Too many rotamers! --- symmetry puzzle

Started by BootsMcGraw

BootsMcGraw Lv 1

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.

BootsMcGraw Lv 1

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 Lv 1

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 Lv 1

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 Lv 1

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

Rav3n_pl Lv 1

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 :)

Tythesly Lv 1

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?