Models, maps, spreadsheets, and ChimeraX .cxs files to reproduce results
in Terwilliger et al, 2022, "Improving AlphaFold modeling using 
experimental density maps"

The directory DataFor25StructuresFigs1and3 contains the data shown in Figs
1 and 3, and the directory Figures contains data and ChimeraX .cxs files
that you can load to see all the panels in Figures 1, 2 and 3.

The DataFor25StructuresFigs1and3 directory and subdirectories have README
files explaining how to reproduce results in the paper.

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VERSION NOTES:

Version 2:  All analyses are from the same version of Phenix (1.20),  Data 
for Figures/Fig1_Fig3/ are in: Figures/Fig1_Fig3_all_using_phenix_1.20

Version 1: The analysis of the 7mlz example was 
carried out, then a fix was made to the software (to catch a problem where 
chains were extended with the wrong sequence and then subsequently rejected 
because the sequences did not match), and all 25 datasets (including 7mlz) 
were re-run  to yield the data in Fig. 1JKL and Fig. 3.

Therefore the 7mlz models illustrated in Fig. 1 A-I are from a different run 
than the 7mlz models used in Figs. 1JKL and Fig. 3E.

The fix did not affect the 7mlz analysis, but the randomization steps in the 
procedure yielded slightly different models.

The full data for the second run using Phenix version 1.20 after fixing this 
bug are located in:
DataFor25StructuresFigs1and3/results_by_structure

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