chime3D                package:made4                R Documentation

_P_r_o_d_u_c_e _w_e_b _g_r_a_p_h _o_f _3_D _g_r_a_p_h _t_h_a_t _c_a_n _b_e _v_i_e_w_e_d _u_s_i_n_g _C_h_i_m_e _w_e_b _b_r_o_w_s_e_r _p_l_u_g-_i_n _f_r_o_m _a _p_d_b _f_i_l_e

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

     'chime3D' produces a html web page with a 3D graph of a pdb file
     that can be rotated and manipulated in a web browser that 
     supports the chime plug-in.

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

     chime3D(pdbfilename, classvec = NULL, title = NULL, filename = "output.html", point.size=40,cols=NULL,  ...)

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

pdbfilename: Input pdb filename, this is an output file from 'html3D'.

classvec: Factor or vector which describes classes in the df. Default
          is NULL. If specified each group  will be coloured in
          contrasting colours

   title: Character, the title (header) of the web page saved if
          writehtml is TRUE. The default is NULL.

filename: Character. The filename of the html to be saved. The default
          is  "output.html".

point.size: Numeric, size of the points in plot. Default is 40

    cols: Vector, of colours to be used.  The length of the vector must
          equal the length levels(classvec), that is the number of
          classes or groups of samples. The default is NULL, colours
          will be choosen using getcol.

     ...: further arguments passed to or from other methods 

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

     Produces a html file, of a 3D graph which can be rotated using the
     FREEWARE chime (win, MacOS).  Will colour samples by classvec if
     given one, and will produce chime script to highlight groups, spin
     on/off,  and include button for restore for example see <URL:
     http://bioinf.ucd.ie/research/microarrays/>.

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

     chime3D output is a html file that can be viewed in any web
     browser that supports the Chime plug-in.

_N_o_t_e:

     Note chime is only available on windows or Mac OS currently. Using
     the chime plug-in on Linux  is slightly complicated but is
     available if the CrossOver Plug-in is installed. Instructions on
     installing this and chime on Linux  are available at  <URL:
     http://mirrors.rcsb.org/SMS/STINGm/help/chime_linux.html>.

     If you wish to view a 3D graph in Rasmol, you will need to execute
     a Rasmol script similar to 



     load pdbfilename.pdb; 
     set axes on; 
     select off; 
     connect;
     set ambient 40; 
     rotate x 180; 
     select *;  
     spacefill 40


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

     Aedin Culhane

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

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

