{"id":353,"date":"2020-11-21T15:24:44","date_gmt":"2020-11-21T15:24:44","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/cellpaint\/?page_id=353"},"modified":"2021-04-02T17:15:58","modified_gmt":"2021-04-02T17:15:58","slug":"cellpaint2-documentation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/cellpaint\/cellpaint2-documentation\/","title":{"rendered":"CellPAINT-2.0 Documentation"},"content":{"rendered":"

CellPAINT 2.0 — Documentation<\/h3><\/h1><\/div>
Download CellPAINT-2.0 at SourceForge<\/span><\/a><\/div>
Use CellPAINT-2.0 on the WWW<\/span><\/a><\/div>
<\/div>
<\/div><\/div>
<\/div>

Frequently-Asked Questions<\/strong><\/h3>\n<\/div>

<\/i><\/i><\/span>How do I open cellPAINT 2.0 on my Mac?<\/span><\/a><\/h4><\/div>
\n

Possible issues opening cellPAINT 2.0 on Mac.<\/span><\/p>\n

Problem 1:<\/b> \u00a0 \u00a0 <\/span>\u201cCannot open app from unidentified developer.\u201d<\/span><\/i><\/p>\n

This problem originates from our app not being signed through the mac gatekeeper yet. Rest assured our app is safe.<\/span><\/p>\n

Solution:<\/b><\/p>\n

Step 1:\u00a0 \u00a0 \u00a0 <\/b>Navigate to or search for the “Terminal” and open it<\/span><\/p>\n

Step 2: \u00a0 \u00a0 <\/b>In the prompt enter: <\/span>chmod +x (drag cellPAINT here)\/Contents\/MacOS\/*<\/span><\/p>\n

Step 3: \u00a0 \u00a0 <\/b>Delete \u201c<\/span>(drag cellPAINT here)\u201d<\/span><\/p>\n

Step 4: \u00a0 \u00a0 <\/b>Drag the cellPAINT app into the terminal where \u201ccellPAINT here\u201d was<\/span><\/p>\n

Step 5: \u00a0 \u00a0 <\/b>Hit enter and run the program normally.<\/span><\/p>\n

Problem 2:<\/b> \u00a0 \u00a0 <\/span>\u201c<\/span><\/i>You do not have permission to open the application.\u201d<\/span><\/i><\/p>\n

This problem seems to be exclusive to users using the new Big Sur OS.<\/span><\/p>\n

Solution:<\/b><\/p>\n

Step 1: \u00a0 \u00a0 <\/b>Navigate to or search for the “Terminal” and open it.<\/span><\/p>\n

Step 2:\u00a0 \u00a0 <\/b>Enter this command into the prompt: sudo chmod -R 755<\/span><\/p>\n

Step 3:\u00a0 \u00a0 <\/b>Drag the cellPAINT app into the terminal after the 775<\/span><\/p>\n

Step 4:<\/b>\u00a0 \u00a0 <\/span>A path should appear after the “775”<\/span><\/p>\n

Step 5:<\/b> \u00a0 \u00a0 Verify there is a space between \u201c775\u201d and the path.<\/span><\/p>\n

Step 6:<\/b> \u00a0 \u00a0 <\/b>Hit enter and run the program normally.<\/span><\/p>\n<\/div><\/div><\/div>

<\/i><\/i><\/span>Can I import non-PDB coordinate files?<\/span><\/a><\/h4><\/div>
\n

Many people are asking to import non-PDB coordinate files.<\/strong> This is not currently implemented but is on our to-do list. For now, you can generate images with any software\u00a0and import them using the \u201cBrowse Image\u201d in \u201cCreate Ingredient.\u201d To be consistent with the other molecules in CellPAINT, be sure to create these at a scale of 6 pixels\/A.<\/p>\n

Here’s how to do it with our program\u00a0Illustrate.<\/a><\/p>\n

Go to the web version of illustrate <\/a>and (1) choose your coordinate file, (2) set the scale to 6 pixels\/A (important!!!), (3) (optional) choose a style, (4) pick a view using the NGL window, (5) click “ILLUSTRATE”, and (6) save the image (drag to a folder or right click and save).<\/p>\n

\"\"<\/p>\n

Then go to CellPAINT and click the little “+” icon at the top. This opens the “CREATE INGREDIENT” window. (1) Choose “BROWSE IMAGE” to find the picture, (2) pick what type of molecule it is, (3) set the scale to 6 pixels\/A (important!!!), (4) change the rotation and offset if needed, and (5) click “CREATE INGREDIENT.” It should show up in your current palette, and you can start drawing!<\/p>\n

\"\"<\/p>\n<\/div><\/div><\/div><\/div><\/div>

If you are still having problems, please visit\u00a0“Tickets” at the CellPAINT SoureForge page<\/a> to report a problem.<\/b><\/h4>\n<\/div>
<\/div>
<\/div><\/div>
<\/div>
<\/div><\/div><\/div><\/div><\/div>

This quick start video covers some of the basic functions of the program as well as some more advanced features:<\/span><\/strong><\/p>\n

0:00 Introduction to cellPAINT-2.0<\/span><\/p>\n

1:19 Basic Tools<\/span><\/p>\n

7:15 Advanced Features<\/span><\/p>\n

16:32 Background Images<\/span><\/p>\n

18:58 Custom Ingredients<\/span><\/p>\n<\/div>

<\/div><\/div><\/div>