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Recipe: Band All Contacts Adaptive v2.3
Created by LociOiling 2 1
Your rating: None Average: 4.4 (46 votes)


Name: Band All Contacts Adaptive v2.3
ID: 102063
Created on: Wed, 05/18/2016 - 13:15
Updated on: Wed, 05/18/2016 - 20:57

Places a band wherever there is a green dot on the contact map with weight greater than a chosen minimum; min weight of 0 bands all contacts. Dialog lets you set band length and strength based on whether the contact is currently made or not. Option to band beta carbons. V2.3 adds options to set band strength based on contact weight and only band beta carbons of hydrophobes merged from Madde's v2.2m. Options to not band structure to itself and not band parallel to structure adapted from Spvincent's Helix Rebuild and Local Quake.

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LociOiling's picture
User offline. Last seen 6 hours 3 min ago. Offline
Joined: 12/27/2012
Merges BACA v2.2 and v2.2m, Band Pruner v0.2, and more

Version 2.3 of Band All Contacts Adaptive merges Susume's Band Pruner v0.2 and Madde's BACA v2.2m with Susume's BACA v2.2. Some functions from Contact Cement 3.0 and Local Quake 5.0 (NC) are also included.

The main dialog has been streamlined a bit to hopefully make it usable on smaller screens.

For both made and unmade contacts, the sliders and checkboxes specify which contacts should be banded, and how they should be banded.

The "Min. Weight" slider specifies the minimum contact weight (or heat) for banding.

The "Dist. Multiplier" slider is used to set the goal length of the bands. The goal length is the bands initial length times the distance multiplier setting. A distance multiplier over 1.0 makes "push" bands.

The "Strength" slider sets the strength of the bands. If the "set strengths according to weights" option is checked, the value of the strength slider is multiplied by the contact's weight to get the band strength.

The "band beta carbons" and "band beta carbons (phobics only)" options band the beta carbon (generally atom 5) instead of the default alpha carbon (atom 2). The beta carbon is the first "elbow" of the sidechain, except for glycine, which has only a hydrogen there. (Poor glycine.) Banding beta carbons may allow things to pivot more easily.

The new "exclusions" section further restricts which contacts get banded. The exclusions apply to both made and unmade contacts.

The two "skip distances" options are taken from Band Pruner v0.2. The corresponding sliders let you set minimum and maximum distances for banding.

The exclusions section also includes two new options. The logic behind these options was adapted from spvincent's Helix Rebuild and Local Quake recipes. These options both depend on a secondary structure that is not all loop.

The "don't band structure to itself" option eliminates bands on the same secondary structure. For example, is segments 2 through 18 form a helix, the recipe won't band any contacts in this range if the option is checked. This option applies to helix, sheet, and loops.

The option "don't band parallel to structure" applies to helixes and sheets, and eliminates bands that are more than +/- 30 degrees from perpendicular to a structure.

Version 2.3 uses the contact scanning logic from Contact Cement to build a table of contact information. The recipe now reports contact statistics to the scriptlog. Lua fans will enjoy the new table-based hydrophobe check. Banding is done based on the contact table.

The "Print contact report" option dumps the contact table information to the scriptlog and a dialog window. The text box in the dialog window can be copied and pasted into a spreadsheet, as in Print Protein 2.0. Thanks to Herobrine's Army to the idea.

The spreadsheet includes banding information, such as whether the contact was banded, the goal length and strength of the band, and the atoms banded. This information is included mainly for debugging purposes.

The "distance" column in the table is the result of structure.GetDistance for the segments in question. Previous testing has shown that this value is the same as length returned for a band.AddBetweenSegments band using the default atoms (which bands alpha carbons). If the beta carbon banding options are used, the length of the initial band will be slightly different.

Thanks for Susume, Madde, spvincent, Bruno Kestemont, and Herobrine's Army for ideas and code. The initial suggestion to merge BACA and Band Pruner came from retiredmichael. Things kind of got out of hand after that.

Joined: 09/24/2012
Groups: Go Science

Thanks Loci.
A suggestion: when an unmade contact is shorter than 7, I think it would be better to set band length bigger than current length (not even smaller as default).

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

Optional set default goal length to minimum 4 for unmade contacts. Current 0 has the risk of crushing too much after contact is achieved (which would give a bonus for unrealistic contacts).

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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, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons