Plane function for beta sheets

Case number:699969-994868
Opened by:AlexBiohazardous
Opened on:Monday, April 1, 2013 - 17:28
Last modified:Monday, April 1, 2013 - 23:41

There are many puzzles where you are required to bring together sheets to create hydrogen bonds.More often than not,one sheet is not on the same plane with its neighbouring sheet making the bonding very difficult and sometimes impossible.The shifting tool almost always makes things worse.
A tool that aligns two or more sheets to a preffered plane would be a life-saver.

ps:Naturally,the sheets tend to bend a little in the final structure.The tool would be used in the beggining to form the H-bonds.

(Mon, 04/01/2013 - 17:28  |  3 comments)

tamirh's picture
User offline. Last seen 9 years 9 weeks ago. Offline
Joined: 05/11/2012

I'm not sure I understand exactly what this tool would do. Could you explain it a bit more?

To bring sheets together, a combination of bands, tweak, and pulling are generally enough. You can also look at to see some useful ways of straigtening out sheets.

Joined: 08/22/2010
Groups: Go Science

Create a coloured plane and force the sheets you choose to align themselves to the plane.

utaca's picture
User offline. Last seen 2 years 3 weeks ago. Offline
Joined: 01/18/2012
Groups: Void Crushers

An easier way to make bonds between sheets:
1. Freeze the sheets
2. Make cutpoints in the middle of the connecting loops
3. Place the sheets with the purple cross into the order you want them, adjust till the bonds appear.
4. Band the neighbours together, always the aas together which shows in the same direction.
5. disable backbone constraints, shake sidechains and wiggle the sheets together.
6. enable backbone constraints, close the cutpoints and run TvdL DRW on the ugly loops
7. unfreeze the sheets, wiggle, disable bands with key "d" , shake and wiggle and evrything should look nice.

I hope you understand my manual.

Happy folding


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