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README.md

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## Usage guide:
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##### About the input
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DeepEMhancer was trained using half-maps. Thus, as input, both half-maps are the preferred option (deepemhancer -i half1.mrc -i2 half2.mrc).<br>
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DeepEMhancer was trained using half-maps. Thus, as input, both half-maps are the preferred option (`deepemhancer -i half1.mrc -i2 half2.mrc`).<br>
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Full maps obtained from refinement process (RELION auto-refine, cryoSPARC heterogenus refinement...) are equally valid.<br>
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However, deepEMhancer will not work correctly if post-processed (masked, sharpened...) maps are provided as input
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(e.g. RELION postprocessing maps).
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##### About the deep learning models (-p option)
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We provide 3 different deep learning models. The default one is the tightTarget model, that was trained using
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tightly masked volumes. This is the default option and all the statistics reported in the publication were obtained
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using this model. Additionally, we provide a wideTarget model that was trained using less tightly masked maps. Finally,
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we have also trained a model (highRes) using a subset of the maps with resolutions <4 Å.<br>
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we have also trained a model (highRes) using a subset of the maps with resolutions <4 Å and fewer empty cubes.<br>
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We recommend our users to try the different options and choose the one that looks nicer to them. As a guidance,
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we suggest to employ the highRes model for maps with overall resolution better than 4 Å and a moderate amount of bad
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resolution regions. If the overall resolution is worse, or the number of low resolution regions is high, the tightTarget
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resolution regions. HighRes solutions tend to be noisier than others, but also more enhanced.
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If the overall resolution is worse, or the number of low resolution regions is high, the tightTarget
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model should do a good job. For cases in which both tightTarget and highRes produce too tightly masked solutions, possibly removing
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some parts of the protein as if they were noise, we recommend to employ the wideTarget model.
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deepEMhancer/__init__.py

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__version__="0.13"
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__version__="0.14"

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