Scene authoring tools: Difference between revisions
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The '''Scene authoring tools''' are used for the creation and editing of molecular scenes. Scenes created using the ''Scene authoring tool'' can then be inserted into [[Proteopedia]] pages. This is a reference page explaining everything. For a tutorial introduction, see [[Proteopedia:DIY:Scenes|Instructions for creating a molecular scene with Proteopedia's Scene Authoring Tools]], and watch the introductory videos. | The '''Scene authoring tools''' are used for the creation and editing of molecular scenes. Scenes created using the ''Scene authoring tool'' can then be inserted into [[Proteopedia]] pages. This is a reference page explaining everything. For a tutorial introduction, see [[Proteopedia:DIY:Scenes|Instructions for creating a molecular scene with Proteopedia's Scene Authoring Tools]], and watch the introductory videos. | ||
==Where are the ''Scene authoring tools''== | ==Where are the ''Scene authoring tools''== | ||
The ''Scene authoring tools'' are accessible when you are editing a page. Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box 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 [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. | The ''Scene authoring tools'' are accessible when you are editing a page. Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box 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 [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. | ||
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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 (e.g. Hemoglobin/Cavity/14). Current scenes have numerical page names (e.g. 77/778341/Ballstick/1). To find out which page is associated with a scene, create the URL of the script by prepending "proteopedia.org/wiki/scripts/" and appending ".spt". e.g. the scene called 77/778341/Ballstick/1 is stored at [https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt]. | 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 (e.g. Hemoglobin/Cavity/14). Current scenes have numerical page names (e.g. 77/778341/Ballstick/1). To find out which page is associated with a scene, create the URL of the script by prepending "proteopedia.org/wiki/scripts/" and appending ".spt". e.g. the scene called 77/778341/Ballstick/1 is stored at [https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt]. | ||
==Controls under the Jmol window== | |||
These controls are available no matter which tab is open. You can select "ALL" or "NONE" to quickly select all or no atoms. To see which atoms are selected, use the controls next to "Show Selected with Halos". 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. | |||
=='selections' tab== | =='selections' tab== | ||
It is advised that you use selection halos while creating or modifying a selection to make sure your selection is the one you want before you change the scene. | |||
The selections tab is 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. | |||
In the "build your selection" box, you can select by group, sites, chains, residue types, residue numbers and chemical elements. For example, you could select all sulfur atoms in cysteine residues of chain B of the model by entering those specifications. The buttons below determine what happens to the selection you just built. You can use it as your new selection ("replace selection") or you can combine it with the previous selection in different ways ("add to selection", "remove from 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)" ) | 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)" ) | ||
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The button 'add to selection' checks the information that was specified by you in the boxes in the 'add to or remove from selection' area and then adds what you specified into the current selection. The 'remove from selection' does the same, but rather than adding to the current selection, it removes from the current selection. | The button 'add to selection' checks the information that was specified by you in the boxes in the 'add to or remove from selection' area and then adds what you specified into the current selection. The 'remove from selection' does the same, but rather than adding to the current selection, it removes from the current selection. | ||
===invert and center=== | |||
The "invert current selection" button selects everything that was not selected. The "center on current selection" places the center of rotation (when you or the reader of the page changes the orientation of the displayed structure with the mouse, or when spinning is on) on the currently selected atoms. | |||
===select within distance=== | ===select within distance=== | ||
The "select within distance" box allows you to select atoms within a specified distance form the currently selected atoms (these will remain selected). For example, if you had a ligand selected, and then specify a distance of 4 A and hit 'go', then all atoms within 4 Angstroms of that ligand would be added to your selection. Your selection would then be composed of the ligand as well as all atoms within 4 Angstroms of it.It also allows you to expand the selection to entire residues (or more generally "groups", i.e entire ligand, or building block of nucleic acids and carbohydrates). | |||
===mouse click selects=== | ===mouse click selects=== | ||
The "mouse click selects" allows you to change the effect of a mouse click from nothing to centering on the atom, or selecting all atoms of the same chemical elements by clicking on one of them, or selecting an entire group("residue/ligand") or an entire chain by clicking on one atom in it. | |||
Choosing 'default' sets it so that mouse clicks on the Jmol applet are set to their default setting in Jmol. In the default setting, clicking does not select or deselect any atoms, but clicking to create measurements is enabled. Choosing 'center' makes it so that any click on an atom, centers both the view and the axis of rotation on the atom. Choosing 'atom' is perhaps the most useful setting for creating selections as each click on an atom either adds it to the selection, or if it is already part of the selection, removes it from the selection. Choosing 'element' makes it so that clicking on an atom will select all other atoms of the same element. Choosing 'molecule' makes it so that clicking on an atom selects all other atoms of the same molecule. | Choosing 'default' sets it so that mouse clicks on the Jmol applet are set to their default setting in Jmol. In the default setting, clicking does not select or deselect any atoms, but clicking to create measurements is enabled. Choosing 'center' makes it so that any click on an atom, centers both the view and the axis of rotation on the atom. Choosing 'atom' is perhaps the most useful setting for creating selections as each click on an atom either adds it to the selection, or if it is already part of the selection, removes it from the selection. Choosing 'element' makes it so that clicking on an atom will select all other atoms of the same element. Choosing 'molecule' makes it so that clicking on an atom selects all other atoms of the same molecule. | ||
=='representations' tab== | =='representations' tab== | ||
This contains commands to draw selected parts of the structure, using different representations. | |||
===set selection representation== | |||
The 'set selection representation' box provides a variety of choices for setting the representation of the current selection. Multiple representations can be turned on for the same selection of atoms (for instance using both wireframe and spacefill can create a 'ball and stick' scheme). Click on the representations that you would like to turn on for your current selection and then press 'set representation'. Every representation that has been checked off (to the left of the representation's name) will be displayed. Some representations have an input field to their direct right. If they do, then you may enter values in order to change the form of the representation, usually its size. If you leave the input field blank, the default will be used. | The 'set selection representation' box provides a variety of choices for setting the representation of the current selection. Multiple representations can be turned on for the same selection of atoms (for instance using both wireframe and spacefill can create a 'ball and stick' scheme). Click on the representations that you would like to turn on for your current selection and then press 'set representation'. Every representation that has been checked off (to the left of the representation's name) will be displayed. Some representations have an input field to their direct right. If they do, then you may enter values in order to change the form of the representation, usually its size. If you leave the input field blank, the default will be used. | ||
Clicking on 'hide selection' turns off all representations for the selection. | Clicking on 'hide selection' turns off all representations for the selection. | ||
===disulfide and hydrogen bonds=== | |||
This box allows you to choose how (covalent) disulfide bonds and (non-covalent) hydrogen bonds are drawn between the selected atoms. For disulfide bonds, you can use a schematic connecting the C-alpha carbon atoms of the backbone (appropriate when showing a backbone representation such as a cartoon) or the actual bonds between two sulfur atoms (appropriate when showing the side chain atoms, e.g. as ball-and-stick). | |||
=='colors' tab== | =='colors' tab== | ||