Help file for making oplot files from O

The molecular graphics program O cannot output raster image files directly, but can output plot description files that can be rendered in other programs. The simplest way to render these is via the Molray interface.

The plot description files ("oplot files") are created using the O plot commands, along with any of the normal O drawing commands, and it is highly recommended that you put all these commands into a macro file whilst building your picture, as you will almost certainly want to make small changes later, and repeating by hand a long series of commands with a small change is doomed to failure. Unfortunately, most O users have now got used to using the new pull-down menus, so they don't know the equivalent command-line instructions that are needed for a macro, so this is why I include some examples here.

Example 1 (mix of cpk and stick figures) :

! ================================================

plot_setup MyMetaFile.plt 1 ; yes  ! Declare name of output file 

read matrix101.mat  ! read in a matrix file to give chosen orientation

read radii.o  ! read in normal atomic radius 

sk_setup cylin smooth ; ;  ! Set rendering to smooth
sk_setup sphere smooth ;
sk_setup stick smooth ; ;

plot_on  ! Start writing to the plot file

mol bnd6 ! use mol bnd6
pa_case atom_z 4 6 7 8 16 gold blue red green ! atom colours (gold prints well) 
centre_atom bnd6 499 O4  ! centre the image

obj mp35 ! create an object
zo 499 499 ! with one residue
end ! end of object

sk_stick mp35 ! Render object bonds
sk_cpk mp35 ! Render object atoms

read cpk_radii.o   ! Read in bigger radii

pa_case atom_z 4 6 7 8 16 green blue red green  ! Set atom colours
select_off bnd6 499 499 ! Exclude the residue we had earlier
select_visible ! Make visible

obj sphere ! Show a sphere
sphere 20.0 ! Radius 20 A
end ! end of sphere

cpk sphere ; ;

read radii.o ! Set back radii for next time

plot_off ! end plotting


Example 2 (Showing two maps ) :


plot_setup two_maps.plt 1 ; yes  ! Declare output file name

read matrix10.mat  ! Read matrix for viewpoint

plot_on  ! Start plotting

map_fil ../cns/m6_sigmaa.dsn6 ! Open a map file
map_obj map1 ! Start a map object

map_par 12 12 12 1.5 blue 0.5 0.0 1 ! Set map parameters (contours at 1.5)
map_cov CBI 1.0 ! Cover object CBI by 1 Å
map_draw ! Draw the map

map_fil ../cns/m6_sigmaa_copy.dsn6 ! Repeat for 2nd map
map_obj map2  ! Start a map object

map_par 12 12 12 2.4 red 0.5 0.0 1 ! Set map parameters (contours at 0.5)
map_cov CBI 1.0 ! Cover object CBI by 1 Å
map_draw ! Draw the map

ske_stick CBI ! Make a stick rendering of the object

plot_off ! Stop plotting


Mark Harris

(The Molray Homepage)