Scene authoring tools
The Scene authoring tools are used for the creation and editing of scenes. Scenes created using the Scene authoring tool can then be inserted into Proteopedia pages.
Where are the Scene authoring toolsWhere are the Scene authoring tools
The Scene authoring tools are accessible when you are editing a page. On the edit page, near the top, you'll see a big text area where all the wikitext of the page lives--here you can change the text of the page. If you scroll down some, near the bottom, you'll find in bold letters Scene authoring tools [+/-]. Click on the plus/minus sign to expand and open the Scene authoring tools.
OverviewOverview
The Scene authoring tools are meant to make scene management easier and to make scene creation easier. Scenes are "frozen" moments in Jmol that can be later restored. A scene stores viewpoint, representations, colors, labels, and generally everything that is necessary to recreate the way things looked when the scene was saved.
The steps of using the Scene authoring tools are as follows:
- Either load an existing scene using the 'load scene' tab, or start fresh with the 'load molecule' tab.
- Manipulate the scene view using the mouse. Change the scene appearance by choosing selections from your scene using the 'selections' tab and setting the appearance of selections using the 'representations', 'colors' and 'labels' tabs.
- Save the scene using the 'save scene' tab, and wikitext for inserting the scene into a Protepedia page will be automatically generated.
So the idea is to begin by either loading an existing scene, or by loading a molecule. Once something is loaded onto the Jmol applet, you can begin to change the viewpoint, the representations, the colors, the labels, and other settings, in order to create a scene that conveys your desired message. When you're done creating the scene, you save it and then put it into the page.
'load scene' tab'load scene' tab
The first input box asks for the page name (on which the scene you wish to load resides). The default page name is the name of the page currently being entered. Next, you proceed to choose the scene name using the drop-down selector (all scenes associated with the entered page name will be listed). Once a scene is selected, all of its versions are available for selection using the drop-down version number menu. When a version number is selected, that version of the scene is loaded onto the Jmol applet that is part of the Scene authoring tools and the description that was given to the scene is also recalled. At the same time, the wikitext that is needed for insertion of the scene into the page is displayed.
Each distinct scene has 3 parameters to distinguish it from all other scenes: pagename, scenename, and versionnumber. A scene's "pagename" is automatically determined by the name of the Proteopedia page on which the scene was initially created. The scenename is given by the user. The versionnumber is incremental: If no scene by the given name exists for the given page, then the first version will be version 1. If there exist previous versions of the same scenename on the same pagename, then the newest saved version will not overwrite older versions of the scene, but will instead be automatically saved as the newest version (by incrementing the versionnumber by one). A scene's full name is in this format: Pagename/Scenename/Versionnumber (ex: Hemoglobin/Cavity/14).
'load molecule' tab'load molecule' tab
The load molecule tab is used to load molecules into Jmol. Currently only one file can be loaded into Jmol at a time through this interface (but Jmol can handle several files at a time).
To load a file that has PDB code, input a PDB code into the first input area and click the load button. The file will be fetched from the PDB database throgh OCA.
To load a file that is not part of the PDB, first upload the file to Proteopedia at Special:Upload (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia). Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia upladed file" and click load.
The "currently loaded" text area displays the name of the currently loaded file in the Jmol applet of the "Scene authoring tools".
'selections' tab'selections' tab
The selections tab is meant to be used to select particular groups of atoms so that you can later change that group's color, representations, or labels. When you choose a representation, a color, or a label using the Scene authoring tools other tabs, the change is almost always applied ONLY to the currently selected atoms. That is why it is important to be aware of what atoms are selected at any given time.
selection halosselection halos
To see which atoms are selected, turn 'selection halos' on using the selection halos checkbox. If you have something selected, you will see your selection highlighted by yellow halos. These halos are NOT part of your scene and have no impact other than to indicate to you what atoms are currently selected.
all or nothing and halosall or nothing and halos
This box contains two buttons and a checkbox. 'Select all' selects all atoms. 'Select none' selects none. 'Selection halos' toggles whether selection halos are shown to highlight the current selection.
add to or remove from selectionadd to or remove from selection
This is the main tool for creating selections. This box allows you to specify groups of atoms to either ADD to the current selection, or REMOVE from the current selection. It is advised to either begin with ALL atoms selected and then use this box to REMOVE atoms to your selection to arrive at your desired selection, or alternatively to begin with NO atoms selected and then use this box to ADD atoms to your selection to arrive at your desired selection.
Each input box allows you to specify certain parameters in order to best choose what to add or remove to/from your selection. There is an imaginary 'AND' (or intersection) connecting each input box (a Boolean AND), but an 'OR' (or union) connecting the chosen elements within each input box. What this means is that if you choose in the 'groups' box the items 'all protein' and 'dna' and in the 'limit to elements' box you type in 'C,O' and click "add to selection", then you will add to your selection all the carbon and oxygen atoms that are part of either the protein or the dna in your loaded file (it's like saying "(all protein OR dna) AND (carbon OR oxygen)" )
The 'groups' box lists various pre-defined groups of atoms by name. The 'limit to chains' box allows you to choose specific chains by the names they are given in the loaded file (ex: A,C,D). The 'limit to resi types' allows specification of residues by their 3-letter codes (ex: PHE,ALA,GLY). The 'limit to residue nos' box allows specification of residues by their number (ex: 18,23-25,32). The 'limit to elements' box allows choosing specific elements or even specific isotopes (ex: Fe,2H,31P). The 'limit to atom nos' box allows specifying atoms by their number. The 'sites' box appears only if your file is a PDB file that has predefined sites that the authors defined when they submitted the file to the Protein Data Bank.
Manipulating Jmol with your mouseManipulating Jmol with your mouse
- Rotate: left click
- Zoom: scroll button or left click + shift
- Drag: right click + ctrl
- Measure distance: dbl click on 1st atom, dbl click on 2nd atom
- Measure angle: dbl click on 1st atom, click on 2nd atom, dbl click on 3rd atom
- Measure dihedral angle:' dbl click on 1st atom, click on 2nd and 3rd atoms, dbl click on 4th atom