Wed Jun  7 16:58:33 2006

split-into-domains created subdirectory for N210-N306 of T0320

Make started Wed Jun  7 17:00:35 PDT 2006
Running on farm09.cse.ucsc.edu

Sat Jun 24 16:12:44 PDT 2006 Firas Khatib

so try2 scores best, followed by try3 and try4 (but none of them score THAT
much better than try1)

looking at try2 it was not able to use all the constraints.
For example, I put in:

HelixConstraint 	L216	P232	0.6

and this became a strand. (presumably so that it could pair up with:
 StrandConstraint	L245	F255	0.6)

I like the helix in try3 (from D258-N286) so I will increase that constraint 
from 0.7 to 0.9

I have taken try2 and increased the constraints to 50 (from 20) and the weights
to:
HelixConstraint 	D258	N286	0.9
HelixConstraint 	S265	K277	0.9
HelixConstraint 	L216	P232	0.7
StrandConstraint	L245	F255	0.6
HelixConstraint 	T297	R300	0.6498

try5 is running on lopez.

in try3 I like the way that Y288-Y292 could form a strand with L245-F255
I will try a similar run to try2 but with those 2 strand constraints higher
and if see if they connect, otherwise I will add h-bond constraints to bring
those 2 potential sheets together.

this will be try6 on lopez with the increased constraints from 20 to 50

HelixConstraint 	D258	N286	0.9
HelixConstraint 	S265	K277	1.0
HelixConstraint 	L216	P232	0.6
StrandConstraint	L245	F255	0.9
HelixConstraint 	T297	R300	0.6498
StrandConstraint	Y288	V294	0.9

I don't like try4 except the final helix from N286-R300, in future I think I
will increase that constraint

Mon Jun 26 11:49:36 PDT 2006 Pinal Kanabar

starting with try5, we did not like the breaks in the chain so we increased
BREAKS from 50 to 80. We also increased CONSTRAINTS from 50 to 80 and got rid
of an overlapping constraint (265-277) and added a strand constraint:

StrandConstraint      P234    F255    because it seemed like 234-244 could
create a sheet with 245-255... we'll see if that works.

We also added: StrandConstraint      Y288    V294 because we liked it in try3
and it seemed to work well in try6 (but the rest of try6 did not score well)
so we will see how this does in try7 (running on camano)


for try8 : we wanted to keep the try6 model and make just 1 change:
 HelixConstraint       D258    K277    1.0  
We kept everthing same except that we removed the overlaping constraint.
try8 is running on lopez.

Mon Jun 26 12:18:01 PDT 2006 Firas Khatib

so try7 was awful, we have increased the try7 constraints from:

 StrandConstraint      P234    F255    6
 StrandConstraint      Y288    V294    6

 StrandConstraint      P234    F255    10
 StrandConstraint      Y288    V294    8

hopefully this will help. try9 is running on orcas