Chimera Commands Index

rmfalias [ depth N ] [ skip_prefix M ] [ rmf filename ]

The rmfalias command creates command-line specifiers for sets of nodes in Rich Molecular Format (RMF) currently open in RMF Viewer. This allows acting on the node sets with Chimera commands. The resulting aliases are of the form:

with up to N levels aliased (default 4, up to the third level of nodes) and the names of M levels omitted from the start of the alias (default 1, omitting filename). The node names are read from the RMF file and shown in the RMF Viewer interface. Certain characters such as dots (periods) and colons are stripped. The resulting aliases are listed in the Reply Log.

For example, nodeset aliases for a file named “myfile.rmf3” could include “P0/Rpb1” and “P0/Rpb1/beads” (N≥4, M=1). Caution is warranted in skipping more than 1 level of prefix (M>1), as that could produce non-unique (duplicate) alias strings. In the case of duplicates, only the last of the potential assignments will apply.

Option keywords for rmfalias can be truncated to unique strings, and their case does not matter. The rmf keyword can be used to limit alias assignment to filename when more than one RMF file is open. The path to the file should not be included in filename.

See also: alias