11. Utility macros
Keyword: utilities

This chapter lists and explains how to use the utility macros, that is
the command files in ">utils/" available also via "MAIN_UTILS:".  

A more up to date information and files are availabe in the "Dialog
mode accessories", in the chapter related to the menu block "UTILS".

11.1. Protein bonds
Keyword: covalent bond generation, calculate bonds, generate bonds

The file ">utils/protein.bond" CALCULATES covalent BONDS between a
protein atoms on the basis of interatomic distances.  In order to
speed up the calculation first only bonds within each single residue
are calculated, then the connections between C and N atoms for
NEIGHBOR residues (residues along the chain) are calculated.  Finally
DISULFIDE bonds are calculated with an explicit distance criterion
2.1AA.

> calculate bond residue
> calculate bond select atom name C N end neighbor
> calculate bond distance 2.1 disulfide 
> return

Covalent bonds are stored in a connectivity table (CTABLE), where each
atom has an entry. Each atom entry contains a list of all its covalent
bond partners.

WARNING: You should not apply this procedure when several disulfide
bonds are overlaping.  This is the case when you want to compare
similar molecules, superimposed to each other.  Apply your own and
calculate the disulfide bridges for each molecule separately.  Use
macros "MAIN_UTILS:calculate.bonds" or
"MAIN_UTILS:calc_segm_bonds.com".

11.2. Show unit cell
Keyword: unit cell

The procedure ">utils/show.cell" reads in fractional coordinates of
cell origins, connects them with covalent bonds and converts them to
the orthogonal world. It then displays in blue lattice of several unit
cells, designates by "ATOM NAMES" crystal origin and the axis.
WARNING: The unit cell parameters should be read before calling the
procedure.

> key old sele all end
> read file >utils/5.cell coor gauss
> key cell_atom sele .not. old end
> calc bond sele cell_atom end dist 1.1
> set coor sele cell_atom end ortho
> ima col 245 sele cell_atom end bond
> ima col 245 sele name atom C[%] .and. cell_atom end atom name
> return

I recommend you to display unit cells as the first image object,
immediately after the "IMAGE INIT" call, delete the unit cell atoms
and save the images into the background:

> image init
> <>utils/show.cell
> delete atom sele cell_atom end
> image from

11.3. Ramachandran plot

The command file ">utils/rama.com" reads in the GRAPH of Ramachandran
plot and displays it in the GRAPH OBJECT 1.  Then a dial set is
defined, which allow you to define the size of the plot and position
it to the desired place.  The dial set is protected from deletion with
the 'SET DIAL 1 FROM 1' command.

> graph
> object 1
> scale 1.0 
> character scale 0.01
> read file >utils/rama.graph
> exit
>  set dial 1 init
>  set dial 1 graph obj 1 translate
>  set dial 4 graph obj 1 scale
>  set dial 5 graph obj 1 char
>  set dial 1 write
>  set dial 1 from 1
> return

The Ramachandarn plot is composed of several image objects, so turn the
ones that disturb you off by clicking their image names on the right
side of the image window.

Similarly as the dials set, it makes sense to put the plot into the
image background in order to prevent its deletion, since as any graph
object it will disappear from the image display as soon a redraw
command will be invoked somewhere within MAIN.  

> image from

After this is done, display your molecules and start manipulating
them.  In order to see where you residue lies click an atom first and
then teh HIS_RAMA.  A cross will appear at the residue position in the
Ramachandran plot. When you rotate about a phi or psi bond the cross
will monitor the rotations.