User:AngelHerraez

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I am a lecturer in Biochemistry and Molecular Biology, long-time designer of web pages with Chime models, mainly proteins and nucleic acids. I am part of the BioROM group, which publishes a free, yearly CD-ROM with materials for computer-assisted teaching and learning in Biochem&MB in Spanish.

My location is the University of Alcalá, in Alcalá de Henares (Madrid province), Spain

You can contact me: angel.herraez AT uah.es

I have finished converting all my old Chime pages into Jmol. Everything is in my website, Biomodel:

  • Biomodel-1 (in Spanish) is a tutorial on structure of biomolecules:
    • amino acids, peptides and proteins
    • DNA
    • RNA
    • DNA-protein complexes
    • RNA-protein complexes
  • Biomodel-2 (in Spanish and English) is a Jmol port of my former Chime version based on Eric Martz's RasMol script "Lipid bilayers and the gramicidin channel".
  • Biomodel-3 (in Spanish and English) is a simpler tutorial on biomolecule structure, aimed for Secondary School students:
    • carbohydrates (mono-, di- and polysaccharides)
    • lipids (fatty acids, triacylglycerol, phospholipids, steroids, lipid bilayer)
    • vitamins
    • amino acids, peptides and proteins
    • nucleic acids (bases, nucleosides, nucleotides, DNA, RNA)
  • Biomodel-4 (in Spanish, English and Portuguese; French and German are in progress, but I need volunteer translators) is a Jmol port of Eric Martz's Chime tutorial "DNA structure".
  • Biomodel-5 (in Spanish) is an assorted collection about biopolymers.
  • Stereoisomerism in sugars and amino acids: a quiz with answers included (in Spanish).


Localization of Jmol

Spanish localization of Jmol

I have translated the texts in Jmol Application and Jmol Applet interfaces into Spanish. They started to be included in Jmol with pre-release 10.00.22, so the Spanish interface is part of Jmol 10.2 (but not of 10.00).

I have also translated Jmol's web site into Spanish.

Forcing Jmol to open in a certain language

Jmol includes several languages (technically called localizations) for the user interface (top menu in the App and pop-up menu in both App and Applet). Jmol will open by default with the interface using the language of your operating system (ref.). However, if you need to change this:

Jmol Application

If you want to force a certain language in the Application, you must start Jmol with 

  java -Duser.language=es -jar Jmol.jar   # forces Spanish (Español)
  java -Duser.language=de -jar Jmol.jar   # forces German (Deutsch)
  java -Duser.language=en -jar Jmol.jar   # forces English
  etc.

Jmol Applet

On Windows:

Open Windows Control Panel > Java icon (opens Java Control Panel) > Java tab > Applet run-time configuration > Show button > on row "JRE", click on the textbox under "Parameters" and type: 

  java -Duser.language=es    # forces Spanish (Español)
  java -Duser.language=de    # forces German (Deutsch)
  java -Duser.language=en    # forces English
  etc.

On other operating systems, I guess you just have to find where Java Control Panel is and do the same.

You can also force the applet in your pages to use English (the default) if you

1) use Jmol.js in your pages (or the split version JmolApplet0-6.jar, not the monolythic JmolApplet.jar)

and

2) omit the JmolApplet_i18n.jar file from the folder where the other files are.

(This method will exclude Jmol localization files, so it will affect not only you and your computer, but anyone seeing your pages, so it is not a very polite option; should be used only for testing.)

Running Jmol applets from the local file system

Advice and FAQ on how to set-up webpages that use Jmol applet and will work both when put on the web server AND when called from hard disk, CD-ROM, etc.: Jmol_Applet_Deployment_Local

Loading molecules from the hard disk: testing page - works locally, but not from the web server so you would have to download the webpage and its accesory files for it to work; uses the signed applet.


Moving from Chime to Jmol

Thousands of pages exist in the web that use Chime for showing and teaching molecules. I have done many, based on Eric Martz's 2-frame template. Here I will try to collect advice of how to port these kind of pages into Jmol based on my experiences.

1.- Remember that the model will load in a different orientation with Jmol, and some default rendering is different, so you need to fix your scripts (see specific sections below).

2.- Using the official Jmol.js is recomendable to ease coding.

3.- If you adopt Jmol.js and were using Eric's button() function, you can maintain your existing code for buttons by including this function after calling Jmol.js: 

function button(scrp) { jmolButton(scrp,"X") }

(it will take existing button(script) code and transform it into a Jmol javascript button with a cross inside it -similar to Chime button-).

Differences in rendering between Jmol and Chime

Default representation in Chime is wireframe, while it is ball & stick in Jmol.

wireframe 0 in Rasmol/Chime leaves thin wireframe, but hides the bonds in Jmol.
wireframe off works the same in both, hiding the bonds.

Because of this, most Rasmol-generated scripts will need "wireframe; spacefill off" added after loading the molecule in order to work similarly in Jmol.


Orientation of axes, translations and rotations: comparing Jmol with Chime

Purpose: establish a method for converting Chime scripts into Jmol scripts in a way that they render the same view of the molecule (by default, they don't).

Since I am unable to find documentation for this, I have set-up a page for testing orientation differences in Chime and Jmol.

Please, post your comments here (is it possible?) or in the jmol-users list.

First assert (already established and discussed previously): axes orientations are different.

First surprise: positive Y atom coordinates (red atom) go up, but positive "translate Y" moves down !! Is this a bug? Am I confused about orientations?

Jmol and frames

Jmol and Jmol.js design is not specially addressed for web pages with frames, but it can cope with it. If you are -like me- a fan of frames for organizing your content (static molecular model area, scrollable text content, no reloading of applet), you can get it:

1.- You must include the call to jmolInitialize() in both frames -otherwise, Jmol will complain-.

2.- In some set-ups, Jmol.js will find the applet in the other frame, but in some cases it will not. (For me, it worked with a model-in-left-frame, text-in-right-frame setup, but failed with model-in-right-frame, text-in-left-frame). You can direct Jmol.js to find the applet by redefining one of its functions: 

function _jmolFindApplet(target) 
{ /*replaces default function in Jmol.js, suggested by Bob Hanson*/
  var applet = _jmolSearchFrames(top.modelframe, target); /*first look for the target in my frame*/
  if (applet == undefined) applet = _jmolSearchFrames(top, target);
  return applet;
}


where modelframe must be the name of your frame containing the applet. You must call this function after you call Jmol.js. Thanks to Bob Hanson who suggested this fix.

Contribution to Jmol documentation

Using the mouse with Jmol (also known as 'mouse gestures')

Coloring schemes in Jmol

(now included in Jmol website)

Atomic and ionic radii in Jmol

(now included in Jmol website)


Molecular surfaces in Jmol

This section is being rewritten to include new capabilities available in Jmol 11) See doc.page

a) There is good support for

- isosurfaces - pMesh surfaces

both need surface data in additional files.

b) Some kind of surfaces can be obtained using "dots" and "set solvent on" (see testing page below).

c) Solid surfaces calculated from atomic coordinates and radii, similar to what is done by Rasmol/Chime: preliminary versions around 10.00.22 had some support for these. .
Now, Bob Hanson's prototype version (10.x.11, june2006) can calculate "molecular surfaces" (solvent-excluded surfaces) and render then as isosurfaces, and save them to jvxl format (Jmol voxel) for later loading them .

Slabbing through molecules in Jmol

After version 10.00.24, slabbed atoms are rendered as solid instead of hollow spheres ('bubbles'). See testing page

Delaying a Jmol applet to be loaded only when user asks for it

This is a prototype code built after Brian Duke's request for a means to incorporate Jmol into Wikipedia without forcing the users to wait for Java and Jmol to load. A text and/or image is shown and, if the user asks for it, it is substituted by a Jmol applet.

You can visit a demo page at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/

Suggestions are welcome.

Contributors

AngelHerraez, NicolasVervelle

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