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Recipe: tlaloc Contract 3.00
Created by Tlaloc 80 650
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Name: tlaloc Contract 3.00
ID: 2690
Created on: Wed, 06/09/2010 - 17:44
Updated on: Mon, 09/20/2010 - 06:09
Description:

Contracts bands and releases finding points. Works iteritively until there is no improvment. This script bands to center the hydrophobic bands, attempting to pull them in.



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Joined: 09/18/2009
Groups: SETI.Germany
Changes

What are the changes you made?

Tlaloc's picture
User offline. Last seen 10 weeks 2 days ago. Offline
Joined: 08/04/2008
Groups: Mojo Risin'
It depends...

I discovered that if I upload changes that I make to the current version, they replace that version on the server with no notice to anyone who already has it. So different people had different versions of 1.0, without any notification that they were different. I uploaded the 2.0 version to make sure everyone got the current changes. So it depended on when you downloaded the v1.0 version on how much different it is from 2.0.

I had made a lot of minor changes to the code to make it more consistent. I also changed the reporting some. I found a few ways to make things more efficient, such as band_disable() with no arguments disables all the bands, without having to iterate through each band one at a time. This makes the code somewhat faster.

The basic algorithm, though, is the same.

All future uploads will change the version number and be a child of the previous version.

Joined: 09/18/2009
Groups: SETI.Germany
pastebin

Yes, sometimes, it is more efficient no to do some more, but fewer things ;)

As the detection of hydrophobics is not prefect, I use a slight change of your version to add them manually:
http://pastebin.de/7534
This example includes segments 1,2,3,4 and 5 as example to the detected ones.

I'm thinking about changing the script for also excluding segments.

Joined: 09/18/2009
Groups: SETI.Germany
More...

I added the feature to exclude Segments.
This example includes segments 1-5 and excludes 4-10 to show that excluding is dominant:
http://pastebin.de/7536

Joined: 09/18/2009
Groups: SETI.Germany
+

This would help in processing if we can get the information later if a segment is hydrophobic or not.

Joined: 09/18/2009
Groups: SETI.Germany
Check this for puzzle 317!

http://pastebin.de/7539

{1,66,76} forces these segmetns also to be banded,
{75,78} excludes these hydrophilic sidechains.

Change "{1,66,76},{75,78}"to "{},{}" to get normal behaviour, and compare banding.

Joined: 09/18/2009
Groups: SETI.Germany
How to get code

Copy the non-colored code of the link (bottom code) back to fold.it to test it.

Tlaloc's picture
User offline. Last seen 10 weeks 2 days ago. Offline
Joined: 08/04/2008
Groups: Mojo Risin'
Now reliably finds the hydrophobics!

With some additional information from the foldit team, I am now able to reliably tell which segments are hydrophobic (see the separately published tlaloc get_aa() function script).

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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, RosettaCommons