T0216 - Domain 1 Wed Jul 28 16:20:15 PDT 2004 George Shackelford The alignments, sequences, and ehl2 predictions using t2k seem a bit better (or bolder) than t04. I'm going to try mostly t2k by itself. I have added a couple of hairpins and the first two rr constraints along with some rr bonus constraints. I'll see what I get as there doesn't seem to be any template to focus on. I should check to see if this domain seems to 'reflect' the first domain. No, it doesn't seem to. Fri Jul 30 16:35:26 PDT 2004 George Shackelford Try2 has some decent sheets, but I'm going to formalize them. TRY3 started on peep. Fri Jul 30 22:04:48 PDT 2004 George Shackelford Try3 showed some bad twists in it. I set up a third sheet, and adjusted the first two. There is an interesting rr constraint (24-151) but I'm going to wait for the first sheets to settle down. Started TRY4 on peep Sat Jul 31 22:04:48 PDT 2004 George Shackelford Try4 seemed to blow up. I think I'll try the technique of undoing the SheetConstraints and trying to set simple constraints for each end of the strands. Starting TRY5 on peep. Sun Aug 1 21:55:16 PDT 2004 George Shackelford Wow! That worked well. Now I need to sort thru and harden what I like, and perhaps select some new ones. E27 I23 F31 L35 is not good, drop the hbond 170-195?? where did this come from? 67-94?? I'm not buying this one adjusting 55 to 64 and dropping hbond OK, I'm going for two really long strands as a sheet. We'll see... TRY6 running on peep. Mon Aug 2 11:25:16 PDT 2004 George Shackelford The long sheet, V21 A36 - K54 D39, didn't seem to work. It broke at 26-30. I also noted that t04 is better at detecting hairpins; I'm going to unlease them and drop the t2k this time. Reenforcing the long strands... TRY7 running on caw Tue Aug 3 12:01:20 PDT 2004 George Shackelford Try7 fell apart. I'm going to install the t04 constraints in toto but remove the 'bogus' helices that appear to be strands. I'll have to deal with them one by one. Doing a new TRY8 on peep. Tue Aug 3 17:37:35 PDT 2004 George Shackelford Try8 is much better but I need to fix up some of the sheets, reenforcing others, and define new connections. Actually ended up just working on the 21-36,39-57 sheet. Starting TRY9 on peep. Wed Aug 4 16:33:37 PDT 2004 George Shackelford I have discovered that the many.frags file is missing and I am assuming that this affects my results. I am going to try and rerun the build for this directory and get stuff up to date. Fri Aug 6 16:35:26 PDT 2004 George Shackelford I have finally gotten the files rebuilt. I'm redoing try9, and then I can start tackling try10. Fri Aug 6 23:46:14 PDT 2004 George Shackelford The rebuild of try9 looks quite different from the first (in old1-218) but is a bit apart. I have labeled my notes on the strands as: # should these next two be combined? StrandConstraint E20 L26 0.6364 # s1 StrandConstraint F31 A36 0.603 # s2 # should these next two be combined? StrandConstraint D39 A46 3.0 # s3a StrandConstraint N50 K57 3.6225 # s3b StrandConstraint K60 R65 0.6023 # s4 StrandConstraint Y101 Y107 0.8 # s5 ?? HelixConstraint E73 S81 2.6412 HelixConstraint K117 A130 0.6182 StrandConstraint V137 K145 0.8 # s6a-b HelixConstraint P198 L212 0.6601 StrandConstraint V148 N155 0.8 # s6c StrandConstraint D166 A176 0.8 # s7b I am only specifying a few sheets right now. I am trying to find good fits and Kevin has notified me that the domains are probably wrong. I wonder if I'll have to start all over.