Difference between revisions of "Label"
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===DESCRIPTION=== | ===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 ''. | |
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===USAGE=== | ===USAGE=== | ||
label (selection),expression | label (selection),expression | ||
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===Users Comments=== | ===Users Comments=== | ||
| + | ====Labels Using ID Numbers==== | ||
The following commnent, | The following commnent, | ||
label SELECTION, " %s" % ID | label SELECTION, " %s" % ID | ||
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label SELECTION, " %s:%s %s" % (resi, resn, name) | label SELECTION, " %s:%s %s" % (resi, resn, name) | ||
which will give you something like "GLU:139 CG" | which will give you something like "GLU:139 CG" | ||
| − | + | ||
| + | ====Lables Using Three Letter Abbreviations==== | ||
| + | * First, Add this to your $HOME/.pymolrc file: | ||
| + | <source lang="python"> | ||
| + | # 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 | ||
| + | </source> | ||
| + | |||
| + | *. Second, instead of: | ||
| + | label n. ca, resn | ||
| + | use: | ||
| + | label n. ca, one_letter[resn] | ||
| + | |||
[[Category:Commands|label]] | [[Category:Commands|label]] | ||
Revision as of 08:19, 9 June 2005
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
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]