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Tue, 03/06/2012 - 06:31
#2
 
Update 1.0.1
The script now find all the S-S distances and pairs them up, closest pair first, then second, then third. Any pair closer than 3.5 is considered a possible bridge and added to the initial defaults. 3.5 is an arbitrary number, but the bigger the cut off, the more the protein will be distorted if band up the pairs to try to make bonds. The algorithm isn't perfect, if 4 Cys are clumped together, they can pair 3 different ways. It will pick the one with shortest distance.
Sat, 06/16/2012 - 22:33
#3
Update 1.1
* Version 1.1.0 June 16 2012 Brow42 |
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04:09:39 GMT
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![](http://128.95.1.228:8000/tracking_pixel.gif?events=scAdd&f=1111&wdata={"x":12, "y":11}){kind=tracking}
This uses bands-to-space to randomly move the ends of your cysteines around, keeping any improvements in the total disulfide score. This is a random-walk hill-climbing algorithm. The last 2 atoms in each cysteine are randomly banded to space and if the total disulfide score increases, the configuration is saved.
Bands will have random strengths and lengths up to the values you specify. You can also include an unbanded wiggle periodically. Bridge wiggle runs until canceled. You can get the best disulfide scoring configuration from quicksave #3, and the recent best is available the usual way.
Defaults are for CASP Roll 3. This recipe will remove bands. This script will run forever, check the output window to view the progress.
Click 'More' to initially band the cysteines. This bands the SS bond to 2.05, the C-S between cysteines to 2.73 and C-C between cysteines to 3.26 (based on CS bond being 1.8). This arrangement should pull the CS bonds to be 90 degrees to the SS bond, and the two CS bonds also at right angles to each other. This seems to score higher.