Mon Jun 21 08:38:58 PDT 2004 T0209 DUE DATE? Mon Jun 21 09:19:36 PDT 2004 Kevin Karplus Neither t2k nor t04 get obvious hits with w0.5, but both favor 1b87A and 1n71A (d.108.1.1). These are not the top scorers with the 3-track HMM, so this looks like it may be a hard fold-recognition target, or even ab initio. None of the 2-track methods is getting a strong hit, and they disagree about what the weak hits are. Mon Jun 21 12:10:04 PDT 2004 Kevin Karplus This looks like hard fold recognition or new-fold. The best hits are getting e-values > 17, so are likely spurious. There may be a super-secondary matck to domain d.117.1.1, but with e-values of 37 or more, the hits are quite dubious. A 239-long new-fold predictions is likely to be hard. Mon Jun 21 13:09:46 PDT 2004 Kevin Karplus try1 finished, and essentially no beta structure was formed. I'll run try2 with more alignments and with lots of very conjectural constraints from the mutual-information predictions. Let's see if anything forms now. Mon Jun 21 17:29:05 PDT 2004 Kevin Karplus On try2, T0209 still looks like spaghetti. It looks like we'll have to turn off the mutual-information constraints and (painfully) assemble the sheets by hand. Tue Jun 22 15:47:45 PDT 2004 Kevin Karplus On the Robetta web site: http://robetta.bakerlab.org/results.jsp?id=1243&p=1 T0209 looks like a 2-domain protein with a split (somewhere between 140 and 160). Sat Jul 3 23:49:10 PDT 2004 Kevin Karplus For try3, I put in strong constraints for the strands and helices and took the strongest of the distance constraints from mutual information. With just the try1 and try2 runs done, the best-scoring model using try3.costfcn so far is robetta-model1, which has formed some fairly good anti-parallel sheets. Hmm, robetta-model8 also scores well, and its sheets look good too, except for the hairpin formed out of the N-terminal strand. I'll steal those sheet constraints for try4. Sun Jul 4 00:27:16 PDT 2004 Kevin Karplus When try3 and try4 are done, we should look to see if they have formed any sheets, then look at the burial, near, and conserved_t2k/t04 colorings, to see if we want to flip any strands over, adding sheet constraints to get pairings we like better. One thing we'll also have to decide is whether E215 and F216 are in the middle of a long strand or are in a turn. The different neural nets disagree somewhat on this. Sun Jul 4 15:19:05 PDT 2004 Kevin Karplus try3 looks like it was trying to form a single long sheet (a half barrel), while try4 just looks like a mess. I think that we may want to do further work starting from the sheet constraints of try3, though some things may need to be tweaked. Mon Jul 5 11:59:49 PDT 2004 Kevin Karplus The try5 optimization seems to have created a mess. Let's try the try3 sheet constraints without tweaking, and drop the mi constraints. Tue Jul 6 08:13:55 PDT 2004 Kevin Karplus Try6 is also a bit of a mess, though there is a beta sheet (with breaks and the ends of the strands). I think that this one will take patient assembly of lots of alternative sheets. Tue Jul 6 16:54:54 PDT 2004 Kevin Karplus Looking at the possible templates, it may be that 1kgiA (Transthyretin (synonym: prealbumin)) beta sandwich; 7 strands in 2 sheets, greek-key, maybe the appropriate template. Since it isn't in our template library, I'll add all the b.3.4.1 templates that ARE in t04.ids or t2k.ids and alignments for them. I added them by editing Makefile to add MANUAL_TOP_HITS, then running make extra_alignments, make read_alignments, and make all-align* This may help us get a better model even without sheet constraints. For try7.costfcn, I removed all sheet constraints, and replaced the "include" constraints with a consensus of the the files that were included ("grep Helix *.constraints" to get helix constraints, add a space after the first amino acid letter, sort on the residue number, manually merge overlapping predictions, eliminate lone predictions, take the extra space back out---do the same for strands). Wed Jul 7 08:08:36 PDT 2004 Kevin Karplus I don't really like try7, though it scores well with the try7 cost fcn. Several of the predicted strands have been folded in the middle, and predicted other structure turned into strands. Thu Jul 8 02:58:56 PDT 2004 Kevin Karplus try8 is scattered, but has some good pieces of sheets. Let's pick up (and extend) the sheet constraints from it, except for the I60 pairing with A90, which I don't really like. Thu Jul 8 20:45:11 PDT 2004 Kevin Karplus try9-opt1 gets some of the strand pairing almost ok, but hasn't formed the hbonds, which suggests that the constraints may not be consistent. The opt2 part of the run is taking much too long---I should probably modify the optimization commands to take less time on the second half of the run---perhaps trying more options in the first half instead. Sat Jul 10 12:03:07 PDT 2004 Kevin Karplus try9 and try10 had some almost-formed sheets that looked promising, so I added them to the sheet constraints for try11, and did a short run, which did not pick them up, but liked the try8-style sheet. I'm doing another short run starting from the models rather than the alignments, to see if crossover can pick anything up. Sat Jul 10 14:27:04 PDT 2004 Kevin Karplus try12 seems to be doing only minor polishing on try11---the cost is not being reduced much and the breaks are only slightly reduced. For try13, I'll try a hand assembly of the strands, based on what I see in try10 and try11. Sat Jul 10 21:28:13 PDT 2004 Kevin Karplus Foo! the try12 run stepped on the try11 results. I was really careless today! Luckily, I can restore them from my laptop. I'm not very impressed with either try12 or try13. Try13 seems to be trying pretty hard to get the strand order I specified, but it also seems to be pretty much wrong. I rather like robetta-model1.pdb for R180-K239, if you accept a turn near E215 and G101-K136 is not bad. robetta-model4 also does a nice job of L100-I139. robetta-model5 comes very close to forming a barrel or sandwich in the N-terminal domain. We just need to make G87-S91 antiparallel to V105-V100 (or thereabouts) and parallel to L4-I12. Or maybe it goes on the other side.... I'll try a robetta-like set of strand constraints for try14. For try15, I'll use the same cost function, but start from existing models. Sun Jul 11 07:44:51 PDT 2004 Kevin Karplus Both try14 and try15 score better than the robetta model5 that was the prvious best with this cost function. Try14 is a bit of a mess, but try15 looks ok---still a lot like robetta5. Let's try two directions for improvement: a 2-domain split at Y141 and twiddling with th strand pairing in the N-domain. When we're done, we'll probably want to submit both the 2-domain prediction and the best of the long-strand predictions. I've started subdirectories 1-140 and 141-end. I don't hold out great hopes for them finding anything, but it doesn't hurt to try. I'd like to try to make the N-terminal domain into a beta sandwich--- perhaps with F89 facing I132 and S91 facing T130. Sun Jul 11 10:00:02 PDT 2004 Kevin Karplus The 1-140 fold recognition matches aren't getting anything good. The top few hits have most of the predicted strands wound up into helices. Maybe try1 will find something, but I doubt it. The 141-end domain is also not finding any good scores, and the lowest costs seem to be different in different searches---indicating that they are just the expected tail of the random distribution, as the E-values already imply. So it looks like splitting into domains for this target isn't going to help. I'll look at the try1 results when they are done, but am not counting on them doing anything. That leaves me trying to design a strand order by hand. The try15 run really didn't do much to the robetta5 model. I suspect that continuous backbones are still too hard for undertaker to break and remodel. There are a few breaks introduced in try15, but not much remodeling, other than moving the domains relative to each other. There is some close of the big hole in the first domain, but no rearrangement of the strands. Looking at the second part (Y141-end) by itself, none of the predictions look great. I think we have a choice of going with something like robetta5 (say the try15 model) or a long hairpin and long helix (something like try8-opt2, though that hairpin needs to be shifted by 1, to pair L213 and I235, F216 and V232. The turn pairing K223 and T226 is good though, so there would need to be a bulge to get the shift of 1. We also might want to constrain I187 to be near L213, to get the helix to pack against the hairpin. Actually, a cut-and paste of the try8-opt2 C-terminus with the try15-opt2 Nterminus looks feasible---pairing F133-P137 antiparallel to W220-F216. I could do a cut-and-paste to make an initial model. For try16, I picked up the sheet constraints from try15 and try8, added the strand pairing F133-P137 antiparallel to W220-F216, and a distance constraint for I187+L213. The try15-try8 chimera scores best, so will be the model that gets tweaked in this optimization. If the result looks any good, I'll try fixing up the N-terminal domain some more. Sun Jul 11 12:49:57 PDT 2004 Kevin Karplus The 1-140 subdomain did not get anything useful on try1. Sun Jul 11 14:13:38 PDT 2004 Here are our collected 2ry structure predictions: HelixConstraint P45 R49 0.704 # T0209.t04.bys.constraints HelixConstraint P45 R49 0.722 # T0209.t04.dssp-ebghstl.constraints HelixConstraint P45 R49 0.7239 # T0209.t04.dssp-ehl2.constraints HelixConstraint P45 R49 0.781 # T0209.t04.str2.constraints HelixConstraint P45 A47 0.688 # T0209.t2k.alpha.constraints HelixConstraint P45 R49 0.74 # T0209.t2k.bys.constraints HelixConstraint P45 V48 0.633 # T0209.t2k.dssp-ebghstl.constraints HelixConstraint P45 R49 0.6373 # T0209.t2k.dssp-ehl2.constraints HelixConstraint P45 R49 0.764 # T0209.t2k.str2.constraints HelixConstraint P45 R49 0.746 # 1-140/T0209.t04.bys.constraints HelixConstraint P45 R49 0.707 # 1-140/T0209.t04.dssp-ebghstl.constraints HelixConstraint P45 R49 0.6822 # 1-140/T0209.t04.dssp-ehl2.constraints HelixConstraint P45 R49 0.629 # 1-140/T0209.t04.str2.constraints HelixConstraint P45 A47 0.618 # 1-140/T0209.t2k.alpha.constraints HelixConstraint P45 R49 0.734 # 1-140/T0209.t2k.bys.constraints HelixConstraint P45 R49 0.633 # 1-140/T0209.t2k.dssp-ehl2.constraints HelixConstraint P45 R49 0.747 # 1-140/T0209.t2k.str2.constraints HelixConstraint E46 R49 0.774 # T0209.t04.alpha.constraints HelixConstraint E46 R49 0.74 # 1-140/T0209.t04.alpha.constraints HelixConstraint E46 V48 0.616 # 1-140/T0209.t2k.dssp-ebghstl.constraints HelixConstraint L51 E52 0.691 # T0209.t04.bys.constraints HelixConstraint L51 E52 0.662 # T0209.t2k.bys.constraints HelixConstraint L51 E52 0.664 # 1-140/T0209.t04.bys.constraints HelixConstraint Q149 E155 0.605 # 141-end/T0209.t04.bys.constraints HelixConstraint S150 E155 0.612 # T0209.t04.bys.constraints HelixConstraint S150 E155 0.61 # T0209.t2k.bys.constraints HelixConstraint S151 A153 0.615 # T0209.t04.alpha.constraints HelixConstraint S151 Q154 0.6094 # T0209.t04.dssp-ehl2.constraints HelixConstraint S151 A153 0.616 # 141-end/T0209.t04.alpha.constraints HelixConstraint F152 Q154 0.604 # T0209.t04.dssp-ebghstl.constraints HelixConstraint F152 Q154 0.712 # 141-end/T0209.t2k.bys.constraints HelixConstraint E167 R176 0.682 # T0209.t04.alpha.constraints HelixConstraint E167 E178 0.859 # T0209.t04.bys.constraints HelixConstraint E167 E178 0.672 # T0209.t04.dssp-ebghstl.constraints HelixConstraint E167 E178 0.7162 # T0209.t04.dssp-ehl2.constraints HelixConstraint E167 E177 0.701 # T0209.t04.str2.constraints HelixConstraint E167 K179 0.66 # T0209.t04.stride-ebghtl.constraints HelixConstraint E167 E177 0.7 # T0209.t2k.alpha.constraints HelixConstraint E167 E178 0.828 # T0209.t2k.bys.constraints HelixConstraint E167 E177 0.711 # T0209.t2k.dssp-ebghstl.constraints HelixConstraint E167 E178 0.6617 # T0209.t2k.dssp-ehl2.constraints HelixConstraint E167 E178 0.676 # T0209.t2k.str2.constraints HelixConstraint E167 E178 0.734 # T0209.t2k.stride-ebghtl.constraints HelixConstraint E167 R176 0.742 # 141-end/T0209.t04.alpha.constraints HelixConstraint E167 E178 0.727 # 141-end/T0209.t04.bys.constraints HelixConstraint E167 E177 0.602 # 141-end/T0209.t04.dssp-ebghstl.constraints HelixConstraint E167 E178 0.6105 # 141-end/T0209.t04.dssp-ehl2.constraints HelixConstraint E167 E177 0.623 # 141-end/T0209.t04.str2.constraints HelixConstraint E167 E178 0.656 # 141-end/T0209.t04.stride-ebghtl.constraints HelixConstraint E167 K175 0.639 # 141-end/T0209.t2k.alpha.constraints HelixConstraint E167 E178 0.648 # 141-end/T0209.t2k.bys.constraints HelixConstraint E167 E177 0.695 # 141-end/T0209.t2k.dssp-ebghstl.constraints HelixConstraint E167 E177 0.7046 # 141-end/T0209.t2k.dssp-ehl2.constraints HelixConstraint E167 E177 0.636 # 141-end/T0209.t2k.str2.constraints HelixConstraint E167 E177 0.715 # 141-end/T0209.t2k.stride-ebghtl.constraints HelixConstraint R180 E192 0.648 # T0209.t2k.str2.constraints HelixConstraint P181 Q193 0.634 # T0209.t04.stride-ebghtl.constraints HelixConstraint P181 E192 0.635 # T0209.t2k.alpha.constraints HelixConstraint P181 E192 0.915 # T0209.t2k.bys.constraints HelixConstraint P181 Q193 0.706 # T0209.t2k.dssp-ebghstl.constraints HelixConstraint P181 E192 0.78 # T0209.t2k.dssp-ehl2.constraints HelixConstraint P181 Q193 0.611 # T0209.t2k.stride-ebghtl.constraints HelixConstraint P181 E192 0.618 # 141-end/T0209.t04.bys.constraints HelixConstraint P181 P195 0.612 # 141-end/T0209.t04.stride-ebghtl.constraints HelixConstraint P181 E192 0.708 # 141-end/T0209.t2k.bys.constraints HelixConstraint H182 Q193 0.648 # T0209.t04.dssp-ehl2.constraints HelixConstraint H182 Q193 0.681 # T0209.t04.str2.constraints HelixConstraint H182 E192 0.65 # 141-end/T0209.t04.alpha.constraints HelixConstraint H182 Q193 0.6765 # 141-end/T0209.t04.dssp-ehl2.constraints HelixConstraint H182 Q193 0.667 # 141-end/T0209.t04.str2.constraints HelixConstraint H182 E192 0.6208 # 141-end/T0209.t2k.dssp-ehl2.constraints HelixConstraint H182 E192 0.662 # 141-end/T0209.t2k.str2.constraints HelixConstraint L183 E192 0.766 # T0209.t04.alpha.constraints HelixConstraint L183 E192 0.921 # T0209.t04.bys.constraints HelixConstraint L183 Q193 0.686 # T0209.t04.dssp-ebghstl.constraints HelixConstraint L183 E192 0.726 # 141-end/T0209.t04.dssp-ebghstl.constraints HelixConstraint L183 L191 0.715 # 141-end/T0209.t2k.alpha.constraints HelixConstraint L183 Q193 0.799 # 141-end/T0209.t2k.dssp-ebghstl.constraints HelixConstraint L183 E192 0.91 # 141-end/T0209.t2k.stride-ebghtl.constraints HelixConstraint A198 Y199 0.619 # T0209.t2k.bys.constraints HelixConstraint A198 Y199 0.609 # 141-end/T0209.t04.bys.constraints HelixConstraint A198 Y199 0.617 # 141-end/T0209.t2k.bys.constraints Boiling those down to the consensus predictions, we get HelixConstraint P45 R49 HelixConstraint S150 E155 HelixConstraint E167 E178 HelixConstraint P181 Q193 There is NO confident prediction of a long helix, making the long helix E167-Q193 in try8 a bit suspect---although some of the predictors continue the helix through E178-P181, none give it a high probability there. These helix constraints are essential the ones I've been using, though some have been extended a bit, based on good supersecondary structure in a model. The collected strand predictions are StrandConstraint D3 L6 0.619 # T0209.t2k.alpha.constraints StrandConstraint D3 I12 0.658 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint D3 H13 0.639 # T0209.t2k.str2.constraints StrandConstraint D3 L6 0.628 # 1-140/T0209.t2k.alpha.constraints StrandConstraint D3 I12 0.693 # 1-140/T0209.t2k.dssp-ebghstl.constraints StrandConstraint D3 H13 0.6018 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint D3 T14 0.606 # 1-140/T0209.t2k.str2.constraints StrandConstraint L4 I12 0.607 # T0209.t04.bys.constraints StrandConstraint L4 P8 0.852 # T0209.t2k.bys.constraints StrandConstraint L4 H13 0.6718 # T0209.t2k.dssp-ehl2.constraints StrandConstraint L4 I12 0.682 # 1-140/T0209.t04.bys.constraints StrandConstraint L4 I12 0.639 # 1-140/T0209.t2k.bys.constraints StrandConstraint T5 L6 0.677 # T0209.t04.alpha.constraints StrandConstraint T5 H13 0.62 # T0209.t04.dssp-ebghstl.constraints StrandConstraint T5 H13 0.6225 # T0209.t04.dssp-ehl2.constraints StrandConstraint T5 H13 0.607 # T0209.t04.str2.constraints StrandConstraint T5 L6 0.67 # T0209.t04.stride-ebghtl.constraints StrandConstraint T5 H13 0.645 # T0209.t2k.stride-ebghtl.constraints StrandConstraint T5 L6 0.65 # 1-140/T0209.t04.str2.constraints StrandConstraint L6 H13 0.621 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint L6 H13 0.613 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint P8 I12 0.615 # T0209.t04.alpha.constraints StrandConstraint I9 H13 0.804 # T0209.t04.stride-ebghtl.constraints StrandConstraint I9 H13 0.6849 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint I9 H13 0.644 # 1-140/T0209.t04.str2.constraints StrandConstraint I9 H13 0.691 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint A10 I12 0.867 # T0209.t2k.bys.constraints StrandConstraint A10 I12 0.677 # 1-140/T0209.t04.alpha.constraints StrandConstraint I11 I12 0.624 # T0209.t2k.alpha.constraints StrandConstraint I11 I12 0.645 # 1-140/T0209.t2k.alpha.constraints StrandConstraint V22 P23 0.698 # T0209.t04.bys.constraints StrandConstraint V22 P23 0.677 # T0209.t2k.bys.constraints StrandConstraint V22 P23 0.775 # 1-140/T0209.t04.bys.constraints StrandConstraint V22 P23 0.708 # 1-140/T0209.t2k.bys.constraints StrandConstraint V33 P41 0.63 # T0209.t04.bys.constraints StrandConstraint V33 L38 0.859 # T0209.t04.dssp-ebghstl.constraints StrandConstraint V33 L38 0.723 # T0209.t04.dssp-ehl2.constraints StrandConstraint V33 L38 0.652 # T0209.t04.str2.constraints StrandConstraint V33 L38 0.752 # T0209.t04.stride-ebghtl.constraints StrandConstraint V33 P41 0.623 # T0209.t2k.bys.constraints StrandConstraint V33 L39 0.634 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint V33 L38 0.6215 # T0209.t2k.dssp-ehl2.constraints StrandConstraint V33 L38 0.747 # T0209.t2k.str2.constraints StrandConstraint V33 P41 0.621 # 1-140/T0209.t04.bys.constraints StrandConstraint V33 L38 0.836 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint V33 L38 0.7322 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint V33 L38 0.71 # 1-140/T0209.t04.str2.constraints StrandConstraint V33 L38 0.725 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint V33 Y42 0.603 # 1-140/T0209.t2k.bys.constraints StrandConstraint V33 L39 0.63 # 1-140/T0209.t2k.dssp-ebghstl.constraints StrandConstraint V33 L38 0.6094 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint V33 L38 0.756 # 1-140/T0209.t2k.str2.constraints StrandConstraint G34 L38 0.814 # T0209.t2k.stride-ebghtl.constraints StrandConstraint G34 L38 0.767 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint I35 L38 0.709 # T0209.t04.alpha.constraints StrandConstraint I35 L38 0.76 # T0209.t2k.alpha.constraints StrandConstraint I35 L38 0.671 # 1-140/T0209.t04.alpha.constraints StrandConstraint I35 L38 0.763 # 1-140/T0209.t2k.alpha.constraints StrandConstraint S55 F63 0.676 # T0209.t04.bys.constraints StrandConstraint S55 F63 0.631 # T0209.t2k.bys.constraints StrandConstraint S55 F63 0.624 # 1-140/T0209.t04.bys.constraints StrandConstraint H56 F63 0.7 # T0209.t04.stride-ebghtl.constraints StrandConstraint H56 D64 0.699 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint H56 F63 0.706 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint H56 F63 0.672 # 1-140/T0209.t2k.bys.constraints StrandConstraint H56 D64 0.678 # 1-140/T0209.t2k.dssp-ebghstl.constraints StrandConstraint H56 F63 0.6769 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint H56 F63 0.72 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint L57 Q62 0.657 # T0209.t04.alpha.constraints StrandConstraint L57 F63 0.743 # T0209.t04.dssp-ebghstl.constraints StrandConstraint L57 F63 0.6822 # T0209.t04.dssp-ehl2.constraints StrandConstraint L57 F63 0.676 # T0209.t04.str2.constraints StrandConstraint L57 Q62 0.665 # T0209.t2k.alpha.constraints StrandConstraint L57 F63 0.784 # T0209.t2k.dssp-ehl2.constraints StrandConstraint L57 F63 0.718 # T0209.t2k.str2.constraints StrandConstraint L57 F63 0.85 # T0209.t2k.stride-ebghtl.constraints StrandConstraint L57 Q62 0.647 # 1-140/T0209.t04.alpha.constraints StrandConstraint L57 F63 0.732 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint L57 F63 0.6677 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint L57 F63 0.657 # 1-140/T0209.t04.str2.constraints StrandConstraint L57 Q62 0.648 # 1-140/T0209.t2k.alpha.constraints StrandConstraint L57 F63 0.69 # 1-140/T0209.t2k.str2.constraints StrandConstraint W71 P77 0.663 # T0209.t04.bys.constraints StrandConstraint W71 P78 0.621 # T0209.t2k.bys.constraints StrandConstraint W71 P78 0.67 # 1-140/T0209.t04.bys.constraints StrandConstraint W71 R79 0.63 # 1-140/T0209.t2k.bys.constraints StrandConstraint Q72 R76 0.704 # T0209.t2k.str2.constraints StrandConstraint Q72 R76 0.663 # 1-140/T0209.t2k.str2.constraints StrandConstraint P73 R76 0.642 # T0209.t04.stride-ebghtl.constraints StrandConstraint P73 V75 0.6158 # T0209.t2k.dssp-ehl2.constraints StrandConstraint P73 R76 0.623 # T0209.t2k.stride-ebghtl.constraints StrandConstraint P73 V75 0.628 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint T74 V75 0.613 # T0209.t04.dssp-ebghstl.constraints StrandConstraint T74 V75 0.6436 # T0209.t04.dssp-ehl2.constraints StrandConstraint T74 V75 0.661 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint T74 V75 0.6042 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint T74 R76 0.612 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint T74 V75 0.6171 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint N83 R85 0.606 # T0209.t04.bys.constraints StrandConstraint N83 S91 0.633 # 1-140/T0209.t04.bys.constraints StrandConstraint N83 S91 0.625 # 1-140/T0209.t2k.bys.constraints StrandConstraint R85 A90 0.656 # T0209.t04.dssp-ebghstl.constraints StrandConstraint R85 A90 0.642 # T0209.t04.dssp-ehl2.constraints StrandConstraint R85 A90 0.712 # T0209.t04.stride-ebghtl.constraints StrandConstraint R85 A90 0.686 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint R85 A90 0.6426 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint R85 A90 0.605 # 1-140/T0209.t04.str2.constraints StrandConstraint R85 A90 0.675 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint V86 A90 0.676 # T0209.t04.str2.constraints StrandConstraint V86 A90 0.681 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint V86 A90 0.692 # 1-140/T0209.t2k.dssp-ebghstl.constraints StrandConstraint V86 A90 0.604 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint G87 S91 0.802 # T0209.t04.bys.constraints StrandConstraint G87 S91 0.792 # T0209.t2k.bys.constraints StrandConstraint G87 A90 0.6685 # T0209.t2k.dssp-ehl2.constraints StrandConstraint G87 S91 0.678 # T0209.t2k.stride-ebghtl.constraints StrandConstraint G87 S91 0.691 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint V88 A90 0.605 # T0209.t2k.alpha.constraints StrandConstraint V88 A90 0.607 # 1-140/T0209.t2k.alpha.constraints StrandConstraint F89 A90 0.606 # T0209.t2k.str2.constraints StrandConstraint R96 N98 0.635 # T0209.t04.bys.constraints StrandConstraint R96 N98 0.634 # T0209.t2k.bys.constraints StrandConstraint R96 N98 0.639 # 1-140/T0209.t04.bys.constraints StrandConstraint R96 N98 0.639 # 1-140/T0209.t2k.bys.constraints StrandConstraint G101 C112 0.757 # T0209.t04.str2.constraints StrandConstraint G101 C112 0.654 # T0209.t2k.stride-ebghtl.constraints StrandConstraint G101 C112 0.759 # 1-140/T0209.t04.str2.constraints StrandConstraint G101 C112 0.76 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint L102 L107 0.714 # T0209.t04.bys.constraints StrandConstraint L102 C112 0.6104 # T0209.t04.dssp-ehl2.constraints StrandConstraint L102 L107 0.708 # T0209.t2k.bys.constraints StrandConstraint L102 C112 0.67 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint L102 C112 0.6787 # T0209.t2k.dssp-ehl2.constraints StrandConstraint L102 C112 0.624 # T0209.t2k.str2.constraints StrandConstraint L102 L107 0.731 # 1-140/T0209.t04.bys.constraints StrandConstraint L102 C112 0.6475 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint L102 C112 0.604 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint L102 L107 0.737 # 1-140/T0209.t2k.bys.constraints StrandConstraint L102 C112 0.636 # 1-140/T0209.t2k.dssp-ebghstl.constraints StrandConstraint L102 C112 0.6866 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint L102 C112 0.712 # 1-140/T0209.t2k.str2.constraints StrandConstraint S103 C112 0.626 # T0209.t04.stride-ebghtl.constraints StrandConstraint S103 I113 0.62 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint K104 C112 0.741 # T0209.t04.dssp-ebghstl.constraints StrandConstraint K104 L107 0.614 # T0209.t2k.alpha.constraints StrandConstraint K104 L107 0.608 # 1-140/T0209.t2k.alpha.constraints StrandConstraint Q109 C112 0.67 # T0209.t04.alpha.constraints StrandConstraint Q109 C112 0.846 # T0209.t04.bys.constraints StrandConstraint Q109 E111 0.679 # T0209.t2k.alpha.constraints StrandConstraint Q109 I113 0.652 # T0209.t2k.bys.constraints StrandConstraint Q109 C112 0.718 # 1-140/T0209.t04.alpha.constraints StrandConstraint Q109 C112 0.845 # 1-140/T0209.t04.bys.constraints StrandConstraint Q109 E111 0.661 # 1-140/T0209.t2k.alpha.constraints StrandConstraint Q109 I113 0.603 # 1-140/T0209.t2k.bys.constraints StrandConstraint I117 L121 0.703 # T0209.t04.alpha.constraints StrandConstraint I117 L121 0.785 # T0209.t04.bys.constraints StrandConstraint I117 D125 0.71 # T0209.t04.dssp-ebghstl.constraints StrandConstraint I117 L121 0.7734 # T0209.t04.dssp-ehl2.constraints StrandConstraint I117 L121 0.686 # T0209.t04.str2.constraints StrandConstraint I117 A123 0.62 # T0209.t04.stride-ebghtl.constraints StrandConstraint I117 L121 0.774 # T0209.t2k.bys.constraints StrandConstraint I117 L121 0.691 # 1-140/T0209.t04.alpha.constraints StrandConstraint I117 L121 0.786 # 1-140/T0209.t04.bys.constraints StrandConstraint I117 G122 0.612 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint I117 L121 0.7863 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint I117 L121 0.696 # 1-140/T0209.t04.str2.constraints StrandConstraint I117 G122 0.602 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint I117 L121 0.782 # 1-140/T0209.t2k.bys.constraints StrandConstraint F118 L121 0.662 # T0209.t2k.alpha.constraints StrandConstraint F118 G122 0.679 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint F118 G122 0.6206 # T0209.t2k.dssp-ehl2.constraints StrandConstraint F118 L126 0.611 # T0209.t2k.str2.constraints StrandConstraint F118 L121 0.9 # T0209.t2k.stride-ebghtl.constraints StrandConstraint F118 L121 0.648 # 1-140/T0209.t2k.alpha.constraints StrandConstraint F118 G122 0.67 # 1-140/T0209.t2k.dssp-ebghstl.constraints StrandConstraint F118 G122 0.6032 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint F118 G122 0.805 # 1-140/T0209.t2k.str2.constraints StrandConstraint F118 L121 0.898 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint V124 L126 0.617 # T0209.t04.alpha.constraints StrandConstraint V124 D125 0.633 # T0209.t04.bys.constraints StrandConstraint V124 D125 0.633 # T0209.t2k.alpha.constraints StrandConstraint V124 D125 0.644 # T0209.t2k.bys.constraints StrandConstraint V124 D125 0.716 # 1-140/T0209.t04.alpha.constraints StrandConstraint V124 D125 0.625 # 1-140/T0209.t04.bys.constraints StrandConstraint V124 D125 0.709 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint V124 D125 0.623 # 1-140/T0209.t2k.alpha.constraints StrandConstraint V124 D125 0.625 # 1-140/T0209.t2k.bys.constraints StrandConstraint V124 D125 0.629 # 1-140/T0209.t2k.str2.constraints StrandConstraint D125 L126 0.646 # T0209.t04.str2.constraints StrandConstraint T130 F133 0.742 # T0209.t04.bys.constraints StrandConstraint T130 F133 0.742 # T0209.t2k.bys.constraints StrandConstraint T130 F133 0.781 # 1-140/T0209.t04.bys.constraints StrandConstraint T130 F133 0.772 # 1-140/T0209.t2k.bys.constraints StrandConstraint P131 I132 0.675 # T0209.t04.alpha.constraints StrandConstraint P131 I132 0.692 # 1-140/T0209.t04.alpha.constraints StrandConstraint I132 P137 0.606 # T0209.t04.dssp-ebghstl.constraints StrandConstraint I132 D134 0.7333 # T0209.t04.dssp-ehl2.constraints StrandConstraint I132 F133 0.614 # T0209.t04.str2.constraints StrandConstraint I132 D134 0.828 # T0209.t04.stride-ebghtl.constraints StrandConstraint I132 F133 0.6205 # T0209.t2k.dssp-ehl2.constraints StrandConstraint I132 D134 0.639 # T0209.t2k.str2.constraints StrandConstraint I132 P137 0.669 # 1-140/T0209.t04.dssp-ebghstl.constraints StrandConstraint I132 I135 0.6481 # 1-140/T0209.t04.dssp-ehl2.constraints StrandConstraint I132 D134 0.631 # 1-140/T0209.t04.str2.constraints StrandConstraint I132 I135 0.62 # 1-140/T0209.t04.stride-ebghtl.constraints StrandConstraint I132 F133 0.6173 # 1-140/T0209.t2k.dssp-ehl2.constraints StrandConstraint I132 F133 0.614 # 1-140/T0209.t2k.str2.constraints StrandConstraint I132 D134 0.65 # 1-140/T0209.t2k.stride-ebghtl.constraints StrandConstraint I135 I139 0.615 # T0209.t04.bys.constraints StrandConstraint I135 I139 0.633 # T0209.t2k.bys.constraints StrandConstraint I135 I139 0.619 # 1-140/T0209.t04.bys.constraints StrandConstraint I135 A140 0.672 # 1-140/T0209.t2k.bys.constraints StrandConstraint S144 E145 0.68 # T0209.t04.bys.constraints StrandConstraint S144 E145 0.698 # T0209.t2k.bys.constraints StrandConstraint L157 F165 0.671 # T0209.t2k.bys.constraints StrandConstraint L157 T166 0.794 # 141-end/T0209.t04.bys.constraints StrandConstraint L157 T166 0.768 # 141-end/T0209.t2k.bys.constraints StrandConstraint V159 T166 0.667 # T0209.t04.bys.constraints StrandConstraint K160 E164 0.611 # T0209.t04.alpha.constraints StrandConstraint K160 E164 0.659 # T0209.t04.dssp-ebghstl.constraints StrandConstraint K160 F165 0.636 # T0209.t04.stride-ebghtl.constraints StrandConstraint K160 V163 0.628 # 141-end/T0209.t04.alpha.constraints StrandConstraint K160 E164 0.783 # 141-end/T0209.t04.dssp-ebghstl.constraints StrandConstraint L161 E164 0.6838 # T0209.t04.dssp-ehl2.constraints StrandConstraint L161 E164 0.7777 # 141-end/T0209.t04.dssp-ehl2.constraints StrandConstraint L161 E164 0.65 # 141-end/T0209.t04.str2.constraints StrandConstraint L161 F165 0.669 # 141-end/T0209.t04.stride-ebghtl.constraints StrandConstraint L161 E164 0.601 # 141-end/T0209.t2k.dssp-ebghstl.constraints StrandConstraint T162 V163 0.639 # T0209.t04.str2.constraints StrandConstraint T162 E164 0.662 # 141-end/T0209.t2k.alpha.constraints StrandConstraint T162 E164 0.6266 # 141-end/T0209.t2k.dssp-ehl2.constraints StrandConstraint T162 E164 0.644 # 141-end/T0209.t2k.stride-ebghtl.constraints StrandConstraint V163 E164 0.665 # 141-end/T0209.t2k.str2.constraints StrandConstraint K203 P204 0.692 # T0209.t04.bys.constraints StrandConstraint K203 P204 0.826 # T0209.t2k.bys.constraints StrandConstraint K203 P204 0.81 # 141-end/T0209.t04.bys.constraints StrandConstraint K203 P204 0.825 # 141-end/T0209.t2k.bys.constraints StrandConstraint R207 I222 0.664 # T0209.t04.bys.constraints StrandConstraint R207 K223 0.629 # T0209.t2k.bys.constraints StrandConstraint R207 F216 0.714 # 141-end/T0209.t04.bys.constraints StrandConstraint R207 I222 0.725 # 141-end/T0209.t04.str2.constraints StrandConstraint R207 F216 0.712 # 141-end/T0209.t2k.bys.constraints StrandConstraint R207 Y214 0.619 # 141-end/T0209.t2k.stride-ebghtl.constraints StrandConstraint I208 K223 0.741 # T0209.t04.dssp-ebghstl.constraints StrandConstraint I208 I222 0.789 # T0209.t04.dssp-ehl2.constraints StrandConstraint I208 I222 0.807 # T0209.t04.str2.constraints StrandConstraint I208 I222 0.826 # T0209.t04.stride-ebghtl.constraints StrandConstraint I208 L213 0.602 # T0209.t2k.alpha.constraints StrandConstraint I208 Y214 0.673 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint I208 Y214 0.6486 # T0209.t2k.dssp-ehl2.constraints StrandConstraint I208 I222 0.724 # T0209.t2k.str2.constraints StrandConstraint I208 L213 0.862 # T0209.t2k.stride-ebghtl.constraints StrandConstraint I208 K223 0.706 # 141-end/T0209.t04.dssp-ebghstl.constraints StrandConstraint I208 K223 0.6631 # 141-end/T0209.t04.dssp-ehl2.constraints StrandConstraint I208 K223 0.689 # 141-end/T0209.t04.stride-ebghtl.constraints StrandConstraint I208 Y214 0.674 # 141-end/T0209.t2k.dssp-ebghstl.constraints StrandConstraint I208 Y214 0.6372 # 141-end/T0209.t2k.dssp-ehl2.constraints StrandConstraint I208 I222 0.637 # 141-end/T0209.t2k.str2.constraints StrandConstraint G210 L213 0.645 # T0209.t04.alpha.constraints StrandConstraint G210 S212 0.698 # 141-end/T0209.t04.alpha.constraints StrandConstraint G210 L213 0.688 # 141-end/T0209.t2k.alpha.constraints StrandConstraint E215 R221 0.634 # T0209.t04.alpha.constraints StrandConstraint F216 R221 0.68 # T0209.t2k.alpha.constraints StrandConstraint F216 I222 0.742 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint F216 I222 0.7215 # T0209.t2k.dssp-ehl2.constraints StrandConstraint F216 I222 0.781 # T0209.t2k.stride-ebghtl.constraints StrandConstraint F216 I222 0.613 # 141-end/T0209.t2k.dssp-ebghstl.constraints StrandConstraint F216 I222 0.6776 # 141-end/T0209.t2k.dssp-ehl2.constraints StrandConstraint F216 K223 0.698 # 141-end/T0209.t2k.stride-ebghtl.constraints StrandConstraint N217 I222 0.715 # 141-end/T0209.t04.alpha.constraints StrandConstraint V218 A224 0.604 # 141-end/T0209.t04.bys.constraints StrandConstraint V218 R221 0.779 # 141-end/T0209.t2k.alpha.constraints StrandConstraint V218 K223 0.742 # 141-end/T0209.t2k.bys.constraints StrandConstraint T226 C229 0.797 # T0209.t04.bys.constraints StrandConstraint T226 E234 0.603 # T0209.t04.dssp-ebghstl.constraints StrandConstraint T226 E234 0.679 # T0209.t04.stride-ebghtl.constraints StrandConstraint T226 E236 0.74 # T0209.t2k.bys.constraints StrandConstraint T226 E234 0.677 # T0209.t2k.str2.constraints StrandConstraint T226 E236 0.661 # 141-end/T0209.t2k.bys.constraints StrandConstraint V227 E234 0.815 # T0209.t04.dssp-ehl2.constraints StrandConstraint V227 E234 0.825 # T0209.t04.str2.constraints StrandConstraint V227 V230 0.605 # T0209.t2k.alpha.constraints StrandConstraint V227 I235 0.752 # T0209.t2k.dssp-ebghstl.constraints StrandConstraint V227 I235 0.6075 # T0209.t2k.dssp-ehl2.constraints StrandConstraint V227 I235 0.641 # T0209.t2k.stride-ebghtl.constraints StrandConstraint V227 V232 0.658 # 141-end/T0209.t2k.alpha.constraints StrandConstraint V227 I235 0.76 # 141-end/T0209.t2k.dssp-ebghstl.constraints StrandConstraint V227 I235 0.623 # 141-end/T0209.t2k.dssp-ehl2.constraints StrandConstraint V227 E234 0.81 # 141-end/T0209.t2k.str2.constraints StrandConstraint V227 I235 0.666 # 141-end/T0209.t2k.stride-ebghtl.constraints StrandConstraint N228 I235 0.663 # 141-end/T0209.t04.str2.constraints StrandConstraint C229 V232 0.71 # 141-end/T0209.t04.alpha.constraints StrandConstraint C229 V232 0.897 # 141-end/T0209.t04.bys.constraints StrandConstraint C229 E236 0.642 # 141-end/T0209.t04.dssp-ebghstl.constraints StrandConstraint C229 E236 0.6029 # 141-end/T0209.t04.dssp-ehl2.constraints StrandConstraint C229 E236 0.71 # 141-end/T0209.t04.stride-ebghtl.constraints StrandConstraint E231 V232 0.793 # T0209.t04.alpha.constraints StrandConstraint E231 I235 0.672 # T0209.t04.bys.constraints StrandConstraint E234 I235 0.615 # 141-end/T0209.t04.alpha.constraints StrandConstraint E234 K237 0.657 # 141-end/T0209.t04.bys.constraints Boiling these down leads to StrandConstraint D3 H13 # S1 StrandConstraint V33 L38 # S2 maybe to L39 or even P41 StrandConstraint H56 F63 # S3 StrandConstraint Q72 R76 # S4 StrandConstraint R85 A90 # S5 StrandConstraint L102 C112 # S6 StrandConstraint I117 D125 # S7 but 121-124 may be a hairpin StrandConstraint P131 D134 # S8 StrandConstraint V159 T166 # S9 StrandConstraint R207 K223 # S10 very long strand---maybe 2? StrandConstraint R207 L213 # S10a StrandConstraint F216 K223 # S10b StrandConstraint T226 E236 # S11 These are essentially the same as the strand constraints I've been using. With 11 strands, I need 6-11 sheet constraints, with the number depending on how many sheets there are. I like a parallel sheet S1-S2-S3, but I need to work on strand phase to get good packing. Antiparallel S3-S4 seems reasonable, the I'm pretty sure of the antiparallel sheet S6-S7-S8, though I need to play with the strand phase to get the hydrophobics on the same face. I'm also pretty comfortable with an S10-S11 hairpin (perhaps with a bulge), but that only takes care of half of S10. What does the other half do? Perhaps it is an antiparallel sheet S10a-S10b-S11. I wrote a rasmol script "strands" to define sets for each of the strands, so that I could select one or two at a time to highlight. Sun Jul 11 20:36:40 PDT 2004 Kevin Karplus try17-opt1 is showing some progress. I think that this may be a viable way to the put the strands together, and just needs some tweaking of the requested pairings. Mon Jul 12 07:55:00 PDT 2004 Kevin Karplus It looks we want to pair S9 parallel to S11 and maybe antiparallel to S5. L161 with V227, T162 with N228 and C229 V163 with V230 E164 with E231 F165 with V232 How about SheetConstraint K160 T162 T226 N228 Hbond T162 SheetConstraint V163 F165 V230 V232 Hbond E164 V86 T166 G87 F165 V88 E164 F89 V163 A90 T!62 How about SheetConstraint V86 A90 T166 T162 hbond V163 Mon Jul 12 14:36:23 PDT 2004 Kevin Karplus try18-opt1 is getting the strands in roughly the places I want, but is getting some bad clashes with T162 and C229 in the same place. Perhaps I put in inconsistent sheet constraints for L161-E164, that put both S11 and S5 on the same side of S9? I was trying to bulge S11, which flips the handedness of the hbonds in mid strand. I should have hbonds free on V227, C229?, V230?, V232, E234 which looks consistent with what I requested. I think that S2 is flipped, since it is trying to bury E37 in the helices. So do I want E37 to line up with P8 or A10? I think it should lineup with I60 on the other side. Currently, we ASK for it to line up with A10 and I60 but undertaker is not succeeding in achieving that. E37 should hbond to I9 and I11, which is as we request. The strand on the other side should be hbonding V36 and L38 to I60, but we have specified inconsistently that I35 hbonds this pair, not V36. Similarly, the s3^vs4 strand should have F61, not I60 as the hbonding residue. Mon Jul 12 17:06:05 PDT 2004 Kevin Karplus try19 was started with the first few strands fixed. try20 was started with the strand5-strand9 pairing slid a bit and some extra distance constraints to try to get the helix before strand9 to be on the face of the sheet. For try21, I'd like to look into the possibility of an s5 || s9 pairing. Mon Jul 12 17:43:57 PDT 2004 Kevin Karplus For the s5||s9 pairing, I'd like to try 83: nqRVGVFAsr 158: pvKLTVEFt SheetConstraint R85 A90 K160 F165 Hbond G87 I don't really like this one so much, since it leaves the conserved F89 floating in space, but I'll try it for try21. Tue Jul 13 01:35:24 PDT 2004 Kevin Karplus try19 is done, and try20 has produced try20-opt1. Both have serious clashes between s9 and s11. Looking at the curvature of S10a,S10b,and s11, I think I'm trying to put it in the wrong place---it should be pairing S11 || S8. S9 can stay with S5, but I'm not sure how it should be aligned. I'll have to put together a new cost function for this, and look at what happens to S9. Maybe I should just have a loose distance constraint betwen F89 and F165, which will probably be close no matter how the strands are oriented. On s8 I have I132 and D134 conserved, which should line up nicely with V232 and E234. SheetConstaint P131 K136 E231 E236 Hbond F133 Tue Jul 13 08:15:31 PDT 2004 Kevin Karplus try22-opt1 is the new best scorer (with the try22 costfcn, of course), but it has some bad clashes between s9 and s11, because s11 hasn't moved fully over to the position I requested for it. Foo! I had made inconsistent requests in try22, putting s11 in two places at once! Fixing the error in try23.costfcn still has try22-opt1 scoring best, giving me some how that we can fix this. Tue Jul 13 13:13:07 PDT 2004 Kevin Karplus try23-opt1 looks quite promising, and suggests yet another strand arrangement: s11 pairs with both s5 and s8 on one side and with s10b and s9 on the other. We can split s11 at E231 to get s11a: T226-V230 s11b: E231-K237 I'd like to flip s8 over so that I135 ^v L119, D134 ^v H120, with L119 and L121 hbonding. (Already in try23.costfcn) That leaves D134 and I132 to hbond probably I132|| V232 ... K136 ||E236, S5 || s11a might be G87 || T226, F89 || N228, A90 ||C229 with G87 hbonding S9 may be T162||E234 E164||E236, with E234 Hbonding. Tue Jul 13 14:39:45 PDT 2004 Kevin Karplus I'm trying those sheet constraints as try24. I just noticed a typo in try23. In the second round of optimization, it is doing 800 conformations per generation, instead of the intended 80. This will make it very slow. Tue Jul 13 16:22:38 PDT 2004 Kevin Karplus try24-opt1 is beginning to look vaguely protein-like. I probably don't have enough time to make a real protein shape out of it, but I should at least try submitting it to VAST. job VS59784 password T0209try24 Tue Jul 13 16:55:22 PDT 2004 Kevin Karplus I got one hit from VAST: 1amuB for the first 100 residues. This turns out to be a little bit of anti-parallel sheet with a helix on one side---not enough to be very useful, as it didn't even include the connecting loops. I'm scoring all the models with a "no-sheets" cost function, and will submit some of the best. I like try24, so I'll make it first, even though it hasn't gotten polished enough to be competitive. The best score is for try16-opt2, which is a "long-strand" model. Next best is try15-opt2 which looks a lot like it was borrowed from robetta. After that is try21-opt2 which juxtaposes the two parts without too horrendous a clash. I'll also include the fully automatic try1-opt2. 1: try24-opt1 2: try16-opt2 3: try15-opt2 4: try21-opt2 5: try1-opt2 Those 5 have been submitted. I might replace try24-opt1 with try24-opt2, if it finishes in time and is better. Wed Jul 14 05:42:44 PDT 2004 Kevin Karplus Try23-opt2 now out scores try16-opt2! We may want to rearrange to drop try21 from the list and put try23 above try16. Actually, l think I just want to replace try24-opt2 with try23-opt2. If I had more time, I'd play with other possibilities, but with only 6 hours left, there doesn't seem to be much point.