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ChimeraX Positions Format

A ChimeraX positions file (format positions, filename suffix .positions) contains one line per model, with 13 comma-separated fields: model name and 12 numbers, corresponding to a 3x3 rotation matrix, and in the fourth column, a translation vector. Ordering is row-by-row, such that the translation vector is given as the fourth, eighth, and twelfth numbers. This is the same matrix format as given by the view matrix command. Only model transformations relative to the scene are described, not global movements, which instead reflect rotations and translations of the camera. The command view matrix can report the camera transformation. Any model that has not been moved relative to the scene will have an identity matrix, as in the first line of this example:

2gbp map 6,-0.33209739031,-0.835019159773,-0.438696166112,55.7338415394,-0.205194478785,0.51790960911,-0.830460632822,20.7421450103,0.920655499753,-0.185775777765,-0.343337750867,-49.6090434768

Saving and Applying Positions Files

Usage: save  filename models  model-specformat positions ] [ childModels  true | false ]
Usage: open  filename models  model-specformat positions ] [ childModels  true | false ] [ matchNames  true | false ]

The models option is required for both saving and opening the file. By default, only top-level models will be included, as normally submodels will have the same transformation as their parent. However, the childModels option allows explicitly including or applying the submodel matrices as well. The matrices will simply be applied in order of occurrence in the file unless matchNames true is used to indicate matching the models by name instead.

See also: view, ChimeraX sessions

UCSF Resource for Biocomputing, Visualization, and Informatics / June 2020