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Mon, 01/09/2017 - 00:02
#2
note on line formats for Mac and Linux
I had to kludge a bit to get the line breaks on Windows correct. When pasted into a Foldit textbox on Windows, the lines apparently retain the CRLF format (0x0d0a). The Lua regular expression used to read the pasted lines allows for a carriage return. On Mac and Linux, the pasted lines will probably have just a newline (0x0a). Hopefully, the code allows for this, but it's not been tested on other platforms. Please send a PM if there are problems.
Wed, 01/11/2017 - 20:59
#3
Great
Interesting to define own structure from Escel sheet, with own preferences.
Mon, 05/18/2020 - 16:11
#4
How to get data out of this
I may be missing something, but I can't work out how to save the output from this routine. My computer won't let me select the output in thd text boxes |
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NetSurfP is yet another web-based secondary structure prediction service. (JPred is another.)
NetSurfP outputs its results in a columnar format. The predictions for helix, sheet, and loop are expressed as probabilities.
(NetSurfP also predicts he "surface accessibility" of a given residue, which seem to be more or less the inverse of the likelihood the residue is buried in the hydrophobic core.)
The formatting for the NetSurfP results doesn't lend itself to being pasted directly into a spreadsheet.
This recipe does two things. First, it converts the NetSurfP output to a tab-delimited format that can be pasted into a spreadsheet. Second, it creates a secondary structure string. Both formats can be found in print protein 2.4.
To use this recipe, run a NetSurfP prediction, then copy the output to the clipboard. (It's not necessary to include the comment lines, but you can if you wish.)
Run the recipe, and paste the NetSurfP output into the textbox on the first screen. When you click OK, the secondary screen displays two text boxes, one containing the spreadsheet output, and one containing the secondary structure string.
The secondary structure string is created by picking the secondary structure type with the highest probability for each segment. The picking logic is quite simple, and doesn't worry about ties or close finishes.
This recipe depends heavily on the NetSurfP output format. Any changes to NetSurfP output will require revisions to the recipe.
Sample NetSurfP output: