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Recipe: print protein 2.0
Created by LociOiling 1 1
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Name: print protein 2.0
ID: 101034
Created on: Thu, 05/21/2015 - 05:29
Updated on: Tue, 05/26/2015 - 19:38
Description:

Updated version of "print protein lua2 V0" by marie_s.



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LociOiling's picture
User offline. Last seen 6 hours 41 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
updated classic

This update to "print protein lua2 V0" by marie_s adds some new reports and a dialog with many new options for controlling the output. A new "copy-and-paste" dialog simplifies getting the segment subscore report, the primary sequence, and the secondary structure. As before, detailed information can be found in the recipe's scriptlog.

Thanks to spvincent, Timo van der Laan, and HerobrinesArmy for code and ideas used in this version. Thanks to brgreening for helping to illuminate the mystery of the total score.

ligands and segment count

The recipe first does detailed checking for ligand sections, looking for any segments with a secondary structure code of "M". The recipe calculates the total score for each range of ligands found. For a "normal" ligand, one "M" segment at the end of the protein, the recipe reduces the segment count by one. The recipe issues a warning message to the scriptlog for any other ligands found. The recipe also issues a warning if the "normal" ligand has a non-zero score, but this may in fact be "normal". A current bug is that the "auto structures" tool may incorrectly convert the last segment to a ligand, which inspired these checks.

scoring information

New in this version, the recipe detects active subscores using the logic found in "Tvdl enhanced DRW". In some cases, this logic may suppress certain subscores, such as disulfides, when they have a low total value across all segments. The recipe reports the active subscores in the main dialog and the scriptlog.

The recipe calculates the "filter bonus" by toggling filters off and on, and then checks the total score. In theory, the total score is 8000 points plus the total of all segment subscores, plus the filter bonus. There's is usually a discrepancy, which is reported as "dark" score.

sequence information

As in previous versions, the recipe reports the primary sequence as a string of single-letter amino acid codes, and the secondary structure as a string with "H" for helix, "E" for sheet, and "L" for loop. The recipe also reports hydrophobicity as a string with "i" for if hydrophobic, and "e" if not hydrophobic.

New in this version, the primary sequence and secondary structure are available in the cut-and-paste dialog at the end.

The recipe issues warning messages to the scriptlog if a non-standard amino acid code or secondary structure code is found. The code "x" is substituted for a non-standard amino acid code. (One previous puzzle had a segment with an amino acid code of "unk", which caused problems.)

modifiable sections

New in this version, the recipe reports on modifiable sections, including locked and unlocked sections, zero-score sections, and mutable sections. The "mutable segments" report is now optional.

Some puzzles have locked sections with movable sidechains or locked sections that are mutable. Some recipes incorrectly assume that "locked" means not modifiable in any way. Locked sections with zero subscores are likely the only truly non-modifiable sections.

segment subscore report

New in this version, the main dialog appears before the segment subscore report is produced. Along with reporting other information, the dialog lets you select which subscores are to be included in the report. The hydropathy index (a fixed value based on the AA code), atom count, and rotamer count can optionally be included.

The main dialog lets you select the delimiter character, with the tab character as the default. The number of decimal places reported is also now adjustable.

The segment subscore report is now available in the cut-and-paste dialog, or in the scriptlog as previously. The report now includes a total line reflecting the column totals for the scoring components.

The fixed-width option found in previous versions, for example reporting "12389" instead of "123.89" or "123,89" has been eliminated.

other report sections

The mini contact table and detailed mutable reports are now optional. These are available in the scriptlog only.

cut-and-paste dialog

When you click "OK" in the main dialog, the segment subscore report and other selected reports are produced. The cut-and-paste dialog then appears, with text boxes for the subscore report, and the primary and secondary structures of the protein. These fields can be copied and pasted into a spreadsheet or another tool.

To copy a given field, click in its text box. Then use ctrl+a on Windows or command+a on Mac to "select all". Then use ctrl-c or command-c to copy. The selected text can then be pasted into the tool of your choice.

The use of the tab character as the default delimiter produces more legible scriptlog output (in most tools), and also simplifies pasting data into most spreadsheets, such as Excel and Open Office Calc. At least US English versions, spreadsheets typically recognize the comma-separated value (CSV) format automatically when pasting, and offer the tab character as the default delimiter.

scriptlog

In this version, key outputs, such as the segment score report and the primary and secondary structures, are available through dialogs.

As before, certain outputs, such as the mini-contact table and the detailed mutable report, and available only in the scriptlog.

The scriptlog file has the name "scriptlog.*trackname*.xml" where *trackname* is the current trackname, or "default" for the default track. The scriptlog file is located in the foldit installation folder, for example c:\Foldit in a Windows environment.

Although the scriptlog is nominally an XML file, with XML tags at the beginning and end, the recipe output is normally just plain text. (A few recipes create XML tags in their output, however.) A normal text editor, such as notepad on Windows, can be used to view the scriptlog. In some cases, you may need to manually select a tool to open the "XML" type. For example, in Windows, right-click the scriptlog file and select "Open with", then "Notepad".

Joined: 09/24/2012
Groups: Go Science
excellent!

Thanks, it's very useful.

Joined: 09/24/2012
Groups: Go Science
suggestion / bug

The windows is too long for a laptop 15". Impossible to click on the "ok" button. Could you divide the dialog in 2 ?

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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