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, ...)

_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

     ...: 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:

