Exception... "Access to restricted URI denied" c

Re: [Jmol-developers] Jmol to Jsmol - issues

2014-07-25 Thread Angel Herráez
Hello Priya Nothing has changed? That's surprising I've visited your page and in the source code I can see nothing related to J(S)mol Can you please give a better pointer? -- Want fast and easy access to all the code in

Re: [Jmol-developers] reg: certificate for java applets - for JMol

2014-07-15 Thread Angel Herráez
nformatician/Data Manager > Innovation Center for Biomedical Informatics (ICBI) > Georgetown University Medical Center, Washington, DC > Email: kb...@georgetown.edu ; krithika...@gmail.com > Phone: 202-687-6850 ; Fax: 202-687-5011 > http://icbi.georgetown.edu/ > --

Re: [Jmol-developers] "move" breaks any further movement

2014-07-09 Thread Angel Herráez
FYI, this was broken between 14.1.10 and 14.1.11 > In 14.1.16 and 14.2.2, issuing a "move" command works, but any > further "moveto" or "zoom" does nothing load $caffeine; moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065} 5.5 {0 0 0} 0 0 0 3 0 0; move 90 0 0 0 0 0 0 0 5 30

[Jmol-developers] "move" breaks any further movement

2014-07-08 Thread Angel Herráez
Dear Bob, In 14.1.16 and 14.2.2, issuing a "move" command works, but any further "moveto" or "zoom" does nothing load $caffeine; moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065} 5.5 {0 0 0} 0 0 0 3 0 0; move 90 0 0 0 0 0 0 0 5 30; // 90 degrees around X moveto 1.0 { 916 -39

Re: [Jmol-developers] language localization fails

2014-07-03 Thread Angel Herráez
> And > http://127.0.0.1/biomodel/JSmol/idioma/ > definitely exists? Oh yes > I'm not sure where the vertical bar in the file:/// path is coming > from, do you? I think it's (at least) a Firefox thing, it's taking the place of the colon after the drive letter. On the other hand, there seems t

Re: [Jmol-developers] language localization fails

2014-07-02 Thread Angel Herráez
tive path broken · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- Open source business process management suite built on

[Jmol-developers] internal version number in JSmol is not updated to Jmol version number

2014-07-02 Thread Angel Herráez
Bob, some internal string needs to be fixed. I am seeing different version numbers in the pop-up menu depending on where I look: About > Jmol > gives the correct version, 14.2.2 2014.06.29 About > System > gives a wrong JSmol version, 14.1.14 Apr 27, 2014 -

Re: [Jmol-developers] language localization fails

2014-07-02 Thread Angel Herráez
Dear Bob, The Jmol JSconsole has provided some hints as why the language is not loading: Loading language resource file:///F|/webs/biomodel/model3j/../JSmol/idioma/es.po FileManager opening 3 file:/F|/webs/biomodel/model3j/../JSmol/idioma/es.po FileManager opening 1 file:/F 0 translations load

Re: [Jmol-developers] problems with custom popup and with language

2014-07-01 Thread Angel Herráez
You are right, I see now that both auto-language and lang-switch are both working fine at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.14.2/jsmol.htm Sorry. So I need to isolate the problem in my page, and will come back if needed. Thanks ---

Re: [Jmol-developers] language localization fails

2014-07-01 Thread Angel Herráez
I agree it's quite tricky. I will have to setup a test page maybe On 1 Jul 2014 at 14:23, Robert Hanson wrote: > > How can we test this? > -- Open source business process management suite built on Java and Eclipse Tu

Re: [Jmol-developers] problems with custom popup and with language

2014-07-01 Thread Angel Herráez
When I enter load menu mine.mnu in the console, I get this output: Available callbacks include: animframeCallback appletreadyCallback atommovedCallback clickCallback dragdropCallback echoCallback errorCallback evalCallback hoverCallback loadstructCallback measureCallback messageCallback minim

Re: [Jmol-developers] problems with custom popup and with language

2014-07-01 Thread Angel Herráez
Precedents, for reference: 29 Jan 2014, 11:55, Bob Hanson wrote: > ___JmolVersion="14.1.8_dev_2014.01.29" > bug fix: show MENU write MENU load MENU all broken in 12.2 > > [feature-requests:#213] custom pop-up menus > Status: open > Created: Tue Jan 28, 2014 11:08 AM UTC by Angel Herraez > Last

[Jmol-developers] problems with custom popup and with language

2014-07-01 Thread Angel Herráez
Jmol 14.2.2_2014.06.29 both in HTML5 and Java modes 1. The pop-up opens in English, not Spanish (I already reported this earlier today) 2. My page applies a language command that is being ignored (in fact, it is somehow applied since the language submenu has Spanish ticked, but the interface i

[Jmol-developers] language localization fails

2014-07-01 Thread Angel Herráez
Hi Bob 14.2.2_2014.06.29 application, the interface opens in English instead of Spanish. The pop-up language shows Spanish ticked, when I click on that the interface changes to Spanish. So the switch works, it's just the initial display where the language is not applied correctly. I haven't te

[Jmol-developers] write("coord") gives original, not transformed, coordinates

2014-06-17 Thread Angel Herráez
Dear Bob, Some time ago we addressed the issue of writing transformed coordinates in MOL format, either using write command or write() function. I think it was fixed in some 14.1.x version, but right now I am finding that zz = write("coord") zz = write("coord", "t.mol") are delivering the ori

Re: [Jmol-developers] is source code missing at SF ?

2014-06-17 Thread Angel Herráez
Thank you, Jaime In fact, my usual target is http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/ but since I got nothing, I climbed up the tree :) -- HPCC Systems Open Source Big Data Platform from L

[Jmol-developers] is source code missing at SF ?

2014-06-16 Thread Angel Herráez
There is nothing at http://sourceforge.net/p/jmol/code/ I used to go there for seeing the code. What has changed? -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Yo

Re: [Jmol-developers] bug in the script for ligand pockets in PDB

2014-06-04 Thread Angel Herráez
> yes, OK, but that's not a general solution. I suppose that happens in Java > and JavaScript? Not sure, but I will try to check today. It is happening in the PDB site, I think it was Java Jmol. I guess I can use the ?_USE=HTML5 there for testing. Why is it not general? Just avoid uppercase i

Re: [Jmol-developers] bug in the script for ligand pockets in PDB

2014-06-04 Thread Angel Herráez
Bob, I think you are not getting my point. I think this happens because there is an upercase "ID" text in the source code of that "gotoligand" function. For some reason, Jmol goes later to convert that to lowercase. But if the "gotoligand" function had just lowercase "id", then I believe no harm

Re: [Jmol-developers] bug in the script for ligand pockets in PDB

2014-06-03 Thread Angel Herráez
Yes, I had read about such a problem. The issue is, however, that it is not a user-given ID with Turkish characters, but the "ID" token in the source code. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph

[Jmol-developers] bug in the script for ligand pockets in PDB

2014-06-03 Thread Angel Herráez
Dear Bob, You're going to love this bug report. It's thrilling! I was today demonstrating the new PDB "ligand pocket" view that uses the "contact" command. Guess what... it breaks in Turkish computers, nothing is displayed but the standard protein rendering. I think I have tracked down the issue.

Re: [Jmol-developers] What is the second Canvas2d for that shows up below the active one when using JSmol?

2014-05-08 Thread Angel Herráez
Hi Removing the assignment of Info.coverImage makes the problem go. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: • 3 signs your SCM is hindering your productivity • Requirem

Re: [Jmol-developers] What is the second Canvas2d for that shows up below the active one when using JSmol?

2014-05-08 Thread Angel Herráez
I'm having a similar problem as Jonathan's. Two canvas2d objects are created. I believe there is something wrong with Jmol.getAppletHtml() The problem does not happen when I use Jmol.getApplet() directly in the div. Note: I am using jquery-1.10.2.min.js plus JSmol.min.nojq.js Symptoms: -

Re: [Jmol-developers] Jmol web site

2014-03-27 Thread Angel Herráez
Not a bit of work, I'm afraid, but quite a lot. There is a lot of information there that is obsolete. I have done --long time ago-- updates to the website files and I committed then, but then Nico had to do the "building" or whatever is the name to get the actual website updated. I may have t

[Jmol-developers] documentation

2014-03-25 Thread Angel Herráez
Bob, the text for set cartoonLadders OFF is duplicated from set cartoonRockets OFF and makes no sense, of course :) -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to

Re: [Jmol-developers] cameraDepth seems broken

2014-03-24 Thread Angel Herráez
Am I getting paranoid, or is "set cameraDepth" again not working? in 14.1.12_2014.03.22, both Java applet and JSmol JmolVersion="14.1.12_2014.03.13" bug fix: set cameraDepth disabled -- Learn Graph Databases - Download

Re: [Jmol-developers] loading binary files in Chrome from local host

2014-03-17 Thread Angel Herráez
Well, even if unexpected it is welcome ;-) > and see what's going on. The message is expected; successful local file > loading is not. I do not consider "localhost" or "http://127.0.0.1"; to be LOCAL -- it should be the same as SERVER. So, the alert should not be displayed and then the file l

[Jmol-developers] loading binary files in Chrome from local host

2014-03-17 Thread Angel Herráez
Dear Bob, You have implemented an alert that says "JSmolCore.js: synchronous binary file transfer is requested but not available" when trying to load a binary file. In Chrome, I get this alert when trying to load a pdb.gz file from disk -- correct. but I also get it when I load the page and fi

[Jmol-developers] bug in translucent background for echo

2014-03-17 Thread Angel Herráez
Translucent background for echos seems broken now: Jmol Application, 13.0.10 #works fine, yellow text on translucent background load =1crn; set echo coment4 50% 50%; echo "example"; color echo yellow; background echo gray translucent 0.4; Jmol Application, 14.0.10 #wrong Background is opaque

[Jmol-developers] cameraDepth seems broken

2014-03-12 Thread Angel Herráez
Hi I cannot make set cameraDepth to work in 14.0.11 or 14.1.8 It does have an effect in Jmol 12.0.5, 13.0.10 (Jmol application) load $cubane set cameraDepth 10 set cameraDepth 2 set cameraDepth 0.2 set cameraDepth 0.02 set cameraDepth 0.002 --

[Jmol-developers] meaning of struts mp.added ?

2014-03-10 Thread Angel Herráez
org\jmol\scriptext\CmdExt.java May I ask the meaning or context of this phrase? {0} struts mp.added -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph database

[Jmol-developers] GuiMao phrases that are split in 2 lines pose a translation question

2014-03-10 Thread Angel Herráez
Any reason for these phrases split between two variables? I am not sure how should I split them when translating. org\openscience\jmol\app\jmolpanel\GuiMap.java "GT_script_button_template.html_LOADING",GT.escapeHTML(GT._("Once the molecule file is fully loaded the image at right will bec

Re: [Jmol-developers] [Jmol-users] last chance before Jmol 14.1.11; JJSME/JSpecView

2014-03-10 Thread Angel Herráez
I usually commit the Spanish updates directly into SVN, so we can test this first without worrying about merging the Launchpad files. Once it works, that's a second part to address. For example, the Capture menu entries have already Spanish translations which I added a few days ago. Now I see th

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