Help:Copying FirstGlance Scenes into Proteopedia

PDB code makes it easy to obtain certain types of molecular scenes more easily than generating those scenes in Proteopedia's homology model. This page explains how to move those scenes into Proteopedia, attaching them to a green link.

spinqualitylabelsall models Selected contacts between an anti-Alzheimer`s drug analog and acetylcholinesterase in 1gpk. Scene generated largely and quite easily in FirstGlance in Jmol. Atoms shown as balls are within non-covalent bonding distances. Usepopupto see details in this scene! Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Procedure This procedure was improved in July, 2024. 1. View the molecule in FirstGlance. If the molecule has a PDB code, search for the page titled with that PDB code in Proteopedia. At that page, click on the link to FirstGlance beneath the molecule, in the Resources block. Or, simply go to firstglance.jmol.org and enter the PDB code. If the model does not have a PDB code (e.g. a homology model), upload the PDB file at firstglance.jmol.org. If you want to color the protein by evolutionary conservation, there are two methods: It is possible to create a green-linked scene with a molecule colored by evolutionary conservation simply by using the button "evolutionary conservation" in the "color" tab of the Molecular Scene Authoring Tools. However, as explained in Caveats, this pre-calculated color scheme may obscure important parts of the conservation pattern. This is explained at Diversity in the MSA and with an example under Average Pairwise Distance. You can use custom settings at the ConSurf Server to limit the MSA largely to proteins of a single function. Some examples are explained at Interpreting ConSurf Results, and the basic ConSurf Server procedure is at the ConSurf Quick Analysis Procedure. 2. Obtain the desired scene in FirstGlance in Jmol. Turn off spinning (even if you want it to spin in Proteopedia), and orient and zoom the molecule as you want it to appear initially. 3. Right-click (Mac: Ctrl-click) on or near the molecule to open JSmol's menu. Select File, Save script with state. A dialog will appear in which you can choose the location on your computer's disk to save the file (type .spt). Take note of the name of the file and where you are putting it. This file contains a state script of JSmol commands that will produce your scene. 4. Delete the load command. Edit the state script file with a plain text editor. Before you use the state script, you must delete the entire load ... command (at the end of the 3rd block of commands), and then save the .spt file with that change. Delete everything shown below in red: the entire command beginning with "load", deleting everything up until the closing bracket "}" (keeping that closing bracket!). The load command may be long, wrapping onto several lines in your plain text editor. function _setFileState() {   set allowEmbeddedScripts false;   ... blah blah blah ...   set smartAromatic true;   load /*file*/"https://www.rcsb.org/pdb/cgi/export.cgi/1GPK.pdb.gz"; } 5. Edit the page in Proteopedia where you want to install the scene from FirstGlance in Jmol. Show the Scene Authoring Tool. 6. Load your molecule: Use the load molecule tab to load your PDB code (or uploaded molecule) into JSmol in the Scene Authoring Tool. 7. Exit load molecule mode by clicking on, for example, the selections tab. Additional options will appear below the molecule. 8. Drag the edited state script file and drop it into JSmol (where the molecule is displayed). Your scene should appear in a few seconds. 9. Use the save scene tab to save your scene. Follow the instructions there to insert a green link into the page to show your scene. Tweaking the Scene from FirstGlance 1gpk was displayed in FirstGlance in Jmol. Selected contacts were visualized in FirstGlance in Jmol using the Contacts.. and Hide.. dialogs, simply by clicking on controls. The scene was transferred into Proteopedia using the above procedure. Then, in Proteopedia's SAT, the sizes of labels were reduced by clicking select all, then in the labels dialog, reducing the size to 12, changing the color to orange, and changing the offsets to 1 and 1 (all without entering any label text or clicking the set label button). Finally, the drug was labeled.

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See Also

• Help:How to Insert a ConSurf Result Into a Proteopedia Green Link
• Help:How to put a PACUPP scene into Proteopedia
• Copying and pasting scripts

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Eran Hodis