Thu Jul 13 09:18:00 PDT 2006
T0377
Make started Thu Jul 13 09:19:35 PDT 2006
Running on lopez.cse.ucsc.edu

Thu Jul 13 15:36:46 PDT 2006 Kevin Karplus

HMMs get strong hit to 1zpwX and not much else.

BLAST gets strong hit to 2ivyA (100% id), which was released 26 June 2006.

I assume that T0377 will be canceled.

Thu Jul 13 15:53:19 PDT 2006 Kevin Karplus

Interestingly, although 2ivyA was in the dunbrack-pdbaa set, it did
not move to the top of the hit list, because of it not being in the
template libraries.  This may indicate a fairly serious flaw in the
protocol for selecting templates.



Date: Thu, 13 Jul 2006 16:03:58 -0700
From: Kevin Karplus 
Subject: T0377 cancellation


I noticed that T0377 was the same as 2ivyA before the CASP team
announced it.

I'm a little worried about the script for combining HMM results,
because 2ivyA did *not* come out as the first hit (it was third), even
though it was in the dunbrack-pdbaa file.  It isn't in the template
library (yet, anyway), so that may have hurt the scoring.  It only
scored a little better than 1zpwX with the t06 w0.5 HMM, but had a
bigger difference with the t2k w0.5 HMM.  These scores (essentially
the only ones available for 2ivyA) were so strong that it should have
had an excellent e-value in the combined "best-scores" file, but it
got dropped WAY down to e-value 17.  That seems like *much* too large
a penalty for not being in the template library, and certainly not
what I had intended.

I suspect a bug in the part of the script that is supposed to detect
whether a template is in the template library or not.

Kevin
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Make started Thu Jul 13 17:34:40 PDT 2006
Running on cheep.cse.ucsc.edu

I *think* I fixed the bug in the best_scores script (and a couple of
other oversights, while I was at it).  Let's see if it does any better now.

OK, 2ivyA is now second to 1zpwX and only a little behind.  Since
there is a small penalty for not being in the template library (to
favor better templates over antiques), this seems quite reasonable.