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1. Test data and solution to all tests. Begin from downloading the file attachment:codim.tar.gz and unpacking it: ''gunzip codim.tar.gz; tar xvf codim.tar; rm codim.tar''. In addition to subdirectory ''data'' containing PDB files and auxiliary programs, subdirectory ''codimtest'' contains precalculated results of most steps of the test example. 2. Instructions for preparation of a test data attachment:Preparation.pdf 3. Direct analysis of 3D test structures using Principal Component Analysis (PCA) and Kmeans clustering: attachment:3DPCA.pdf 4. Proper codimensional PCA, including resampling of structures, PCA, computation of factorial coordinates, Kmeans clustering of factorial coordinates, calculation of initial structures, multireference alignment of 3D structures. attachment:codimPCAtest.pdf 
1. Test data and solution to all tests. Begin from downloading the file [[attachment:codim.tar.gz]] and unpacking it: ''gunzip codim.tar.gz; tar xvf codim.tar; rm codim.tar''. In addition to subdirectory ''data'' containing PDB files and auxiliary programs, subdirectory ''codimtest'' contains precalculated results of most steps of the test example. 2. Instructions for preparation of a test data [[attachment:Preparation.pdf]] 3. Direct analysis of 3D test structures using Principal Component Analysis (PCA) and Kmeans clustering: [[attachment:3DPCA.pdf]] 4. Proper codimensional PCA, including resampling of structures, PCA, computation of factorial coordinates, Kmeans clustering of factorial coordinates, calculation of initial structures, multireference alignment of 3D structures. [[attachment:codimPCAtest.pdf]] 
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 '''First eigenvector:''' Ratchetlike subunit rearrangement of the complex and inward movement of L1 protein attachment:EIG1_142027877.gif  '''Third eigenvector:''' anticorrelated substoichiometry of Esite tRNA and EFTu attachment:EIG3_142129885.gif   '''First eigenvector:''' Ratchetlike subunit rearrangement of the complex and inward movement of L1 protein {{attachment:EIG1_142027877.gif}}  '''Third eigenvector:''' anticorrelated substoichiometry of Esite tRNA and EFTu {{attachment:EIG3_142129885.gif}} 
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How to analyze conformational variability of macromolecules using codimensional PCA
02/04/2012

We provide an example of application of codimensional PCA to simulated 70S ribosome data. We follow information included in the Supplemental Material of "Identifying conformational states of macromolecules by eigenanalysis of resampled cryoEM images" by Penczek et al, Structure 19, 15821590, 2012. This page includes:
Test data and solution to all tests. Begin from downloading the file codim.tar.gz and unpacking it: gunzip codim.tar.gz; tar xvf codim.tar; rm codim.tar. In addition to subdirectory data containing PDB files and auxiliary programs, subdirectory codimtest contains precalculated results of most steps of the test example.
Instructions for preparation of a test data Preparation.pdf
Direct analysis of 3D test structures using Principal Component Analysis (PCA) and Kmeans clustering: 3DPCA.pdf
Proper codimensional PCA, including resampling of structures, PCA, computation of factorial coordinates, Kmeans clustering of factorial coordinates, calculation of initial structures, multireference alignment of 3D structures. codimPCAtest.pdf
Analysis of CryoEM Structure of the T. thermophilus 70StRNAEFTuGDPKirromycin Complex. Penczek, P. A., Kimmel, M., and Spahn, C. M. (2011) Identifying conformational states of macromolecules by eigenanalysis of resampled cryoEM images, Structure 19, 15821590. 

First eigenvector: Ratchetlike subunit rearrangement of the complex and inward movement of L1 protein 
Third eigenvector: anticorrelated substoichiometry of Esite tRNA and EFTu 

Flexible architecture of IP3R1. Ludtke, S. J., Tran, T. P., Ngo, Q. T., MoiseenkovaBell, V. Y., Chiu, W., and Serysheva, II. (2011) Structure 19, 11921199. 



