Re: [Jmol-users] Change vibration scale from xyz embedded script

-- Please consider the environment before printing this e-mail. Dear Keith Refson, Do you want me to add all the new feature that Bob has introduced in Jmol in J-ICE? http://j-ice.sourceforge.net/ We can show vibrations in a nice way as well as convolute IR, RAman spectra. Let me know

[Jmol-users] error in Jmol applet release

Dear Bob, something weird is happening. Today i recompiled the developer version of Jmol with the new features for VASP me and Bob had recentely introduced. In local all the new VASP features do perfectly work. Once I upload Jmol on my web page http://j-ice.sourceforge.net/ondemand/index.html

Re: [Jmol-users] error in Jmol applet release

Shoot ah I forgot.. -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44

Re: [Jmol-users] error in Jmol applet release

I did it nothing happens. -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0)

Re: [Jmol-users] error in Jmol applet release

Can you add this change yourself because. I am confuseed at a certain point. You had moe experience. You find the last revision in the trunk. By the way can you help me? with the question I asked Thanks, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa

Re: [Jmol-users] error in Jmol applet release

Those I have are very big. I zip two of them OUTCAR_MD.zip under vasp test. 6 Mb I hope they are not too big. Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of

Re: [Jmol-users] Several questions

Bob, what do you mean by that? 4) Bob the Z-matrix functions you kindly sent me doesn't work for crystals and surfaces. To be precise it works but loosing entirely the structure periodicity.Have a try Are you saying you want to add an atom in every unit cell using internal coordinates? Then

[Jmol-users] change atom name and label

Hey Bob, how can I change the an element name? Imagine having one H and I want it to be changed to F. Thanks, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building,

[Jmol-users] pdb problems

Hi Bob 1) can you please check this pdb which was supposed to be a crystal but Jmol views it as a molecule. Is it the pdb file malformed ? 2) If you can open it you will see that there are atom outside the cell. The question is the following: I would like only atoms inside the cell how

[Jmol-users] Uncaught Error: Chrome and opera under linux

Dear all I am experiencing this sort of error using my J-ICE interface when I use chrome under linux. This problem doesn't appear for its windows release. jmol/Jmol.js:410Uncaught Error: Error calling method on NPObject! like 410 is marked below with , function jmolScript(script,

Re: [Jmol-users] Uncaught Error: Chrome and opera under linux

This is how my index page looks like jmolInitialize(., jmol/JmolAppletSigned0.jar); jmolSetAppletColor(white); jmolApplet( [ 440, 440 ], load output/hematite.out ; set messageCallback 'myMessageCallback';message DONE;); -- Please

Re: [Jmol-users] Several questions

I am sorry, it just works great! I was wondering if I want to leave atom in the plane and remove only the atom above or below. it's there any way to exclude them ? Secondly, I have also introduce in J-ICE an option to remove atoms around an atom, something like: select within( distance, { x

Re: [Jmol-users] Several questions

Thanks Angel . Can you give me more info? You probably didn't see it yesterday. Could you please add to the wiki page ? I would like to inform you that I have released my first project, which entirely relies on Jmol. Its name is J-ICE which stand for: a Jmol interface for crystallographic and

Re: [Jmol-users] Several questions

I am sorry the structure beneath the map but not the map. I mean I don't get the superimposed map -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury,

Re: [Jmol-users] Several questions

It'does not work when you replicated the isosurface for crystals. I tried with a slab. -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2

[Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties

Dear all, I would like to inform you that I have released my first project, which entirely relies on Jmol. Its name is J-ICE which stand for: a Jmol interface for crystallographic and electronic properties. J-ICE allows users to visualize, to build and to manipulate complex input/output

Re: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties

Thanks -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456

Re: [Jmol-users] Several questions

thanks again -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456

Re: [Jmol-users] Several questions

I tried select WITHIN(distance,planeType, planeDesignation) with slab and polymer. This doesn't make difference between negative and positive numbers in slab and polymer once defined the plane. Thanks, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa

[Jmol-users] Several questions

Dear all, I got several questions to ask 1) I was wondering whether is possible or not to re-set the origin of the unitcell. The command set unitcell {1/2 1/2 1/2 } do that. Apparently is just a graphical nice feature.In fact, I noticed that whenever I operate an expansion of the cell with

Re: [Jmol-users] internal coordinate (z-matrix) addition of an atom to a molecule

That's great -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456

Re: [Jmol-users] supercells

yes I think it is! This is how the supercell works in CRYSTAL A supercell is obtained by defining the new unit cell vectors as linear combinations of the primitive cell unit vectors (See SUPERCON for crystallographic cell vectors reference). The point symmetry is defined by the number of

Re: [Jmol-users] supercells

Yes that's great for the time being! Any how have a look there. -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom

[Jmol-users] error loadin jmol

Dear All, I have just now recompiled the Jmol code with the new gettext features. When I copy the singned applet files and all the rest built from the buld direcory and I try to open my page I get this error: Error: jmolInitialize is not defined Source File:

Re: [Jmol-users] error loadin jmol

I got it to work -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456

Re: [Jmol-users] decimal places

Dear Rob, Why do I get this ? when I use something like that jmolScript('showSelections TRUE; select none; label on ; set picking on; set picking DISTANCE; set picking SELECT atom;'); jmolScript(measure ON; set measurements ON; set showMeasurements ON; set measurements +

[Jmol-users] fractional coordinates

Hello there, I am trying to do operation on fractional coordinate but I can't' work them out: like divide each of them by 10 xy = for(i;{1.1}.fz; i /10) What's wrong ? The console complains about {1.1}. What am I supposed to do? Thanks -- Please consider the environment before printing

Re: [Jmol-users] decimal places

Ok Sorry Bob, anyway I need 5 decimal places and than I will round them up! 2 are not enough though -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent,

[Jmol-users] decimal places

Dear all, do you know how to set the number of decimal places when I set : set picking MEASURE DISTANCE or ANGLE etc ? should this command be followed by this ? label [%.5x] ? Thanks, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104

Re: [Jmol-users] decimal places

Thanks but how they act on the measure ? should I put something like measure.label[] ? -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2

Re: [Jmol-users] decimal places

because if I use set MeasureCallback It seems I cannot format the string as it's preformatted! For instance [Fe/1 #4, Fe1/1 #3, 2.9 Å] -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram

Re: [Jmol-users] decimal places

1) Yes I came across this command before but this just but I didn't use it because it just increment the number of 0 and doesn't add anything more than that? is there any keyword to make the measure more accurate? 2) if I have my fractional coordinates and I want to operate just on one of

[Jmol-users] Again on the isosurface

Dear All, is it possible to plot isosurfaces from a periodic CUBE file onto a plane? I tried with the following command isosurface ?.CUBE hkl {1/2 1/2 1/2} map ?.CUBE but I wasn't successful! I can see some point is it because the resolution of the cube file ? thanks, Piero -- Please

[Jmol-users] still problem with certain geometries CUBE files

Dear All, Bob We had recently spoken about CUBE files with periodicity, I still have a problem in overlapping correctly my map on the crystal structure. The case I am talking about is the rombohedral Fe2O3. Particularly in the last change you (Bob), did into the CUBE class, you applied a

[Jmol-users] how to remove white lines in array

Hi there, is any hidden :) Jmol command to remove blank lines once in a Jmol array? for instance white lines appear in such cases : var script = var array = [ + varA + , + varB + , ' varC + ']; + =

Re: [Jmol-users] how export in fractional coordinates

apparently is the 2nd option a Jmol bug because by typing : print {1.1}.length = 10 print {1.2}.length = 20 print {1.1 and 1.2}.length = 10 I sent you the file too. Thanks, Piero Bob, I sent the file to you -- Please consider the environment before printing this e-mail. Pieremanuele

Re: [Jmol-users] how export in fractional coordinates

ok Thanks a lot huh! -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0)

[Jmol-users] how export in fractional coordinates

Dear all, How can I export the fractional coordinates of one specif frame having loaded in Jmol a structure with several model? I am asking that question because I experienced the following drawbacks: Ok if I type var xyzCoord = {1.1}.label( %16.9[xyz]); print xyzCoord i get Fe

Re: [Jmol-users] error with jmolColorPickerBox

yes you are right -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0)

[Jmol-users] error with jmolColorPickerBox

Dear all, On firefox this script works, even though I get an error like Warning: Expected number or percentage in rgb() but found '['. Error in parsing value for 'background'. Declaration dropped. Source File: Line: 0 var colorScript = [setAtomColor, 'atomColor'];

[Jmol-users] how can I update the color range of given isosurface

Dear all, is anyway to reset the color range for a loaded map. Should I just re-type isosurface color range newMin newMax map ? If the surface i loaded from ajvxl file ?? I am asking this because I would not like to reload the two files (i.e. dens.cube, pot.cube ) but just update what is

[Jmol-users] work out in two separate text boxes mapped data range min and max when plotting an isosurface

Dear all I'd like to print in two separate textboxes the mapped data range min and max (see below) when I plot a new map with Jmol. isosurface1 created with cutoff=0.02; number of isosurfaces = 1 color range 0.0 0.3; mapped data range -0.06706063 to 0.88033277 Do you have any suggestion? I

Re: [Jmol-users] New version of jmolColorPickerBox that may solve Piero's problem

I got your script I was trying to use it my HTML page has the script set like that script type='text/javascript' var Colorscript = new Array (setAtomColor); jmolColorPickerBox(Colorscript, 'rgb(100,100,100)'); /script The array Colorscript should be the array which include

Re: [Jmol-users] New version of jmolColorPickerBox that may solve Piero's problem

Yes but still it doesn't work! Thanks -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk

[Jmol-users] again jmolColorPickerBox

Thanks Jonathan I got your script and I was trying to use it. My HTML page has the script set like that script type='text/javascript' var Colorscript = new Array (setAtomColor); jmolColorPickerBox(Colorscript, 'rgb(100,100,100)'); /script The array Colorscript should be the array

[Jmol-users] orientation along miller plane

Dear all, is in Jmol anyway to orient one crystal along miller planes. Reading through the Jmol interactive scripting documentation i can't figure out any way to do that Thanks, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104

Re: [Jmol-users] problem setting element colors with JmolColorPickerBox

Dear Jonathan, In the end will you make the extension? when you have something ready I am willing to test it. Thanks , Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building,

Re: [Jmol-users] problem setting element colors with JmolColorPickerBox

Dear Jonathan, I think is mostly the second one as the function you see below print html text which is static. However the variable scriptColor must be changed as the user deal with the page. var scriptColor =; function createAppearanceGrp(){ var strApp=form id='appearanceGroup'

Re: [Jmol-users] problem setting element colors with JmolColorPickerBox

yes u pass it to Jmol with strApp+=JmolColorPickerBox( + scriptColor + ,[255,255,255]); \n Sorry it's been replaced with an x in the original text. -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical

[Jmol-users] jmolscrpt to list out elements label in Jmol

Dear all; what Jmol command should I use to work out the atom type like Mn, O ... once I loaded a structure on Jmol? Is any jmolScript available ? -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical

Re: [Jmol-users] jmolscrpt to list out elements label in Jmol

yes but this way you select just element number 3. Let day my structure loaded is NaCl, I would like that my script prints just Na and Cl. How can I do ? Thanks -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of

[Jmol-users] Problems having two flot graphs in the same page

Dear all, it is possible to use two flot graphs in the same page? did anyone try it before? Bob regarding your function plotEnergies if I create a similar one which point to another div, do you think is going to work along plotEnergies (see the page I sent you)? I got the plotEnergies

[Jmol-users] select item with javascript

Dear All, Does anyone know how to select item in listboxes with javascript ? I don't mean to get the value given a selected element in a listbox. Thanks -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical

Re: [Jmol-users] select item with javascript

Thanks -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456

[Jmol-users] povray map

Dear all, why when I tray to export a povray file of a periodicezed map (.*.Cube) what I get is just the map within the unit cell? Why can I not see the periodicization ? Many Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building,

[Jmol-users] color scale for isosurfaces

Dear All, I am plotting isosurface from cube files. Does exist a way to plot a scale of color into the image? By the way Bob your improvement on the cube files works fantastically. Now I can do my maps with periodicity in one shot Thanks a lot, Piero -- Pieremanuele Canepa Room 104

[Jmol-users] legend in isosurface

Dear All, I am plotting isosurface from cube files. Does exist a way to plot a scale or legend of color into the image? By the way Bob your improvement on the cube files works fantastically. Now I can do my maps with periodicity in one shot Thanks a lot, Piero -- Pieremanuele Canepa Room

Re: [Jmol-users] Unexpected behavior

There was a little error into the reader. Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456

[Jmol-users] Unexpected behavior

Dear Bob, I am developing a bit my internet page. if I want to print all frequency features of one vibration mode all I need is the follow command print getProperty(auxiliaryInfo.models[3].modelProperties) if I want the specific frequency it becomes print

Re: [Jmol-users] problem filling an html list

Dear Angel, I do apologize for the slow replay. The original e-mail I sent several weeks ago was what you find below Dear All I have a javascript function LoadModels() which should load the models in an external HTML list ! How can I let the list be populated when I load the page? This would

[Jmol-users] (no subject)

Dear all, In the page I am working on I create a button to load new files as below: input TYPE=button NAME=load_structure class='button' value=Load file *.out/*out.gz OnClick='jmolScript(load ?; script scripts/name.spt; background white) + removeAllModels() + loadModels()' function

[Jmol-users] load models into an external list

Dear all, In the page I am working on I create a button to load new files as below: input TYPE=button NAME=load_structure class='button' value=Load file *.out/*out.gz OnClick='jmolScript(load ?; script scripts/name.spt; background white) + removeAllModels() + loadModels()' function

Re: [Jmol-users] (no subject)

The last one doesn't work. It comes up with an error JmolApplet0,,, Zapped! why ? Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0)

Re: [Jmol-users] (no subject)

Dear Bob, I tried this one because it looks to me the more feasible. This gives me that error I told you. Thanks Piero function onClickLoadStruc() { jmolScriptWait(load ?; script scripts/name.spt; background white) removeAllModels() loadModels() } -- Pieremanuele Canepa Room 104

Re: [Jmol-users] (no subject)

Te error I see on the jmol deck is java.Security.AccessControlException: access.denied (java.io.FilePermission ... this happens per each file? How comes ? all the best, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of

Re: [Jmol-users] (no subject)

It's strange because all work if I use the normal jmolScript as below function onClickLoadStruc() { jmolScript(load ?; script scripts/name.spt; background white) removeAllModels() loadModels() } This just happens when I employ jmolScriptWait() -- Pieremanuele Canepa Room 104

Re: [Jmol-users] (no subject)

I realized that the file is correctly read with jmolScript(load ? ) wherever it is, whereas it has to be in the same directory as the applet if the command jmolScriptWait(load ? ) . Why ? How can I solve it ? What I am tiring to do is an online visualizer. So I cannot set a set

Re: [Jmol-users] (no subject)

Are you sure because nothing seems to change! -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456

Re: [Jmol-users] (no subject)

Quick mind Bob my functions are. Then what's wrong ? Thanks, Piero function loadModels(selectbox){ removeAllModels() var Info = jmolGetPropertyAsArray(auxiliaryInfo.models) if(!Info){ alert(No models available) return } for(var

Re: [Jmol-users] problem filling an html list

Rob, Angle I did as you said. What I see is: the file location as b, the name of the file as c and the title of the file as d. What's the way to exploit these info to fill the list ? Many thanks, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences,

Re: [Jmol-users] problem filling an html list

Bob, can you give me the INTERNET url not your local? file:///C:/jmol-dev/workspace/Jmol-documentation/script_documentation/index.htm?ver=11.10search=callback#setcallback Thanks, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building,

Re: [Jmol-users] problem filling an html list

Bob, Angel which function is going to be function myfunc(appId,b,c,d) { alert([appId, b, c, d]) } I cannot find any explanation on http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.10search=callback#setcallback . Thanks ,piero -- Pieremanuele Canepa Room 104 Functional Material

Re: [Jmol-users] problem filling an html list

Bob, I can't find where is referring to the function we were speaking some day ago. function myfunc(appId,b,c,d) { alert([appId, b, c, d]) } thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury,

Re: [Jmol-users] problem filling an html list

Exactly that's what I am doing, i am using the div as you said ! how does set loadStructCallback work ? Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail:

[Jmol-users] problem filling an html list

Dear All I have a javascript function LoadModels() which should load the models in an external HTML list ! How can I let the list be populated when I load the page? This would have to happen just after the jmolApplet([520,520] has been called! I can make it to work if I do as below

[Jmol-users] load file

Dera All, I try to within a javascript the following operation load { x x x} where x x x are values read from textbox in my html page Then the javascript function would be : function setPackaging(){ jmolScript(load + '' + { +

[Jmol-users] load structure in HTML page

Dear All, I try to within a javascript the following operation load { x x x} where x x x are values read from textboxes in my HTML page Then the javascript function would be : function setPackaging(){ jmolScript(load + '' + { +

Re: [Jmol-users] load file

It has to be like that, with spaces such as ' ' , otherwise I would have not worked ! function setPackaging(){ jmolScript('load {' + document.pack.par_a.value + ' ' + document.pack.par_b.value + ' ' +