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Recipe: Contact Cement 1.01
Created by LociOiling 2 1
Your rating: None Average: 4.2 (21 votes)


Name: Contact Cement 1.01
ID: 49061
Created on: Mon, 05/05/2014 - 19:04
Updated on: Thu, 07/17/2014 - 19:23

Checks for contacts with non-zero heat. Displays fun facts about any such contacts found. Bands any contacts above a user-specifed heat cutoff. Version 1.01 includes fixes Bruno Kestemont made in version 2.02

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LociOiling's picture
User offline. Last seen 9 hours 56 min ago. Offline
Joined: 12/27/2012
bands and more

The recipe displays the minimum, maximum, mean, and median heat of the non-zero contacts it finds.

The heat cutoff slider allows you to band any contacts at or above the specified heat. The initial cutoff value is the mean contact heat, which seems to be 1 in the limited testing conducted so far.

The bands created have default length and strength.

If you don't wish to band the contacts, simply click cancel.

The contacts are also listed in the scriptlog in comma-separated value (CSV) format, suitable for import into spreadsheets and such.

Joined: 09/24/2012
Groups: Go Science

This saves a lot of hand folding time !

lincher's picture
User offline. Last seen 6 years 7 weeks ago. Offline
Joined: 02/20/2014
Ideas and Suggestion to this awesome recipe

Thank you for sharing and making this neat and clear recipe.

To further it, it would be nice to see an :
1- Upper threshold for Contacts.
2- Make the bond strength linked to the heat map
3- Only work on certain protein segments at a time

These are my 2 cents.

LociOiling's picture
User offline. Last seen 9 hours 56 min ago. Offline
Joined: 12/27/2012
minor update to original

This version of Contact Cement includes some fixes Bruno Kestemont made in Contact Cement 2.02.

The original version of Contact Cement crashed if all contacts had the same strength. The original version also misreported the median contact heat.

As a banding tool, this version has been made obsolete by recent enhancements to the contact map tool. The contact map tool now allows you to band either all contacts or only empty contacts.

This version of the recipe is still useful, since it prints out a complete list of contacts in comma-delimited (CSV) format. The list can be easily imported into a spreadsheet or another tool for further analysis.

This version is also useful as a simple starting point for more ambitious contact tools.

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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