Label

DESCRIPTION

label labels one or more atoms properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space are:

• name
• resn
• resi
• chain
• q
• b
• segi
• type (ATOM,HETATM)
• formal_charge
• partial_charge
• numeric_type
• text_type

All strings in the expression must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered. To clear labels, simply omit the expression or set it to .

USAGE

label (selection),expression

COLOR

Set a label's color by

set label_color, color

where color is a valid PyMol color.

EXAMPLES

label (chain A),chain
label (n;ca),"%s-%s" % (resn,resi)
label (resi 200),"%1.3f" % partial_charge

Users Comments

Labels Using ID Numbers

The following commnent,

label SELECTION, " %s" % ID 

labels the SELECTION with atom ID numbers.

You can make more complicated selections/lables such as

label SELECTION, " %s:%s %s" % (resi, resn, name)

which will give you something like "GLU:139 CG"

Lables Using Three Letter Abbreviations

• First, Add this to your $HOME/.pymolrc file:

# start $HOME/.pymolrc modification
one_letter =3D {'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
# end modification

• . Second, instead of:

label n. ca, resn

use:

label n. ca, one_letter[resn]