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The BioEM software requires a model, a set of experimental images and a input-parameter file. The names of these files are passed to the *bioEM* executable via the commandline, as well as their format specifications.
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### Model file
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The name of the file containing the model has to be provided in the commandline when bioEM is executed using the keyword
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- --Modelfile arg
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- --Modelfile *arg*
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where *arg* is the model filename.
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There are two types of model file formats that are read by BioEM:
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1. *Text file*: with format ”%f %f %f %f %f”. The first three columns are the coordinates of the sphere centers in ångström, the fourth column is the radius in ångström, and the last column is the corresponding number of electrons. (Format: x --- y --- z --- radius --- number electrons ).
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