FAQ

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PyRod seems not to make any progress. Is it stuck?

In case you analyze a big portion of the protein and many frames, PyRod can become very memory expensive. Check the system monitor for the python processes. If memory is full, you will have to cancel the PyRod job (CTRL-C) and change the parameters, e.g. less frames or smaller grid. You can also use the trajectory analysis component with dmifs only set true resulting in dramatically reduced memory usage. However, pharmacophore generation will not be possible.

The centroid component can take very long for finding the centroid, when a lot of protein conformation match the pharmacophore. Either wait or make the pharmacophore feature scores more restrictive as described in the centroid config file.