The program reads in spherical virus electrondensity maps and project the densities along defined radial vectors onto a sterographic sphere. The projected density can be represented as contour lines or as gradient of colors. The program can also read atomic coordinates from a PDB and project chosen residues as roadmap onto the same sterographic sphere. The residues can be labeled and colored in various way. The program is still actively developped. If you have any problem of using it. Please contact the author at Chuan (River) Xiao.
Studies of receptor binding to the surface of parvoviruses presented a problem of how to visualize the interaction between the two complex molecular surfaces. The program RIVEM (Radial Interpretation of Viral Electron density Maps) was developed to project an asymmetric receptor density radially onto a unit sphere using spherical coordinates. The stereographic diagram of the projected densities allows a clear visualization of the receptor footprint on the icosahedral virus surface. A spherical "roadmap" function was incorporated into RIVEM so that virus surface residues were projected within the same unit sphere and therefore superimpose onto the projected receptor densities. The program offers a powerful way to visualize and study the correlation between atomic structures and electron density maps in a generic variety of model systems.
Two spherical coordinate systems were defined in the RIVEM program (see figure below) to match the two different standard icosahedral orientations (see figure inset icosahedrons). This allowed users to visualize their results without having to rotate the map or the atomic coordinates before using the program. In system 1, the definitions of the two polar angles are similar to those used in (Rossman and Blow, 1962), which can facilitate the comparison between Xray crystallography studies and cryoEM studies, because these definitions were also used in many Xray crystallography programs such as the general rotation function program GLRF (Tong and Rossmann, 1997). In system 2, the output results are similar to those of the ROADMAP program (Chapman, 1993), in which X axis points north and Y axis is towards the east on the final 2D diagram.
Options  explanations 

S polar  Define the polar system,default is 1 polar = 1: Theta(Psi) is rotate from X Phi is rotate from Y toward Z polar = 2: Theta(Psi) is rotate from Y Phi is rotate from X away from Z 2 is the same as Rossmann&Blow,1962 
Pbeg[in] begPhi  Plot start with begPhi,default 0.0 
Pend endPhi  Plot start with endPhi,default 180.0 
Tbeg[in] begTheta  Plot start with begTheta,default 0.0 
Tend endTheta  Plot start with endTheta,default 180.0 
D delta_angle  Define the increment step of angle,default 1.0 degree 
Xbeg[in] begX  Plot start with begX in Angstrom, default 3.402823E+38 
Xend endX  Plot start with endX in Angstrom, default 3.402823E+38 
Ybeg[in] begY  Plot start with begX in Angstrom, default 3.402823E+38 
Zbeg[in] begZ  Plot start with begX in Angstrom, default 3.402823E+38 
Zend endZ  Plot start with endX in Angstrom, default 3.402823E+38 
O  Turn off map countour plotting, only plot roadmap, map filename should be omitted, otherwise it will be regarded as the PDB input 
Options  explanations 

E add_map_n  Define the number of additional maps, mimimum is 1,maximum is 9 default is no additional map will be read 
eX mapfilename  Readin the additional maps to superimpose on the original map, X support from 0 to add_map_n1 if you have 1 additional map, X should be 0 (C language style) 
A[X] average  Use the NCS to average the map (average=1) or apply values from one asymmetric unit to other asymmetric unit(average=2) to the other asymmetric unit. X: if exist corespondent to the additional maps 
I[X]  Use icosahedral recalculated radius instead of the original radius X if exist coorespondent to the additional maps, this option require m to input the icosahedral matrices 
R[X]fix fixR  Define the perticular radius that need to plot,see Rmode,default 0.0A X if exist coorespondent to the additional maps 
R[X]beg[in] begR  Define the starting radius in A for density projection,default 0.0A X if exist coorespondent to the additional maps 
R[X]end endR  Define the end of the radius in A for density projection,default is the maximum diagonal radius of the map X if exist coorespondent to the additional maps 
R[X]step delta_R  Define the increment step of the radial projection, default is the map voxel size, X if exist coorespondent to the additional maps 
R[X]mod[e] Rmod  Define the radial interpretation mode,default is 1
X if exist coorespondent to the additional maps * be careful to use and interprete the plot that use Rmod=0 because the sum of the density will have much larger dynamic range than the original map. Choose the contour settings of C carefully. Using small delta_R will further increase the range. It will also affect the c color_method option 4 and 5 that color the residues with density map 
S polar  Define the polar system,default is 1 polar = 1: Theta(Psi) is rotate from X Phi is rotate from Y toward Z polar = 2: Theta(Psi) is rotate from Y Phi is rotate from X away from Z 2 is the same as Rossmann&Blow,1962 
Pbeg[in] begPhi  Plot start with begPhi,default 0.0 
Pend endPhi  Plot start with endPhi,default 180.0 
Tbeg[in] begTheta  Plot start with begTheta,default 0.0 
Tend endTheta  Plot start with endTheta,default 180.0 
D delta_angle  Define the increment step of angle,default 1.0 degree 
Xbeg[in] begX  Plot start with begX in Angstrom, default 3.402823E+38 
Xend endX  Plot start with endX in Angstrom, default 3.402823E+38 
Ybeg[in] begY  Plot start with begX in Angstrom, default 3.402823E+38 
Zbeg[in] begZ  Plot start with begX in Angstrom, default 3.402823E+38 
Zend endZ  Plot start with endX in Angstrom, default 3.402823E+38 
O  Turn off map countour plotting, only plot roadmap, map filename should be omitted, otherwise it will be regarded as the PDB input 
C[X] contour_start contour_end contour_step line_type color  Contour the map X in certain line type and color, X corespond to the additional map number Line_type
Color

p PDB_filename  Give the name for the PDB file for the Roadmap 
a maximum_atom_number  Define the maximum_atom_number,default is 500000 
B border_width border_color  Define the roadmap outline line width and border color, default line width will be automatic determined by the program based on the angular step, delta_angle(see D); color option see C, default color will be black(16) 
b add_atom_move  add additional atom movement in A, default 0.0, default atom radius is van der Waals radius plus the affect of temperature (B) factor 
l label_size label_color  Turn on label of the residues on the roadmap and define the label size and label color; label color option see C; when label_size equal 0 the program will automatic determine it based on the angular step, delta_angle(see D) 
rmin[imum] r_min  Define minimum radius for atom coordinates, atoms with radius smaller than r_min will not be read in 
rmax[imum] r_max  Define maximum radius for atom coordinates, atoms with radius larger than r_max will not be read in 
rfix r_fix  Define the perticular radius to find the closest atom 
rmod[e] r_mod  Define the mode of the roadmap, default is 1

xmin[imum] x_min  Define X minimum for atom coordinates, atoms with X smaller than x_min will not be read in 
xmax[imum] x_max  Define X maximum for atom coordinates, atoms with X larger than x_max will not be read in 
ymin[imum] y_min  Define Y minimum for atom coordinates, atoms with Y smaller than y_min will not be read in 
ymax[imum] y_max  Define Y maximum for atom coordinates, atoms with Y larger than y_max will not be read in 
zmin[imum] z_min  Define Z minimum for atom coordinates, atoms with Z smaller than z_min will not be read in 
zmax[imum] z_max  Define Z maximum for atom coordinates, atoms with Z larger than z_max will not be read in 
c color_method  Turn on coloring the residues on the roadmap
* Only the original input map density can be used to color the roadmap residues(color_method 4 and 5), all the additional map can only be plotted with contoure lines using C ** The name of the PDB file that controls the residue color needs to be started with letter instead of number. Otherwise it might be read as a numbered option 1 to 5 
G color_mid_point  Define the color middle point for RGB color gradient option G and g are related to how to make a RGB gradient. The formula of a RGB gradient is the same as described in VMD http://www.ks.uiuc.edu/Research/vmd/vmd1.7.1/ug/node76.html 
g color_min  Define the color minimum for RGB color gradient option G and g are related to how to make a RGB gradient. The formula of a RGB gradient is the same as described in VMD http://www.ks.uiuc.edu/Research/vmd/vmd1.7.1/ug/node76.html 
dmin d_min  Set the lowest plot value for the RGB gradient, related to the color_method, it can be the smdallest radius or the lowest density default will be lowest radius calculated during the plot or the negative maximum absolute value of the lowest and highest density (MAX(abs(density_min),abs(density_max))).For density,the input d_min smaller or equal to zero 
dmax d_max  Set the highest plot value for the RGB gradient, related to the color_method, it can be the largest redius or the highest density positive maximum absoluted value of the lowest and highest density (MAX(abs(density_min),abs(density_max))). For density, the input d_max must larger than zero 
s plot_axis  Plot the icosahedral axis with plot_axis_color. plot_axis default is 0, not ploting the axes are defined in the matrix_file input by option m

sc axis_color  define axis_color, default is 16(black) see C for color code 
ss symbol_size  define symbol_size, default is 6, can be 1 to 12 
sb asu_border_color  define asymetric unit border color, default is 16 (black), see C for color code 
sl asu_border_linetype  define asymetric unit border_linetype, default is 3 (solid,width 1.0), see C for linetype definition 
m matrix_file  Read in the matrices for the PDB and the maps (include additonal maps), the matrix_file should be in CNS ncs.def matrix format, see examples* *Both NCS and map (include additional maps) rotationaltranslational matrices are read from the matrix_file 
M matrix_max  Define the maximum matrix number, default is 100 
N axis_number axis(1)_theta axis(1)_phi axis(1)_fold axis(1)_size axis(1)_color ...... axis(axis_number)_theta axis(axis_number)_phi axis(axis_number)_fold axis(axis_number)_size axis(axis_number)_color 
Draw additional defined symmetry symbols axis_number define how many axes. Each axis is controled by five parameters: theta, phi, fold, size and color; theta, phi should be in the plot range, fold options are 2,3,4,5,6. Check C for color codes 
L line_number line(1)_theta_start line(1)_phi_start line(1)_theta_end line(1)_phi_end line(1)_color line(1)_type ...... line(line_number)_theta_start line(line_number)_phi_start line(line_number)_theta_end line(line_number)_phi_end line(line_number)_color line(line_number)_type 
Draw defined additional line (great cycle curved line) by inputting start and end polar angles and line type. The polar angle should be inside the plotting range. Check C for color codes and line types 
F label_number label(1)_theta label(1)_phi lable(1)_size label(1)_color label(1)_text ...... label(label_number)_theta label(label_number)_phi label(label_number)_size label(label_number)_color label(label_number)_text 
Put a text label at input polar angle, the angle need to be in the plot range. No space is allowed in label_text, use quotation marks. Check C for color codes 
v verbose_level  Define the verbose level. Default verbose_level=1

h  Print the help manual 
If you meet any bugs or problems of the programs, please email xc@purdue.edu.
contact webmaster  Last Update : 09/27/2010
Copyright © 2007, Rossmann's lab, all rights reserved.