Too many rotamers! --- symmetry puzzle

Case number:845813-991061
Topic:Game: Tools
Opened by:BootsMcGraw
Status:Closed
Type:Bug
Opened on:Thursday, November 10, 2011 - 05:59
Last modified:Tuesday, June 5, 2012 - 03:00

While running the classic Acid Tweeker script, the output shows the number of possible positions (rotamers) of each sidechain it manipulates.

When I ran this script on the Symmetry puzzle, amino acid # 14 (lysine) was shown to have 328 possible positions! (See attached photo.)

Now I know that lysine is the contortionist of the sidechains, but I don't think it can bend *that many* ways.

A bug, perhaps, introduced with the newest update? I have never seen this, before tonight.

AttachmentSize
toomanyrotamers.png29.09 KB
(Thu, 11/10/2011 - 05:59  |  9 comments)


beta_helix's picture
User offline. Last seen 2 days 1 hour ago. Offline
Joined: 05/09/2008
Groups: None

assigning...

mimi's picture
User offline. Last seen 27 weeks 5 days ago. Offline
Joined: 11/17/2008
Groups: Contenders

Got a similar thing, 541 positions for a glutamate

Joined: 12/06/2008
Groups: Contenders

It's not just the symmetry puzzles. I have the same thing happening on # 477. The arginine at sidechain # 3 supposedly has 290 positions. Survey says "X!"

Bug bug bug bug.

mimi's picture
User offline. Last seen 27 weeks 5 days ago. Offline
Joined: 11/17/2008
Groups: Contenders

Think it has to do with setting of Shake Accuracy slider
I've has it now with a couple of different puzzles and a couple of different scripts.
With some sidechains I have had over 2000 positions shown in the output

infjamc's picture
User offline. Last seen 1 day 10 hours ago. Offline
Joined: 02/20/2009
Groups: Contenders

Foldit developers:

Please correct me if I'm wrong, but I'm wondering if the shake accuracy setting is related to the "extra rotamers" options in Rosetta? I know from prior first-hand experience working with Rosetta 3.x that hundreds or even thousands of rotamers could be generated for a single residue if a high "extra rotamer" level is used.

(See also: Rosetta's rotamer packing options at http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/opt_packing.html )

spmm's picture
User offline. Last seen 2 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers

GU has reported the same thing on the nanog - a histidine with 109 positions, not sure what his sliders were set to.

Joined: 06/17/2010

max=0
for i=1,get_segment_count() do
n=get_sidechain_snap_count(i)
if n>max then max=n end
end
print(max)

my 480:
shake=0 => 40
shake=1 => 2123
shake=2 => 793
shake=3 => 287
shake=4 => 101

481:
shake=0 => 42
shake=1 => 2433
shake=2 => 869
shake=3 => 309
shake=4 => 113

Looks like setting "1" is a killer :)

Joined: 10/19/2011
Groups: Go Science

what do you think the shake accuracy and wiggle accuracy should be set to when using recipies? I dont think that recipes can manipulate those right?

Joined: 12/06/2008
Groups: Contenders
Status: Open » Closed

A moot point, now that the sliders were taken away from us.

Closing this feedback.

Sitemap

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