User:AngelHerraez

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.

Contact: angel.herraez AT uah.es

Now, when I have some time, I'm switching my pages into Jmol.

I have ported my tutorial "Biomodel-3" (biochemical molecules for secondary school) into Jmol 10.00. It can be accessed at http://www2.uah.es/biomodel/model3j/ (in Spanish)

My new Jmol version of Eric Martz's Chime DNA tutorial is ready both in Spanish and English: Biomodel website.

"Lipid bilayers and the gramicidin channel" using Jmol is now available both in English and Spanish at Biomodel website

Spanish localization of Jmol

I have translated the texts in Jmol Application and Jmol Applet interfaces into Spanish, as well as Jmol's web site. They are included in Jmol starting with pre-release 10.00.22, and that includes official release Jmol 10.2.

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')

• Mouse_Manual in English
• Manual_Ratón in Spanish

Coloring schemes in Jmol

(now included in Jmol website)

Atomic and ionic radii in Jmol

(now included in Jmol website)

Molecular surfaces in Jmol

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. See testing page This has been removed from current releases (10.00.46).

Slabbing through molecules in Jmol

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

Contributors

AngelHerraez, NicolasVervelle