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Recipe: print protein 2.3
Created by LociOiling 2 1
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Name: print protein 2.3
ID: 102242
Created on: Sat, 11/12/2016 - 02:37
Updated on: Sat, 11/12/2016 - 03:03
Description:

Updated version of "print protein lua2 V0" by marie_s. Version 2.1 includes rulers. Version 2.2 fixes a bug and adds average subscore per segment. Version 2.3 adds density analysis for Electron Density puzzles and makes the main dialog shorter.



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LociOiling's picture
User offline. Last seen 20 hours 30 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
density analysis plus shorter main dialog

Print Protein 2.3 adds analysis of the density component for Electron Density puzzles.

Version 2.3 also has a shorter main dialog, to avoid the problem of a "too tall" dialog on screens with limited vertical resolution. Several less-used options have been relocated to a second dialog accessed via the "More" button on the main dialog.

The density analysis has several sections. The density report appears as a default option on puzzles with a density component.

The first section of density analysis looks at density by amino acid type. Some amino acids outscore others. For example, tyrosine might average a density subscore near 50, but glycine might have average density under 20. The "density by AA" section lists each amino acid found in the puzzle, the number of segments with that AA, the total density score of those segments, and the mean density for that AA. It also lists the worst density score and the corresponding segment number, and best density score and segment number.

The next three sections are similar, but show the density component for "aromatics" (rings) versus non-aromatics, aliphatics versus non-aliphatics, and hydrophobics versus hydrophilics.

Aromatic AAs typically have a much higher density score than non-aromatics. Aliphatics typically score lower than non-aliphatics. Hydrophobics and hydrophilics are close, with hydrophobics typically scoring a bit better.

The aromatics are "f" phenylalanine, "h" histidine, "w" tryptophan, and "y" tyrosine.

For this recipe, aliphatics are "v" valine, "l" leucine, and "i" isoleucine. (Not included: "g" glycine and "a" alanine.)

The first four sections of the density analysis are output in spreadsheet-ready format, similar to the main segment report.

The final section is the "density deviation" report. For each segment, this section shows a "+" if the density subscore is higher than the average for that AA, a "-" if lower, and an "=" if the density subscore is close to the mean.

The density deviation report looks something like this:

"density deviation (above/below mean density by AA)"
1234567890123456789012345678901234567890123456
-++-++-+++-+=+-+---+++=+++++++++++-+----+-=---

The density deviation section is intended to provide a quick indication of which sections are scoring best in terms of density.

The density analysis items are available for copy-and-paste, and can also be retrieved from the scriptlog.

In version 2.3, it appears that the copy-and-paste option for the density analysis interferes with the copy-and-paste for the main report. The source of the problem is not obvious. If you want copy-and-paste for both sections, simply re-run the recipe with the "density analysis" box on the main dialog unchecked to get the full segment-by-segment report. The issue with copy-and-paste will hopefully be resolved in a furture release.

LociOiling's picture
User offline. Last seen 20 hours 30 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
copy-and-paste fixed in 2.4

The new print protein 2.4 fixes the problem with copy-and-paste by presenting the density analysis in a separate dialog. Version 2.4 also corrects the column selection logic, which broke if you selected the "More" button in version 2.3.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons