rmsf                  package:bio3d                  R Documentation

_A_t_o_m_i_c _R_M_S _F_l_u_c_t_u_a_t_i_o_n_s

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

     Calculate atomic root mean squared fluctuations.

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

     rmsf(xyz)

_A_r_g_u_m_e_n_t_s:

     xyz: numeric matrix of coordinates with each row corresponding to
          an individual conformer. 

_D_e_t_a_i_l_s:

     An often used measure of conformational variance.

_V_a_l_u_e:

     Returns a numeric vector of RMSF values.

_A_u_t_h_o_r(_s):

     Barry Grant

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

     Grant, B.J. et al. (2006) _Bioinformatics_ *22*, 2695-2696.

_S_e_e _A_l_s_o:

     'read.dcd', 'fit.xyz', 'read.fasta.pdb'

_E_x_a_m_p_l_e_s:

     data(kinesin)
     attach(kinesin)

     r <- rmsf(xyz)
     plot( r[aln$ali["d1bg2__",]!="-"], typ="h", ylab="RMSF (A)")

