Difference between revisions of "User:AngelHerraez"

From Jmol
Jump to navigation Jump to search
m (Molecular surfaces in Jmol)
(Personal information)
 
(26 intermediate revisions by the same user not shown)
Line 1: Line 1:
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 [http://www.biorom.uma.es BioROM] group, which publishes a free, yearly CD-ROM with materials for computer-assisted teaching and learning in Biochem&MB in Spanish.
+
[[Image:Angel_%26_Bob_BCCE2010.jpg|thumb|right|alt=Angel & Bob|Angel Herráez (left) and Bob Hanson (right), during the [[Events#BCCE%202010|2010 BCCE]]. Angel is wearing the official BCCE cowboy hat -- August in Texas is hot!]]
 +
= Personal information =
 +
I am a lecturer / associate professor in Biochemistry and Molecular Biology, long-time designer of web pages with Chime models, mainly proteins and nucleic acids. I am part of the [http://www.biorom.uma.es 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
+
My location is the University of Alcalá, in Alcalá de Henares (Madrid province), Spain
  
Now, when I have some time, I'm switching my pages into Jmol.
+
[http://orcid.org/0000-0002-9900-6845 ORCID: 0000-0002-9900-6845]
  
I have ported my tutorial "Biomodel-3" (biochemical molecules for secondary school) into Jmol 10.00. It can be accessed at
+
You can contact me: angel.herraez AT uah.es
http://biomodel.uah.es/model3j/  (in Spanish)
 
  
My new Jmol version of [http://molvis.sdsc.edu/dna/index.htm Eric Martz's Chime DNA tutorial] is ready both in Spanish and English: [http://biomodel.uah.es/model4/ Biomodel website].
+
[https://sourceforge.net/u/aherraez/profile/ SourceForge user page].
  
"Lipid bilayers and the gramicidin channel" using Jmol is now available both in English and Spanish at [http://biomodel.uah.es/model2/ Biomodel website]
+
I have finished converting all my old Chime pages into Jmol and then JSmol. Everything is in my website, [http://biomodel.uah.es Biomodel]:
  
= Localization of Jmol =
+
* Biomodel-1 (in Spanish and English) 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 / High 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, Portuguese, French, German, Romanian and Italian) 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).
 +
* Intermolecular hydrogen bonding in liquid water and in ice, including interactive 3D models and an animation, and a simulation of the water-ice transition (in Spanish and English).
  
== Spanish localization of Jmol ==
+
= Publications on 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.
+
* Angel Herráez, Robert M. Hanson, and Leslie Glasser: '''Interactive 3D phase diagrams using Jmol'''. Journal of Chemical Education 86(5): 566 (2009)
 +
:The [http://biomodel.uah.es/personal/2009/phase-diagrams/phase-diagrams.htm supplementary material] described in this [http://jchemed.chem.wisc.edu/journal/issues/2009/May/abs566.html Letter] illustrates the use of Jmol to plot experimental 3D data, together with interactive labeling and captioning, generation of projections of the data onto a plane, highlighting data subsets...
  
== Forcing Jmol to open in a certain language ==
+
* Angel Herráez: '''How to use Jmol to study and present molecular structures, Vol.1'''. <nowiki>ISBN 978-1-84799-259-8</nowiki>. Published by Lulu.com (2007).
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).
+
: A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels.  
Jmol will open by default with the interface using the language
+
: [http://biomodel.uah.es/Jmol-handbook.htm Info and links to preview and on-line shop]
of your operating system ([http://java.sun.com/j2se/corejava/intl/reference/faqs/index.html#set-default-locale ref.]). However, if you need to change this:
 
  
=== Jmol Application ===
+
* Angel Herráez: '''Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1'''. <nowiki>ISBN 978-1-84753-710-2</nowiki>. Published by Lulu.com (2007).
If you want to force a certain language in the Application, you must start Jmol with
+
: (In Spanish)
 +
: [http://biomodel.uah.es/Jmol-manual.htm Info and links to preview and on-line shop]
  
  java -Duser.language=es -jar Jmol.jar  # forces Spanish (Español)
+
* Angel Herráez: '''Biomolecules in the computer: Jmol to the rescue'''. Biochemistry and Molecular Biology Education 34(4): 255-261 (2006).
  java -Duser.language=de -jar Jmol.jar  # forces German (Deutsch)
+
: A review of Jmol project and features, in comparison to Rasmol and Chime. doi:10.1002/bmb.2006.494034042644
  java -Duser.language=en -jar Jmol.jar  # forces English
+
: [http://www3.interscience.wiley.com/cgi-bin/abstract/113449000/ABSTRACT Abstract and open-access full text]
  etc.
 
  
=== Jmol Applet ===
+
= Localization of Jmol =
On Windows:
 
  
Open Windows Control Panel > Java icon (opens Java Control Panel) > Java tab > Applet run-time configuration > Show button >
+
== Spanish localization of Jmol ==
on row "JRE", click on the textbox under "Parameters" and type:
+
I have translated and maintain the Spanish versions of the interface in Jmol Application and Jmol Applet, as well as of Jmol's web site.
  
  java -Duser.language=es    # forces Spanish (Español)
+
== Forcing Jmol to open in a certain language ==
  java -Duser.language=de    # forces German (Deutsch)
+
See [[Jmol_Application#Forcing_Jmol_to_open_in_a_certain_language]]
  java -Duser.language=en    # forces English
+
and [[Jmol_Applet#Forcing_JmolApplet_to_open_in_a_certain_language]]
  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 =
 
= Running Jmol applets from the local file system =
Line 87: Line 89:
 
''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).
 
''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 [http://web.madritel.es/personales2/anherraez/pruebas/jmol/test-axes-rot.htm page] for testing orientation differences in Chime and Jmol.
+
Since I am unable to find documentation for this, I have set-up a [http://biomodel.uah.es/Jmol/axes-rot/inicio.htm page] for testing orientation differences in Chime and Jmol.
  
Please, post your comments here (is it possible?) or in the jmol-users list.
+
''These differences in behaviour seem to depend on the molecular file format.''
  
'''First assert''' (already established and discussed previously): axes orientations are different.
+
Please, post your comments in the jmol-users list.
  
'''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 frames ==
Line 108: Line 109:
 
   return applet;
 
   return applet;
 
  }
 
  }
 
+
''note: this function needs update to match current version of Jmol.js'' '''Current versions of Jmol.js no longer need this patch.'''
  
 
where ''modelframe'' must be the name of your frame containing the applet.
 
where ''modelframe'' must be the name of your frame containing the applet.
 
You '''must''' call this function '''after''' you call Jmol.js.
 
You '''must''' call this function '''after''' you call Jmol.js.
 
''Thanks to Bob Hanson who suggested this fix.''
 
''Thanks to Bob Hanson who suggested this fix.''
 +
  
 
= Contribution to Jmol documentation =
 
= Contribution to Jmol documentation =
Line 120: Line 122:
 
* [[Mouse_Manual]] in English
 
* [[Mouse_Manual]] in English
 
* [[Manual_Ratón]] in Spanish
 
* [[Manual_Ratón]] in Spanish
 +
  
 
== Coloring schemes in Jmol ==
 
== Coloring schemes in Jmol ==
  
 
(now included in [http://www.jmol.org/jscolors/ Jmol website])
 
(now included in [http://www.jmol.org/jscolors/ Jmol website])
 +
  
 
== Atomic and ionic radii in Jmol ==
 
== Atomic and ionic radii in Jmol ==
Line 130: Line 134:
  
  
= Molecular surfaces in Jmol =
+
== Molecular (and other) surfaces in Jmol ==
  
a) There is good support for
+
This section has been rewritten to include new capabilities available in Jmol 11, and is available on a [http://biomodel.uah.es/Jmol/surfaces page] outside this wiki, and as
 +
[http://www.jmol.org/docs/surface/ part of Jmol's website].
 +
It includes documentation and a testing/demo page.
  
- isosurfaces
 
  
- pMesh surfaces
+
= Slabbing through molecules in Jmol =
  
both need surface data in additional files.
+
After version 10.00.24, slabbed atoms are rendered as solid instead of hollow spheres ('bubbles'). See
 +
[http://biomodel.uah.es/Jmol/slab/inicio.htm testing page]
  
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 [http://biomodel.uah.es/pruebas/jmol/surface/inicio.htm testing page]
+
= Delaying a Jmol applet to be loaded only when user asks for it =
This has been removed from current releases (10.00.46).<br />
 
Now, Bob Hanson's prototype version (10.x.11, june2006) can calculate solvent-accesible surfaces and render then as isosurfaces, and save them to jvxl format (Jmol voxel) for later loading them (see [http://biomodel.uah.es/pruebas/jmol/surface/proto/inicio.htm new testing page]).
 
  
= Slabbing through molecules in Jmol =
+
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/Jmol/pop-in/
 +
 
 +
A similar solution is implemented in [http://www.jmol.org/ Jmol website] and is also used in pages built using the '''''PopIn''''' template within the '''''Export to Web''''' module included in Jmol application.
 +
 
 +
Suggestions are welcome.
 +
 
 +
 
 +
= Jmol in Wikipedia =
 +
 
 +
Discussion is going on at http://en.wikipedia.org/wiki/Wikipedia_talk:Using_Jmol_to_display_molecular_models
  
After version 10.00.24, slabbed atoms are rendered as solid instead of hollow spheres ('bubbles'). See
+
Preliminary tests:
[http://biomodel.uah.es/pruebas/jmol/slab/inicio.htm testing page]
+
* [[User:AngelHerraez/Sandbox/Caffeine|Sandbox/Caffeine]]
 +
*: But it needs MediaWiki version 1.12+, and JmolWiki has <s>1.11</s> 1.14 now. I'm going for it!
 +
* [[User:AngelHerraez/Sandbox/SklogWiki|Sandbox/SklogWiki]]

Latest revision as of 15:48, 23 November 2016

Angel & Bob
Angel Herráez (left) and Bob Hanson (right), during the 2010 BCCE. Angel is wearing the official BCCE cowboy hat -- August in Texas is hot!

Personal information

I am a lecturer / associate professor 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

ORCID: 0000-0002-9900-6845

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

SourceForge user page.

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

  • Biomodel-1 (in Spanish and English) 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 / High 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, Portuguese, French, German, Romanian and Italian) 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).
  • Intermolecular hydrogen bonding in liquid water and in ice, including interactive 3D models and an animation, and a simulation of the water-ice transition (in Spanish and English).

Publications on Jmol

  • Angel Herráez, Robert M. Hanson, and Leslie Glasser: Interactive 3D phase diagrams using Jmol. Journal of Chemical Education 86(5): 566 (2009)
The supplementary material described in this Letter illustrates the use of Jmol to plot experimental 3D data, together with interactive labeling and captioning, generation of projections of the data onto a plane, highlighting data subsets...
  • Angel Herráez: How to use Jmol to study and present molecular structures, Vol.1. ISBN 978-1-84799-259-8. Published by Lulu.com (2007).
A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels.
Info and links to preview and on-line shop
  • Angel Herráez: Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1. ISBN 978-1-84753-710-2. Published by Lulu.com (2007).
(In Spanish)
Info and links to preview and on-line shop
  • Angel Herráez: Biomolecules in the computer: Jmol to the rescue. Biochemistry and Molecular Biology Education 34(4): 255-261 (2006).
A review of Jmol project and features, in comparison to Rasmol and Chime. doi:10.1002/bmb.2006.494034042644
Abstract and open-access full text

Localization of Jmol

Spanish localization of Jmol

I have translated and maintain the Spanish versions of the interface in Jmol Application and Jmol Applet, as well as of Jmol's web site.

Forcing Jmol to open in a certain language

See Jmol_Application#Forcing_Jmol_to_open_in_a_certain_language and Jmol_Applet#Forcing_JmolApplet_to_open_in_a_certain_language

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.

These differences in behaviour seem to depend on the molecular file format.

Please, post your comments in the jmol-users list.


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;
}

note: this function needs update to match current version of Jmol.js Current versions of Jmol.js no longer need this patch.

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 (and other) surfaces in Jmol

This section has been rewritten to include new capabilities available in Jmol 11, and is available on a page outside this wiki, and as part of Jmol's website. It includes documentation and a testing/demo page.


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/Jmol/pop-in/

A similar solution is implemented in Jmol website and is also used in pages built using the PopIn template within the Export to Web module included in Jmol application.

Suggestions are welcome.


Jmol in Wikipedia

Discussion is going on at http://en.wikipedia.org/wiki/Wikipedia_talk:Using_Jmol_to_display_molecular_models

Preliminary tests: