New tool: "Force bond"

Case number:845813-987454
Topic:Game: Tools
Opened by:Madde
Opened on:Friday, March 12, 2010 - 17:08
Last modified:Monday, June 27, 2011 - 21:25

1. I'd like to have a tool to force [bondable atom X] to form a bond with [bondable atom Y].
2. For proteins with Cysteines I'd like a tool to force [Cysteine X] to form a disulfide bridge with [Cysteine Y].

(Fri, 03/12/2010 - 17:08  |  2 comments)

infjamc's picture
User offline. Last seen 18 hours 32 min ago. Offline
Joined: 02/20/2009
Groups: Contenders

I second this request. Currently, the bond forcing tool can only be approximated by going into full-atom mode and banding the two specific atoms, with the distance set to a short (but non-zero) value and the band strength set to something very high (if 1.5 isn't enough, then 10 with a recipe would usually do the trick). However, this approach tends to have the side-effect of messing up the rest of the structure...

beta_helix's picture
User offline. Last seen 3 hours 40 min ago. Offline
Joined: 05/09/2008
Groups: None
Type: Suggestion » Suggestion

maybe re-assigning this will get it implemented sooner :-)


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