kinesin                package:bio3d                R Documentation

_B_i_o_3_d _E_x_a_m_p_l_e _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     These data sets contain the results of running various bio3d
     functions on example data.  The main purpose of including this
     data (which may be generated by the user by following the extended
     examples documented within the various bio3d functions) is to
     speed up example execution.  It should allow users to more quickly
     appreciate the capabilities of functions that would otherwise
     require raw data input and processing before execution.

_U_s_a_g_e:

     data(kinesin)

_F_o_r_m_a_t:

     Five objects from analysis of the 'kinesin' sequence and structure
     data:


   _a_l_n is a list with two components: 'ali', a character alignment
        matrix, and 'id', a character vector of ids/names. This is the
        output of running 'read.fasta' on the example alignment
        "kinesin_xray.fa". 

   _p_d_b_s is a list of class '"3dalign"' containing aligned PDB structure
        data.  This is the output of running 'read.fasta.pdb' with the
        'aln' object. 

   _c_o_r_e is a list of class '"core"' obtained by running the function
        'core.find' on the 'pdbs' object.

   _x_y_z is a numeric matrix of "core fitted coordinates" obtained by
        running the function 'fit.xyz' on the 'pdbs' object, using the
        "core atom indices" contained in 'core'. 

   _p_c._x_r_a_y is a list object containing PCA results obtained by running
        the function 'pca.xyz' on the "core fitted coordinates"
        contained in the 'xyz' object. 

   _s_s_e secondary structure annotation of a representative kineisn
        structure, 1bg2, as obtained from the function 'dssp' 

_S_o_u_r_c_e:

     FASTA alignment and PDB structure data from the bio3d "example"
     directory.  A related but more extensive dataset formed the basis
     of the work described in (Grant, 2007).

_R_e_f_e_r_e_n_c_e_s:

     Grant, B.J. et al. (2006) _Bioinformatics_ *22*, 2695-2696. Grant,
     B.J. et al. (2007) _J. Mol. Biol._ *368*, 1231-1248.

