Custom Residue Labeling

Custom residue labels can be generated using Actions... Label... residue... custom in the Chimera menu. Alternatively, custom labels for both atoms and residues can be defined with the command labelopt. See also: 2D Labels, attributes

In the custom labeling dialog, Residue label contents can be described with arbitrary text and/or substitution codes of the form %(descriptor)format. A literal percent symbol % can be specified with %%.

The descriptor can be any of the following:

name - residue name
1-letter code - one-letter residue code for standard amino acids, residue name for other residues
specifier - residue number, insertion code, and chain ID
number - residue number
insertion code - residue insertion code
chain - chain ID

or the name of any residue attribute.

The format can be several things, described as components #3-7 of a conversion specifier in the Python documentation, but useful possibilities include:

s - string
.Nf - floating-point number with N digits after the decimal point, for example .2f to give numbers like 122.57 and –1.66
+.Nf - as above but always signed, for example +.2f to give numbers like +122.57 and –1.66

Clicking the button for a descriptor inserts its substitution code at the current cursor position in the Residue label field. Arbitrary text, including spaces, can be entered before, after, and between substitution codes, and substitution codes can be entered manually. For example, the following would label lysine, residue 8 in chain C as “wt K8”:

wt %(1-letter code)s%(number)s

If the custom label definition includes a descriptor that is not applicable to a particular residue (not all residues have an insertion code or chain ID, for example), nothing will be inserted in that part of the label for that residue.

OK performs the labeling and dismisses the dialog, whereas Apply performs the labeling without dismissing the dialog. Close simply dismisses the dialog. Help opens this manual page in a browser window.

UCSF Computer Graphics Laboratory / June 2012