Wed Jul 28 10:21:43 PDT 2004
T0253

DUE 22 Aug 2004


Thu Jul 29 05:19:10 PDT 2004 Kevin Karplus

T0253 looks like a comparative model with 1g2qA (c.61.1.1) as the template.

Thu Jul 29 09:50 PDT 2004 Kevin Karplus

Observation:

The reason (at least a reason) try1 was so messed up was that the
alignment all-align.a2m.gz was not getting properly created before
try1 was run.  I moved try1 to no_align1, and am rerunning try1 after
creating all-align.a2m.gz properly.


Fri Jul 30 05:25:28 PDT 2004 Kevin Karplus

Redone try1-opt2 looks ok, but strand S1 (roughly) L20-D23 is not part
of a sheet, nor is K185-Q190.  In fact, s1 may fit between the two
strands V172-S180 and K185-Q190, but I need to look at the 90-degree
bend that the rest of the sheet is making.

The predicted contacts do not look very consistent, but some of them
seem quite good.


Sun Aug  8 14:12:15 PDT 2004 Kevin Karplus

Haven't looked at this for a while, but I now see that the t04
structure predictions are more consistent with the try1-opt2
structure, so we may not have to do anything drastic to the model, but
just polish it up.

I redid the make and make extra_alignments, so we now have
a t04.many.frag file, which I'll use in try2.


Sat Aug 14 15:10:41 PDT 2004 Kevin Karplus

try2-opt2 scores best with an unconstrained costfcn, but I think that
the N-terminal helix could be a bit better packed---other than that it
looks pretty good.

I'll try a polishing run from the existing models.


Sat Aug 14 21:37:57 PDT 2004 Kevin Karplus

try3 does a bit better than try2, mainly from phobic_fit and break, I think.
try3-opt2.repack-nonPC also has the lowest Rosetta energy.

I'll submit now
	try3-opt2	# lowest unconstrained
	try3-opt2.repack-nonPC	# lowest Rosetta energy
	try1-opt2	# full auto
	T0253-1g2qA-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5
	T0253-1o57A-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5