Testing Sidechain Accuracy

Started by auntdeen

auntdeen Lv 1

Since I still can't seem to fold my way out of a paper bag, at thom001's suggestion, I ran the following tests on Sidechain Accuracy, using puzzle 512. Although I have a September client available, it would not load that puzzle.

All testing was done from a reset of 512. Testing was done with Sidechain Flipper v2.2 (global script), stopped after the 6th segment was processed. The tests would strongly suggest that:

1) the current Main client is either not accessing the correct number of rotamers, or is not processing them properly (that score is lowest, other than October client).

2) for use during sidechain improvement scripts, the BSSA & ESSA sliders are apparently worthless - the best setting is, for both, at 1 rather than the defaults.

Although these results are only from the beginning of the script, it is likely that there would be more differences if run to end.

Current Main:
1=6 (improve)
2=1
3=9
4=1
5=20
6=18 (improve)
score = 9867

Current new Beta (run with BSSA & ESSA defaults):
1=10 (improve)
2=1 (says immediate improvement but didn't)
3=9
4=1
5=20
6=18 (improve)
score = 9870

Current new Beta (run with BSSA & ESSA at 1.0):
1=10 (improve)
2=1
3=19
4=1
5=37
6=28 (improve)
score = 9875

Current new Beta (run with BSSA & ESSA at 0):
1=1
2=1
3=1
4=1
5=1
6=1
score = no improvement

Current new Beta (run with BSSA at 1.0 ESSA at 0):
1=10 (improve)
2=1
3=1
4=1
5=1
6=1
score = 9856

Current new Beta (run with BSSA at 0 & ESSA at 1.0):
1=1
2=1
3=19
4=1
5=37
6=28 (improve)
score = 9873

November Beta:
1=6 (improve)
2=1 (says immediate improvement but didn't)
5=9
4=1
5=20
6=18 (improve)
score = 9873

October Beta:
1=6 (improve)
2=1
3=9
4=1
5=20,
6=19 (improve)
score = 9858

auntdeen Lv 1

To make it a bit more clear for anyone who has not been staring at these results all morning…

The sequential numbers are the segment numbers the script was analyzing, and working on for improvement - the number after that is the number of rotamers found to work with.

So "6=19" is segment 6 - 19 rotamers found.

phi16 Lv 1

You've lost me beta. I'd love to help but I don't understand how. Which starting model? Model of what? Which scripts? Any? OK. Which clients? How can I identify which client I'm using? How would you know? Is there a client ID# somewhere?

krulon Lv 1

Running the latest Beta for the past couple of days….acid tweeker v1.3 seems to have been reporting more sidechain positions than I thought were possible:

Below is from some scriptlogs

Puzzle 508
Sgmnt: 8 positions: 95
Sgmnt: 36 positions: 83

Puzzle 510
Sgmnt: 12 positions: 64

I can not find a scriptlog, but the other day I stopped acid tweeker because it was on a segment that had over 100 positions.

Rav3n_pl Lv 1

Cant enter this contest using "old" main clients:
6522e6aa85e1b44433d58aff6c06017f
07e7a001798eb97fd84dd779e2b9fb3a
(binary version)

krulon Lv 1

I went back to Puzzle 510b and ran acid tweeker v1.3 set to run just the sidechain_manipulate() function with the "guts" commented out. This modified script only reports the number of sidechains. Then I moved the sliders for wiggle accuracy and shake accuracy. Setting the shake accuracy to 1 made the script report more sidechain positions.. I think the Shake Accuracy function is not working properly

		Shake Acc = 0	Shake Acc =1	 Sgmnt:	2	positions:	13	37	 Sgmnt:	3	positions:	3	3	 Sgmnt:	4	positions:	5	13	 Sgmnt:	5	positions:	17	17	 Sgmnt:	6	positions:	5	13	 Sgmnt:	7	positions:	15	43	 Sgmnt:	8	positions:	10	28	 Sgmnt:	10	positions:	7	19	 Sgmnt:	11	positions:	8	8	 Sgmnt:	12	positions:	29	75	 Sgmnt:	14	positions:	17	49	 Sgmnt:	15	positions:	7	19	 Sgmnt:	16	positions:	5	13	 Sgmnt:	17	positions:	5	5	 Sgmnt:	18	positions:	10	28	 Sgmnt:	19	positions:	25	25	 Sgmnt:	20	positions:	4	4	 Sgmnt:	22	positions:	10	10	

kenjung Lv 1

Shake accuracy may not be the best name for the option, but the behavior is intended.

The real label would be "Add extra rotamers up to the Xth C-C bond* of every side chain". For example, alanine has only one C-C bond (the first one coming out from the backbone) whereas leucine has 2 C-C bonds (the last C-CH3 bond doesn't count).

So if you change ShAcc to 1, then alanine and leucine will both get extra rotamers that have more unusual positions around the first C-C bond.

If you change ShAcc to 2, then alanine and leucine will both get extra rotamers around the first C-C bond (because ShAcc 2 implies ShAcc 1), and leucine will get extra rotamers around the second C-C bond, but not alanine, because it doesn't have a second C-C bond.

Extra rotamers are generally beneficial. In the Baker lab, the default setting we use is ShAcc 2.

  • The real term for this is Chi angle, and it refers to the dihedral angle around each C-C bond in the amino acid. Chi angles are typically numbered from 1-4, where 1 is the closest to the backbone.