Wed Jun 30 08:30:28 PDT 2004
T0224

Due 20 Aug 2004


Wed Jun 30 09:23:27 PDT 2004	Kevin Karplus

T0224 looks like a new-fold or distant fold recognition.


Wed Jun 30 18:46:00 PDT 2004	Kevin Karplus

The SAM-T02 server sent an empty alignment for 1cn4A.
I'm going to treat this as a known-bug problem and not try to hand
pick a different alignment.



Sun Aug 15 19:50:59 PDT 2004 Kevin Karplus

No one has done anything on this target for 2 weeks.
I'd better do something with it today!

The try1-opt2 run does not look bad, other than the predicted strand
for G34-L39 being a helix.  The model is not very consistent with the
rr constraints, but the rr constraints are all pretty weak.
I'll reclassify this target as a fold-recognition target.

The t04 prediction has that region as a helix, I should make t04 be
the preferred alignment method for this target.

I'll make extra_alignments to make sure that the top several t04 hits
are included in the alignment set.


Sun Aug 15 21:57:22 PDT 2004 Kevin Karplus

I killed try2 on abyss, since the machine was overloaded.
I'll start it again on a less busy machine (coo).

Also, since the Template.atoms file was already generated, I'll
comment out the printing of it again in try2.under.


Sun Aug 15 23:05:36 PDT 2004 Kevin Karplus

try2 has finished, but it did worse than try1 on the try2 costfcn.
Perhaps it is time to do some polishing with the try2 costfcn, then
again with an unconstrained cost function.


Mon Aug 16 08:16:35 PDT 2004 Kevin Karplus

try3 looks pretty good---about as good as we are likely to get.

I'll submit
	try3-opt2	best unconstrained cost
	try3-opt2.repack-nonPC	best Rosetta energy
	try1-opt2	full auto
	T0224-1jx7A-t04-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5 	best t02 template (3rd with t04)
	T0224-1m6yA-t04-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5 	best t04 template

Thu Nov 18 23:34:38 PST 2004	Martina Koeva

Based on the smooth gdt scores:

best sam-t04
best submit
model1
auto
align
robetta best
robetta1