Attribute Assignment Files

Attribute assignment files are simple user- or program-generated text files that can be read using the open command to create attributes and assign their values to atomic structures in ChimeraX. The format can be indicated with filename suffix .defattr or the open command option format defattr. It is the same format as used by Chimera, although the atom specification strings within may differ. See also: setattr

Several example files are provided. Existing attributes can be saved in this format by using the save command or the general file-saving dialog shown with File... Save in the main menu or the Save File button in Render/Select by Attribute.

Example commands showing how such a file could be used:

open 1pho
open kdHydrophobicity.defattr
color byattribute kdHydrophobicity palette ^RdYlBu
select ::kdHydrophobicity>2.0

File Format

A hash symbol # at the beginning of a line indicates a comment. Basic properties of an attribute are described in control lines of the form:

identifier: value

Possible control line contents:

identifier	value	description
attribute (required)	alphanumeric string without spaces; can include underscores; cannot begin with a digit	attribute name, existing or new
match mode (optional)	any (default) non-zero 1-to-1	expected matches per assignment line (an error message will be sent to the Log when a line's match behavior differs from the match mode)
recipient (optional)	atoms (default) residues chains structures^† bonds pseudobonds	level of attribute assignment
none handling (optional)	None (default) string delete	treatment of values given as none or None: as the Python value None, as a string, or as removal of any assignment of that attribute from the specified item

^† Either structures or molecules (for backwards compatibility with Chimera files) can be used to indicate an attribute of atomic models.

The attribute assignments are described in assignment lines of the form:

(Tab)atom-spec(Tab)attr-value

Any kind of atom specification can be used.

Control lines and comments can be interspersed with assignment lines, except that the attribute control line should precede all assignment lines for the corresponding attribute.

Allowed attr-value types are:

integer

boolean (true or false, case-independent)

color – an attribute whose name ends with color (case-independent) will be interpreted as a color-valued attribute. Colors can be specified in the same ways as in commands.

string – a string of any characters except tabs; values that might be interpreted as one of the other types should be enclosed in quotation marks

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Example Files

A simple text format is used for attribute assignment. These files can be opened with the open command to assign the corresponding attributes.

percentExposed.defattr creates a new residue attribute, percentExposed, and assigns values previously calculated by Getarea for the protein structure 121p (see raw results). See also: measure sasa
midasrad.defattr assigns atomic radii, i.e., sets values for the existing atom attribute radius. The first assignment line applies to all atoms. Subsequent lines reassign the radii for specific elements. Remember that atoms in models opened after the assignment will have the default radii instead of those in the assignment file. See also: size
Several files of amino acid hydrophobicity scales are provided;
- kdHydrophobicity.defattr – Kyte-Doolittle (see also custom presets)
- wwHydrophobicity.defattr – Wimley-White
- hhHydrophobicity.defattr – Hessa et al.
- mfHydrophobicity.defattr – Moon-Fleming
- ttHydrophobicity.defattr – transmembrane tendency (contributed by Shyam M. Saladi)

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2024