Tue Jul 27 11:16:03 PDT 2004
T0252

DUE -- CANCELLED


Wed Jul 28 10:34:46 PDT 2004 Kevin Karplus

Comparative model with 1mkiA as the template, lots of same-superfamily
hits to include if needed.


Thu Jul 29 03:01:19 PDT 2004 Kevin Karplus



The try1 model seems a bit scattered.
T0252 is mainly helical, but there seems to be a hairpin trying to
form around G272.

The rr constraints may be useful on this target.

Wait a sec---there are excellent fold-recognition results in the
undertaker alignments---why did try1 throw them away??
The Hbond cost functions SHOULD have hung onto that sheet!

We probably want to read in only the 1mkiA alignments before do the
TryAllAlign, then read in the rest of the alignments.


MANUAL_TOP_HITS:= 1mkiA 1i2sA 4blmA 1iysA 1iyoA 1ghpA 1hzoA 1alq 1bza 1n9bA 1pioA 1fqgA 1bsg 3blm 1g6aA 1m40A 1ermA 1btl 1bueA 1e25A 1ei5A 1o7eA 1pi4A 1nrfA 1fsyA 1nzoA 1nj4A 1ga0A 2bltA 1rgzA 1l0gA 3pte 1ci9A 1k38A 1mwxA 1pwgA 1mplA 1hvbA 1rgyA 1m6kA
PREFERRED_AL_METHOD:=t04



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 05:23:36 PDT 2004 Kevin Karplus

Redone try1-opt2 looks pretty good, except for exposing I30 and L33.
Repacking with bigger break penalties might help pull it in closer.

rr does not look like it will be very useful.


Thu Sep 23 05:01:58 PDT 2004 Kevin Karplus

Based on smooth_GDT(maxd=10Ang, maxw=5), the order here is 
robetta4 (61.0196), robetta2, robetta3, robetta5, robetta1(59.4619)
try2-opt1 (58.8993),... try2-opt2 (58.7706)

Looking at all-atom RMSD, the robetta4 model is looking very good at
3.4721, followed by robetta5 at 3.6919, and try1-opt1-scwrl at 3.9083.

I think that the smooth_GDT curve is set to emphasize very good fits
too much.


Fri Sep 24 21:47:40 PDT 2004 Kevin Karplus

With the improved smooth_GDT, we get
name			length	missing_atoms	rmsd	rmsd_ca	GDT	smooth_GDT
robetta-model4.pdb.gz	310	 0.0000		 3.4721	 2.8686	-75.2427	-70.0984
robetta-model5.pdb.gz	310	 0.0000		 3.6919	 3.1244	-74.4337	-69.3478
robetta-model3.pdb.gz	310	 0.0000		 6.0423	 5.5189	-74.4337	-69.3070
robetta-model2.pdb.gz	310	 0.0000		 4.2240	 3.6874	-74.7573	-69.3069
robetta-model1.pdb.gz	310	 0.0000		 5.7922	 5.2332	-72.5728	-67.7041
T0252.try1-opt2.pdb.gz	310	 0.0000		 3.9349	 3.3346	-71.8447	-67.0906
T0252.try1-opt2.repack-nonPC	310	0.0000	 3.9873	 3.3346	-71.8447	-67.0906

robetta did better than our full-auto.
Since this was cancelled, we didn't put much effort into it.