Comparative size of proteins.
Introduction and help.

Proteins available

The page provides a set of selected protein examples in the drop-down menus. You may load any of them in either the left- or right-hand side panel.

Structural models are displayed to the same scale, in spacefill rendering in order to give a better idea of the volume of the molecule. Models may be freely rotated in 3D by mouse or finger. You may also use the pop-up menu in Jmol if you wish to change the rendering. Zooming is disabled since this is technically needed to keep both models in the same scale, which is the major purpose of this page. You can only zoom in or out, both models at a time, using the row of buttons located below the models.

You can load any other protein structure that is in the Protein Data Bank by entering its 4-character PDB ID in the text slot and clicking the button. Please note that in this case the displayed values of molecular mass and number of amino acid residues may be inaccurate or even plain wrong, since they are calculated from information in the model (residue numbering may have gaps or duplicates, and mass of hydrogen atoms is grossly estimated since X-ray results do not include them).

System requirements

• The page should work in any kind of computer with a modern web browser. Internet Explorer must be version 9 or later (although IE7 and IE8 may work with the Java modality of Jmol).
• The page should work in mobile devices such as tablets and phones, subject to their use of an HTML5-compliant browser. Please bear in mind that the computing power of the device and browser may restrict responsiveness, particularly with larger proteins.
• The page may be loaded in one of two modes: using Java or not. Java-less mode will work in any device that supports HTML5, while Java mode is more agile but needs a computer with the Java plugin installed and enabled for the browser used.
  • Java is considered a potentially harmful software platform and hence it may be disallowed in some systems or institutions, or you may personally prefer not to use it. We can assure that Jmol will do no harm to your system, but it is your decision to trust it. You will usually receive one or more warnings when trying to load the page, that you need to accept if you want the page contents to be displayed.
  • In tablets and other mobile devices, the page will use by default the non-Java mode (as these systems do not regularly support Java).
  • In computers (Windows, MacOS or Linux) the page will by default load in the Java mode. You may switch to the non-Java mode using the link at the bottom of the page, or adding a parameter in the URL (explained below).

Choosing Jmol mode

As described above, the page may be run in Java mode (using Jmol applets) or in non-Java, HTML5, JavaScript mode (JSmol). The default mode depends on detection of the system being used, but may be overriden using the links at the bottom of the page or adding an option in the url (use=HTML5 or use=Java).

Language of the interface

The page is prepared in English and Spanish (more languages may be easily added; please contact the author if you are interested). By default, the system's language will be detected and used. You may override this by adding an option in the url (lang=en or lang=es).

Examples:
http://biomodel.uah.es/en/scale/?lang=en
http://biomodel.uah.es/en/scale/?use=HTML5
http://biomodel.uah.es/en/scale/?use=Java
http://biomodel.uah.es/en/scale/?use=HTML5&lang=en
http://biomodel.uah.es/en/scale/?lang=es&use=Java