Tutorial 7: Fitting a flexible ligand into a difference electron density map
- Overview
- Setup
- Running the program
- References
Overview
This tutorial describes how to use the LigandFit wizard
to automatically place an ATP molecule in a difference map. An older tutorial
covering use of LigandFit on the command line is still available.
Setup
The dataset for this tutorial is "N-ethylmaleimide sensitive factor + ATP",
which can be automatically created as a project in the Phenix GUI. Three
files are included: a ligand-free model, experimental data (MTZ file), and
the ligand itself. Once you have created the project, open the LigandFit GUI
under the "Ligands" category. The files can be added to the input list by
dragging them from the desktop, or by clicking the "Add file" button and
selecting them from the browser window.
The space group and unit cell will be automatically loaded from the data
file, and suitable column labels added to the "Input labels" menu. In this
case, we only have amplitudes available, so these will be used as input, and
LigandFit will calculate an Fo-Fc map using model phases. However, in many
cases you will obtain optimal results by using an mFo-DFc map such as those
output by phenix.refine or phenix.maps.
For this example, the rest of the parameters can be left on default settings;
consult the full documentation for explanation of what
these mean. The only exception is "Number of processors"; if you have
multiple processor cores available, you can set this higher. Note that since
the ligand structure has already been
characterized in the PDB, we could simply enter the three-letter residue name
("ATP") under "Ligand code", instead of supplying the ATP as a PDB file.
However, this will increase the runtime, since eLBOW will
be run to generate coordinates.
Running the program
Click "Run" on the toolbar ot launch LigandFit. A new tab will appear
showing the log output:
LigandFit will start several child processes to sample a wide variety of
ligand conformations. The "Parallel jobs" tab will show the output of the
individual runs as they progress; the best result will be selected for
real-space refinement and be copied to the main output directory.
At the end of the run, the summary tab will list the essential output files
and the statistics for the final result, and active the buttons to launch
other programs.
Clicking "Open in Coot" will start Coot and load the difference map, starting
model, and ligand structure. Click on the result in the summary tab to
zoom in on the ligand in Coot. Further refinement is essential, but we can
see that the fit is already very good. (The excess difference density near
the phosphate atoms belongs to an unmodeled magnesium ion and coordinating
waters.)
References
- Automated ligand fitting by core-fragment fitting and extension into density. T.C. Terwilliger, H. Klei, P.D. Adams, N.W. Moriarty, and J.D. Cohn. Acta Cryst. D62, 915-922 (2006).
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