2011-01-19 1a2b test data for model-building

This directory contains the raw data for tests carried out on
model-building of the 1a2b structure starting from a variety of templates.
The tests evaluate the Rosetta+Phaser+Autobuild method for determination of
challenging structures by MR and rebuilding with structure-modeling
and autobuilding.  See the paper

"Increasing the Radius of Convergence of Molecular Replacement by
Density and Energy Guided Protein Structure Optimization" Frank DiMaio,
Thomas C. Terwilliger, Randy J. Read, Alexander Wlodawer, Gustav
Oberdorfer, Eugene Valkov, Assaf Alon, Deborah Fass, Herbert L. Axelrod,
Debanu Das, Sergey M. Vorobiev, Hideo Iwai, P. Raj Pokkuluri & David Baker
(2011, Nature, in press)

which describes these tests and all the approaches that were applied. 
For this test case the subdirectories contain raw data that can be used
to rerun each test case with phenix.mr_rosetta and the final models from
mr_rosetta and from DEN refinement.  The subdirectories also contain
a script that will run phenix.mr_rosetta.

Models in these directories are (for example in 2ew1A directory):

 -- MODELS BEFORE AUTOBUILD --

DEN model: 2ew1A/refine_den_1a2b.pdb

Torsion-angle SA model: 2ew1A/refine_SAtmpl_1a2b.pdb  

Best rosetta model refined with phenix.refine (model that led to the 
final mr_rosetta model, taken at beginning of autobuild just after 
refinement with phenix.refine).:  2ew1A/2ew1A_rosetta_refined_nh.pdb 

 -- MODELS AFTER AUTOBUILD --

DEN model, after autobuild: 2ew1A/autobuild_den_1a2b

Torsion SA model, after autobuild: 2ew1A/autobuild_SAtmpl_1a2b.pdb

Final rosetta-based model 2ew1A/2ew1A_mr_rosetta_nh.pdb 


The sequence identity with 1a2b and the map correlations (correlation of 
model with 2Fo-Fc map from refined 1a2b structure) obtained using 
the superimposed template ("template"), the best Rosetta model ("Rosetta"), 
the model after DEN refinement ("DEN"), and the model after 
Torsion-space SA or Cartesian -space SA  refinement are
listed below (copied from the file all_targets.xlsx).

	seqid	Template	Rosetta	DEN	Torsion-space SA	Cartesian-space SA
2EW1	29%	0.54	0.75	0.69	0.68	0.68
2G6B	35%	0.53	0.72	0.65	0.65	0.66
1YZN	29%	0.52	0.73	0.68	0.64	0.65
1UKV	29%	0.52	0.72	0.65	0.62	0.65
3CPH	31%	0.51	0.73	0.63	0.63	0.65
3BFK	31%	0.51	0.7	0.6	0.63	0.65
2RHD	32%	0.51	0.7	0.58	0.6	0.62
2FOL	31%	0.51	0.68	0.58	0.61	0.63
1G16	29%	0.51	0.7	0.63	0.59	0.64
3GFT	33%	0.5	0.76	0.67	0.65	0.65
2A5J	34%	0.5	0.72	0.64	0.63	0.64
1Z0A	35%	0.5	0.73	0.64	0.64	0.65
1RRP	28%	0.5	0.76	0.63	0.65	0.66
2BKU	28%	0.49	0.73	0.6	0.66	0.67
1Z06	28%	0.49	0.72	0.58	0.62	0.64
1YZT	30%	0.44	0.71	0.57	0.6	0.58
2EFC	36%	0.41	0.71	0.64	0.61	0.6
1UPT	16%	0.38	0.67	0.41	0.51	0.5
3LVQ	20%	0.36	0.64	0.43	0.49	0.51
2FH5	15%	0.36	0.49	0.39	0.43	0.44
3C5H	15%	0.35	0.5	0.24	0.41	0.44
2ZEJ	22%	0.35	0.54	0.21	0.42	0.45
3A1S	16%	0.34	0.52	0.2	0.35	0.41
2WJI	14%	0.34	0.57	0.11	0.43	0.44
2H57	15%	0.34	0.64	0.27	0.44	0.41
1FZQ	19%	0.33	0.57	0.31	0.39	0.46
3DPU	21%	0.31	0.45	0.17	0.36	0.42
3K53	20%	0.3	0.49	0.22	0.36	0.4
2B6H	14%	0.3	0.51	0.35	0.28	0.4
2H18	19%	0.29	0.59	0.25	0.45	0.43
1MR3	18%	0.29	0.54	0.24	0.4	0.38
2CXX	15%	0.28	0.49	0.3	0.34	0.32
1F6B	22%	0.27	0.44	0.26	0.39	0.34
1SVI	11%	0.25	0.41	0.14	0.35	0.35
3I8S	15%	0.23	0.3	0.26	0.25	0.3
2GJ8	22%	0.22	0.33	0.25	0.23	0.28
1YZG	22%	0.2	0.27	0.14	0.26	0.25
3L0I	30%	0.18	0.22	0.29	0.16	0.25
3L82	7%	0.1	0.07	0.09	0.1	0.08