{"id":253,"date":"2019-09-12T17:06:23","date_gmt":"2019-09-12T17:06:23","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/cellpaint\/?page_id=253"},"modified":"2019-09-12T18:25:17","modified_gmt":"2019-09-12T18:25:17","slug":"cellpaintexo-tutorial","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/cellpaint\/cellpaintexo-tutorial\/","title":{"rendered":"cellPAINTexo Tutorial"},"content":{"rendered":"

Custom Sprites for cellPAINTexo using Mesoscope<\/h2>\n<\/div>

This tutorial will walk you through use of Mesoscope to build custom sprites for use in cellPAINTexo<\/p>\n

cellPAINTexo and Mesoscope are both currently under active development, so please expect some snags as you’re using them.<\/p>\n<\/div>

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Launch a session with Mesoscope, beta version, at http:\/\/mesoscope.scripps.edu\/beta<\/a><\/p>\n

In the “Start Recipe” menu, select New->Empty Recipe<\/p>\n<\/div>

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Add a new compartment to recipe, and two new ingredients.<\/p>\n

You may need to change the size of the graphical representation with the center wheel on your mouse.<\/p>\n

You can also drag elements around on the canvas to change their location. Drag one ingredient inside the compartment, and one on the membrane surrounding the compartment (as shown).<\/p>\n

By default, the whole recipe has the name “root” and the compartment has the name “newCompartment0”. You can change names by right click on the background or in the compartment.<\/p>\n<\/div>

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Now we can specify PDB files for each ingredient. A very simple process is shown here. Mesoscope as many other options that can be used to find and curate your structures.<\/p>\n

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  1. double click in the “pdb” column of the spreadsheet, and type in the PDB ID: 1dgb.<\/li>\n
  2. type a descriptive name in the “name” column: CAT<\/li>\n
  3. if you specify “polymer” in the selection box, it will omit water molecules from the sprite<\/li>\n
  4. orient the molecule using the NGL viewer<\/li>\n
  5. click the “Illustrate” button. After a minute or two, Mesoscope will ask you to save the image file<\/li>\n<\/ol>\n<\/div>
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    Now do the same thing for the membrane-associated ingredient:<\/p>\n

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    1. input 1pv6 in the “pdb” column. Mesoscope will pick up the membrane location from OPM, and show the membrane with a blue and red disk<\/li>\n
    2. change the name to “GLUT1”<\/li>\n
    3. type “polymer” into the select box<\/li>\n
    4. orient the molecule so that the membrane is horizontal<\/li>\n
    5. click “Illustrate” to generate and save the sprite<\/li>\n<\/ol>\n<\/div>
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      You can also use the “coarse illustration” option to create a smoother illustration of the molecule<\/p>\n<\/div>

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      When all molecules are specified and sprites have been illustrated, export the recipe using Export Recipe->cellPACK recipe. This will write a .json file.<\/p>\n<\/div>

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      Put the .json file and all of the sprite .png files in one folder on your computer.<\/p>\n<\/div>

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      Now we’re ready to read the files into cellPAINTexo. You can get the program at\u00a0https:\/\/sourceforge.net\/projects\/cell-paint\/<\/a><\/p>\n

      Use the little folder icon to open the .json file. You’ll need to specify the file type at the bottom of the popup window.<\/p>\n<\/div>

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      You’ll need to click on the little arrow at the top to navigate to the new sprites and compartment. You should find a membrane sprite, and the two new ones.<\/p>\n<\/div>

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      You can change the colors of the sprites by selecting the little magnifying glass, then clicking on a sprite in the image. This will pop up a window with color sliders. You’ll need to start with the saturation (S) slider first.<\/p>\n<\/div>

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