There are in principle two different ways to label atoms or residues.
The one is with world oriented labels, the other with screen oriented labels.
World oriented labels are labels that have a fixed position with respect
to the atom they belong to. This means that if you have a label besides
a atom, and you then rotate the molecule 90 degrees around the X or Y
axis, you will no longer be able to read the label because it is pointing
into the screen. Screen oriented labels will always be parallel to the screen.
So they are alway readable.
World oriented labels are normal MOL-items. That means that they can be
moved around with the MOVITM option in the GRAFIC menu. These labels are
meant for picture and plot purposes. The screen oriented labels are more
for all day work. These are the labels that you get by default when you
pick an atom. The special coding done to keep them screen oriented makes
that you can not always do everything with them what you really want when
you make pictures or plots.
There are several ways to obtain screen oriented labels. The most straigth
forward one is to give GO in the GRAFIC menu, and pick an atom. If you then
pick an alpha carbon you get the residue type and number. If you pick another
atom, the atom type and residue number will be shown.
If you first pick .YES and thereafter an atom, you will be prompted for the
screen oriented label to be placed near the atom you picked. This label can
be at most eigth characters long.
If you first pick .NO and thereafter an atom, you can only pick alpha carbons.
In case you pick something else, you will get a warning, but nothing happens.
The picks of .YES or .NO stay active till you pick another menu command like
eg. .WAIT.
Another way to label atoms is from the text terminal. The following options
are available for screen oriented labels:
Remember that .NOID removes the picked labels from the screen.
The command PCKRES will cause WHAT IF to repeatedly prompt you for single
residues. The residues you give will get their alpha carbon labeled with
the residue type and the residue number. This is equivalent to picking
the alpha carbon at the screen. (See above). As usual you should give 0
(zero) to stop being prompted for new residues.
The command PCKATM will cause WHAT IF to prompt you for a residue. Thereafter
all information about this atom will be shown to you. You will then
be prompted for the atom in this residue to be labeled. The atom you give
will be labeled just as if you picked it at the screen. (See above).
WHAT IF will kepp prompting you for new residues till you give 0 (zero)
somewhere.
The command PCKRNG will cause WHAT IF to prompt you for a residue range and
for the number of residue to be skipped. If you answer this question
with zero, then all alpha carbons in the given range will be labelled just
as if you picked them at the screen. (See above). If you give 1 (one) as the
skip value then every second one will be lebeled, etc.
The command PCKTYP will cause WHAT IF to prompt you for a residue range and
for residue types. All alpha carbons of the requested residue types
in the given range will be labelled
just as if you picked them at the screen.
The command PCKTXT will cause WHAT IF to prompt you for a residue. Thereafter
all information about this residue will be shown. You will then be prompted
for the atom in the residue to be labeled. Finally you will be prompted for
the text to be put near this atom (in a screen oriented manner). This text
may not exceed 8 characters. As usual, WHAT IF will keep prompting
for new residues until you give 0 (zero) somewhere.
The command PCKINI is equivalent to picking .NOID at the PS300 screen
command menu. It will cause WHAT IF to remove all screen oriented pick
labels from the screen and from WHAT IF's memory.
This command is irreversible.
The command SHOPCK will cause WHAT IF to tell you which labels are presently
at the screen, what index in your colour map they have,
and where (in X, Y and Z) they are.
The command MOVPCK will cause WHAT IF to tell you which labels are presently
at the screen, and what index in your colour map they have.
You are than asked to give the number of a label, and you can add a translation
to this label. If you give as translation 1.0 1.0 0.0 then that label will
at the screen (and in subsequent plots) be placed 1 Angstrom along X and
1 Angstrom along Y away from its atom.
You will also be asked to give a new colour number. Here you give a whole
number from 1 till 15. As I can not see from here how you set the lower
entries of your colour map, I can not predict what colour the label will get.
I suggest you experiment a bit....
If there is a colour that you like better than the default colour used by
WHAT IF (normally red) you can put this colour number in the file ICONFI.FIG
(see the installation notes about this file).
In contrast to screen oriented lables, it is also possible to make world
oriented labels. World stands for the world at the screen. These labels
are handy if you want to put long texts in a plot, without having the
text character crossing any atomic bonds for example. The informative
value of these labels during working sessions is very low, since they
are most of the times not readable at all.
However, these labels are MOL-items, therefore you can do every thing with
them what is possible with items in general.
The following world view label options are available:
The command LABRES will cause WHAT IF to prompt respectively for the
residue, the text to put near the alpha carbon of this residue, the
character scale, and the colour. Thereafter you will be prompted for the
mol object number and the mol-item name.
As usual WHAT IF keeps prompting you for new input till you give 0 (zero).
You are suggested to look at the APLVIE command in the PORNO menu
to see how you get the view at the screen such that the labels
pop up orthogonal to the user, and thus readable...
The command LABRNG will cause WHAT IF to prompt respectively for the
residue range, the text to put near the alpha carbons of these
residues, the
character scale, and the colour. Thereafter you will be prompted for
the
MOL-object number and the MOL-item name. All Alpha carbons in the
given range will get the given text placed near to their alpha carbon.
You are suggested to look at the APLVIE command in the PORNO menu
to see how you get the view at the screen such that the labels
pop up orthogonal to the user, and thus readable...
The command LABATM will cause WHAT IF to prompt respectively for the
residue, the atom name, the text to put near the alpha carbon of
this residue, the
character scale, and the colour. Thereafter you will be prompted for the
mol object number and the mol-item name. This option is not realy needed
since you can of course use the LABRES option and then move the text to
the desired position with the MOVITM option in the GRAFIC menu, but
a little luxury can never be bad.
As usual WHAT IF keeps prompting you for new input till you give 0 (zero).
You are suggested to look at the APLVIE command in the PORNO menu
to see how you get the view at the screen such that the labels
pop up orthogonal to the user, and thus readable...
The option PCK1LC will prompt you for a range of residues. It
puts a 1-letter code label indicating the residue type at
every alpha carbon in this range. (The residue number is not
indicated). WHAT IF can only display a limited number normal
labels (normally the default parameter is set at 40). PCK1LC
can display many more labels, typically this parameter is set
at maximally 2000 1-letter code labels. (See also INI1LC).
These labels can not be operated on by the MOVPCK, neither can they
be plotted. They are also not saved by the SAVSTA command in the
SOUP menu.
The option INI1LC will remove all the one letter code labels that were generated
with the PCK1LC command (see PCK1LC above).