StarMap is an easy-to-be-used mediator between the popular structural display program ChimeraX and the refinement program Rosetta. StarMap provides a graphical interface within ChimeraX to control and execute Rosetta-based refinements. It includes options for symmetry, local refinements, as well as independent map validation.

A series of analytical outputs, including precise magnification calibration (pixel size calibration) and Fourier shell correlations (FSC) to assess the overall quality of the refinement and resolution (map versus model FSC) are being calculated. Furthermore, per-residue Z-scores provide a fast guide to evaluate and improve local refinements as well as to identify flexible and potentially functional sites in large macromolecular complexes.

In StarMap v1.2 we have integrated support for MEDIC (Model Error Detection in Cryo-EM), a robust statistical model that identifies local backbone errors in protein structures built into cryo-EM maps by combining local fit-to-density with deep-learning-derived structural information.

The MEDIC integration is based on PyRosetta, can be used in addition or independent of the StarMap v1.1 workflow and integrates a ChimeraX MEDIC result viewer to easily inspect problematic areas.

Manuscript

If you use StarMap please read and cite:

• Lugmayr W., Kotov V. et al. StarMap: A user-friendly workflow for Rosetta-driven molecular structure refinement. Nat. Protoc. (2022). https://doi.org/10.1038/s41596-022-00757-9

• DiMaio F. et al. Atomic-accuracy models from 4.5-A cryo-electron microscopy data with density-guided iterative local refinement. Nat. Methods 12, 361-365 (2015). https://www.nature.com/articles/nmeth.3286

• Reggiano G. et al. Robust residue-level error detection in cryo-electron microscopy models. Structure (2023). https://doi.org/10.1016/j.str.2023.05.002

If you are interested in the history and background of StarMap please read:

• Kotov V., Lugmayr W. How to solve a molecular tangram? Behind the paper: https://protocolsmethods.springernature.com/posts/how-to-solve-a-molecular-tangram

Software releases

The actual GitHub code release is: StarMap 1.2.23 (see CHANGELOG.txt for changes).

The official ChimeraX 1.4+ (Qt6) version of the plugin is available via the ChimeraX Toolshed (Tools->More Tools...).

Installations using ChimeraX 1.3 (Qt5) are available in the dist folder of this site.

  chimerax -m pip install --user ChimeraX_StarMap-1.2.23-py3-none-any.whl

Development notes

Here are some starting notes on how this tool is developed.

First have a look at the file dev_functions.source for example development environment settings. These functions are compatible with BASH and ZSH.

The user interface is done with the Qt Designer of Qt5 and the script qt5_to_qt6.sh will replace some code statements.

Create a development environment

Edit the shell function starmap_create_env to fit to your needs and call the following statements in your terminal:

  source dev_functions.source
  starmap_create_env

Install and setup Rosetta.

Set your development environment

Here we use the shell statements in the starmap_dev_chimerax_centos9 function by calling the following statements in your terminal:

  source dev_functions.source
  starmap_dev_chimerax_centos9

Just edit or add your own functions.

Use Makefile targets to develop and test StarMap

We work with Makefile targets to do tasks.

Install and test your changes

  make bundle-install

will generate the documentation and install it directly into your user space of your development ChimeraX application for testing.

Make an installable Python wheel file

  make wheeldist-qt5

will generate the documentation and make a installable Python wheel file for ChimeraX 1.3.

Change the user interface

  make designer
  make test_gui

will open Qt Designer if you want to change the user interface. The second test target will show the user interface as pop-up window as it would appear in ChimeraX.